Query 005710
Match_columns 681
No_of_seqs 263 out of 1677
Neff 6.8
Searched_HMMs 46136
Date Thu Mar 28 12:34:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005710.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005710hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02766 crypt_chrom_pln cryp 100.0 8E-123 2E-127 1040.2 41.3 474 8-481 1-474 (475)
2 COG0415 PhrB Deoxyribodipyrimi 100.0 1E-116 3E-121 958.1 38.2 455 5-483 2-459 (461)
3 PRK10674 deoxyribodipyrimidine 100.0 2E-111 5E-116 944.7 42.5 459 6-484 3-468 (472)
4 TIGR03556 photolyase_8HDF deox 100.0 5E-111 1E-115 941.7 42.5 456 6-483 2-470 (471)
5 TIGR02765 crypto_DASH cryptoch 100.0 5E-101 1E-105 854.1 40.4 413 5-433 1-429 (429)
6 KOG0133 Deoxyribodipyrimidine 100.0 8.4E-89 1.8E-93 746.3 20.9 483 1-492 1-501 (531)
7 TIGR00591 phr2 photolyase PhrI 100.0 1.5E-87 3.3E-92 750.9 28.8 392 3-429 21-454 (454)
8 PF03441 FAD_binding_7: FAD bi 100.0 2.2E-84 4.7E-89 679.9 14.1 272 208-484 1-276 (277)
9 COG3046 Uncharacterized protei 100.0 3.6E-38 7.7E-43 329.2 26.7 383 6-407 3-421 (505)
10 PF00875 DNA_photolyase: DNA p 100.0 8.5E-34 1.9E-38 275.6 15.8 156 7-163 1-157 (165)
11 PF12546 Cryptochrome_C: Blue/ 99.8 5.9E-20 1.3E-24 165.8 4.0 117 510-626 1-121 (121)
12 PF04244 DPRP: Deoxyribodipyri 98.4 7.7E-07 1.7E-11 90.8 9.5 147 8-160 1-156 (224)
13 TIGR00289 conserved hypothetic 83.8 18 0.00038 37.2 12.5 97 22-128 16-116 (222)
14 COG2102 Predicted ATPases of P 79.2 24 0.00051 36.1 11.2 99 20-128 14-117 (223)
15 cd01994 Alpha_ANH_like_IV This 76.5 34 0.00074 34.2 11.7 96 22-128 15-119 (194)
16 cd01989 STK_N The N-terminal d 75.2 41 0.00089 31.0 11.3 84 18-101 11-110 (146)
17 TIGR00290 MJ0570_dom MJ0570-re 72.2 51 0.0011 33.9 11.8 98 21-128 15-116 (223)
18 cd01988 Na_H_Antiporter_C The 71.0 52 0.0011 29.4 10.7 83 21-103 14-103 (132)
19 PF01902 ATP_bind_4: ATP-bindi 70.7 19 0.00042 36.8 8.3 98 21-128 15-116 (218)
20 cd00293 USP_Like Usp: Universa 70.3 54 0.0012 28.6 10.4 73 30-102 28-101 (130)
21 TIGR03679 arCOG00187 arCOG0018 70.2 62 0.0014 32.9 12.0 96 22-128 13-117 (218)
22 PF08218 Citrate_ly_lig: Citra 69.6 20 0.00044 35.4 7.7 107 22-130 17-144 (182)
23 cd01987 USP_OKCHK USP domain i 65.2 60 0.0013 28.9 9.7 78 19-103 12-94 (124)
24 PRK12652 putative monovalent c 63.6 56 0.0012 36.0 10.7 96 31-128 37-148 (357)
25 PRK09982 universal stress prot 60.2 1.4E+02 0.0031 27.5 12.1 108 20-129 17-137 (142)
26 PF10087 DUF2325: Uncharacteri 58.1 46 0.001 29.1 7.3 69 60-132 12-84 (97)
27 PRK10116 universal stress prot 53.5 1.8E+02 0.0038 26.5 12.0 116 14-130 11-138 (142)
28 COG2205 KdpD Osmosensitive K+ 51.6 1.6E+02 0.0035 35.9 12.2 107 19-132 260-375 (890)
29 PRK10490 sensor protein KdpD; 51.2 85 0.0018 39.0 10.6 94 30-130 279-373 (895)
30 cd00466 DHQase_II Dehydroquina 49.2 1.1E+02 0.0024 29.1 8.6 77 59-140 25-108 (140)
31 PF06574 FAD_syn: FAD syntheta 47.9 17 0.00038 35.1 3.2 104 26-131 32-145 (157)
32 COG1139 Uncharacterized conser 47.3 53 0.0011 36.9 7.0 68 58-129 65-133 (459)
33 PF13167 GTP-bdg_N: GTP-bindin 46.5 1.5E+02 0.0033 26.3 8.6 64 57-126 7-83 (95)
34 PRK05395 3-dehydroquinate dehy 46.5 1.2E+02 0.0026 29.1 8.4 77 58-139 26-109 (146)
35 PRK13015 3-dehydroquinate dehy 44.8 1.2E+02 0.0026 29.1 8.1 75 60-139 28-109 (146)
36 COG3053 CitC Citrate lyase syn 44.5 1E+02 0.0022 33.0 8.2 98 24-123 166-283 (352)
37 TIGR01088 aroQ 3-dehydroquinat 44.4 1.3E+02 0.0027 28.8 8.1 76 59-139 25-107 (141)
38 PRK15005 universal stress prot 41.5 2.2E+02 0.0048 25.9 9.6 44 58-102 70-115 (144)
39 PRK15456 universal stress prot 39.0 2.4E+02 0.0053 25.7 9.5 80 21-101 19-112 (142)
40 TIGR00273 iron-sulfur cluster- 39.0 58 0.0013 36.8 6.0 68 57-128 50-118 (432)
41 TIGR00268 conserved hypothetic 38.5 1.5E+02 0.0032 30.8 8.6 72 60-133 2-75 (252)
42 PRK14719 bifunctional RNAse/5- 36.8 84 0.0018 34.7 6.7 61 66-127 37-99 (360)
43 PRK08057 cobalt-precorrin-6x r 35.2 2.1E+02 0.0046 29.8 9.1 47 82-130 53-99 (248)
44 PF00582 Usp: Universal stress 35.1 2.7E+02 0.0058 24.2 8.8 52 78-129 86-139 (140)
45 COG3590 PepO Predicted metallo 35.1 21 0.00045 41.2 1.7 44 382-432 476-519 (654)
46 PF05889 SLA_LP_auto_ag: Solub 32.7 75 0.0016 35.3 5.4 120 3-138 99-230 (389)
47 PLN02347 GMP synthetase 32.5 1.7E+02 0.0036 34.2 8.5 77 55-132 214-293 (536)
48 PF13911 AhpC-TSA_2: AhpC/TSA 32.0 89 0.0019 27.9 5.1 42 60-102 2-44 (115)
49 TIGR00884 guaA_Cterm GMP synth 31.2 2.2E+02 0.0048 30.7 8.7 74 55-132 2-80 (311)
50 PF04104 DNA_primase_lrg: Euka 30.0 45 0.00097 35.0 3.1 48 335-383 110-157 (260)
51 COG2217 ZntA Cation transport 29.8 1.3E+02 0.0027 36.4 7.1 64 60-129 542-605 (713)
52 PF13407 Peripla_BP_4: Peripla 29.4 2.3E+02 0.0051 28.4 8.3 73 55-132 12-89 (257)
53 PF13727 CoA_binding_3: CoA-bi 29.2 94 0.002 29.3 5.0 45 83-129 130-174 (175)
54 cd06313 PBP1_ABC_sugar_binding 29.2 3.7E+02 0.0079 27.4 9.8 73 55-132 13-89 (272)
55 TIGR01490 HAD-SF-IB-hyp1 HAD-s 29.0 2.2E+02 0.0047 27.7 7.7 44 57-101 89-132 (202)
56 PF02571 CbiJ: Precorrin-6x re 28.5 2.3E+02 0.005 29.5 8.0 56 74-131 45-101 (249)
57 PRK14010 potassium-transportin 27.6 2.2E+02 0.0048 34.2 8.6 63 58-126 444-506 (673)
58 PRK08535 translation initiatio 27.0 3.7E+02 0.008 29.0 9.5 93 23-132 137-231 (310)
59 PRK09590 celB cellobiose phosp 26.9 3.8E+02 0.0082 24.1 8.0 67 55-130 16-82 (104)
60 PRK01122 potassium-transportin 26.5 2.3E+02 0.005 34.1 8.5 61 58-124 448-508 (679)
61 cd06295 PBP1_CelR Ligand bindi 26.4 4.1E+02 0.0088 26.9 9.5 71 55-131 24-95 (275)
62 TIGR02990 ectoine_eutA ectoine 26.4 2.8E+02 0.0061 28.7 8.2 50 82-134 107-156 (239)
63 cd06312 PBP1_ABC_sugar_binding 26.1 4.7E+02 0.01 26.4 9.9 73 55-132 14-91 (271)
64 PF01220 DHquinase_II: Dehydro 26.0 5.3E+02 0.011 24.7 9.1 69 67-140 38-109 (140)
65 TIGR00715 precor6x_red precorr 25.6 4E+02 0.0088 27.9 9.2 46 83-130 54-99 (256)
66 PF03392 OS-D: Insect pheromon 24.6 27 0.00058 31.0 0.2 13 417-429 83-95 (95)
67 TIGR02634 xylF D-xylose ABC tr 24.2 5.2E+02 0.011 27.0 10.0 73 55-132 12-88 (302)
68 cd06305 PBP1_methylthioribose_ 24.0 4.6E+02 0.0099 26.3 9.4 73 55-132 13-89 (273)
69 cd06811 PLPDE_III_yhfX_like Ty 23.7 3.3E+02 0.0072 30.2 8.7 71 17-101 7-84 (382)
70 PRK13384 delta-aminolevulinic 23.5 5.7E+02 0.012 27.8 9.8 65 12-78 8-81 (322)
71 PF06415 iPGM_N: BPG-independe 23.4 2.6E+02 0.0057 28.8 7.1 75 58-132 14-104 (223)
72 PF07476 MAAL_C: Methylasparta 22.9 4.3E+02 0.0093 27.4 8.3 89 32-128 104-194 (248)
73 TIGR01497 kdpB K+-transporting 22.8 3.9E+02 0.0085 32.2 9.4 62 57-124 448-509 (675)
74 cd06322 PBP1_ABC_sugar_binding 22.8 5.3E+02 0.012 25.8 9.5 72 55-131 13-88 (267)
75 PRK00074 guaA GMP synthase; Re 22.7 3.1E+02 0.0067 31.8 8.4 75 55-132 201-279 (511)
76 PF00702 Hydrolase: haloacid d 22.6 2.2E+02 0.0047 27.7 6.4 41 56-97 128-168 (215)
77 PRK15118 universal stress glob 22.6 5.9E+02 0.013 23.1 9.3 68 61-129 68-137 (144)
78 cd01545 PBP1_SalR Ligand-bindi 22.6 3.4E+02 0.0074 27.2 8.0 73 55-132 13-89 (270)
79 cd01538 PBP1_ABC_xylose_bindin 22.5 5.4E+02 0.012 26.4 9.7 73 55-132 13-89 (288)
80 cd06323 PBP1_ribose_binding Pe 22.5 5.5E+02 0.012 25.5 9.6 73 55-132 13-89 (268)
81 cd01540 PBP1_arabinose_binding 22.4 5.1E+02 0.011 26.3 9.4 73 55-132 13-88 (289)
82 PF05368 NmrA: NmrA-like famil 22.1 2.5E+02 0.0054 28.1 6.8 64 63-129 36-100 (233)
83 cd06294 PBP1_ycjW_transcriptio 22.0 3.9E+02 0.0083 26.8 8.3 71 55-131 18-91 (270)
84 COG0299 PurN Folate-dependent 21.8 6.6E+02 0.014 25.5 9.3 103 18-133 38-143 (200)
85 TIGR00083 ribF riboflavin kina 21.6 4.1E+02 0.0089 28.4 8.5 97 30-129 29-135 (288)
86 cd06279 PBP1_LacI_like_3 Ligan 20.9 4.9E+02 0.011 26.6 8.9 71 55-132 18-88 (283)
87 PF01171 ATP_bind_3: PP-loop f 20.5 2.2E+02 0.0048 27.7 5.9 36 95-130 30-65 (182)
88 PRK10660 tilS tRNA(Ile)-lysidi 20.4 2.2E+02 0.0048 32.2 6.5 68 62-130 7-82 (436)
89 PRK15408 autoinducer 2-binding 20.4 6.3E+02 0.014 27.2 9.9 73 55-132 37-114 (336)
90 cd02953 DsbDgamma DsbD gamma f 20.2 5E+02 0.011 22.2 7.6 20 22-41 3-22 (104)
No 1
>TIGR02766 crypt_chrom_pln cryptochrome, plant family. At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.
Probab=100.00 E-value=8.4e-123 Score=1040.24 Aligned_cols=474 Identities=84% Similarity=1.462 Sum_probs=412.0
Q ss_pred EEEEcCCCCCCCCHHHHHHHHcCCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeCCChHHHHH
Q 005710 8 IVWFRRDLRVEDNPALAAGVRAGAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRSTDSVSSLL 87 (681)
Q Consensus 8 LvWFRrDLRl~DN~AL~aA~~~~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~g~~~~~L~ 87 (681)
||||||||||+||+||.+|++.++||||||+||.++.....++++++||++||.+|+++|+++|++|+++..|+++++|.
T Consensus 1 l~WFRrDLRl~DN~aL~~A~~~~~vlpvyi~dp~~~~~~~~~~~~~~fl~~sL~~L~~~L~~~G~~L~v~~~g~~~~~l~ 80 (475)
T TIGR02766 1 IVWFRRDLRVEDNPALAAAARAGPVIPVFVWAPEEEGQYYPGRVSRWWLKQSLAHLDQSLRSLGTCLVTIRSTDTVAALL 80 (475)
T ss_pred CEecCCCCCcchHHHHHHHHhCCCEEEEEEechHHhccccccHHHHHHHHHHHHHHHHHHHHcCCceEEEeCCCHHHHHH
Confidence 69999999999999999999877999999999987655556777788999999999999999999999875579999999
Q ss_pred HHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecCCeeeCCcccccccCCcccchHHHHHHHHcCCCCCCC
Q 005710 88 EVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNADLLYEPWDVNDAQGQPFATFAAFWEKCLSMPFDPDA 167 (681)
Q Consensus 88 ~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~~~L~~p~~i~~~~g~~~~~f~~f~~~~~~~~~~p~~ 167 (681)
+|+++++|++||+|++|++++..||++|+++|++.||.++.|++++|++|+++.+..|++|++|++||++++..+.++..
T Consensus 81 ~l~~~~~i~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~~~~l~~p~~i~~~~~~~~~~ft~f~~~~~~~~~~~~~ 160 (475)
T TIGR02766 81 DCVRSTGATRLFFNHLYDPVSLVRDHRAKEVLTAQGISVQSFNADLLYEPWEVYDELGRPFTMFAAFWERCLSMPYDPES 160 (475)
T ss_pred HHHHHcCCCEEEEecccCHHHHHHHHHHHHHHHHcCCEEEEecCCEEEChhhhcccCCCCCCeecHHHHHHHhccCCCCC
Confidence 99999999999999999999999999999999999999999999999999999988899999999999998876433322
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCccccchhchhhhhcCCCCcCHHHHHHHHHHHhcCcCCcccccccCCCCCCCCCCchhh
Q 005710 168 PLLPPKRINSGDMSRCPSDTLVFEDESEKGSNALLARAWSPGWSNADKALTTFINGPLIEYSKNRRKADSATTSFLSPHL 247 (681)
Q Consensus 168 p~~~p~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~gGe~~A~~~L~~Fl~~~l~~Y~~~Rn~p~~~~tS~LSPyL 247 (681)
+.+.|..+.......++.+++++...............|+|||++|+++|+.|+++++.+|+++||.|+.++||+|||||
T Consensus 161 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gGe~~A~~~L~~Fl~~~~~~Y~~~Rd~p~~~~tS~LSPyL 240 (475)
T TIGR02766 161 PLLPPKKIISGDVSKCSADDLGFEDDSEKGSNALLARAWSPGWSNADKALTEFINGPLLEYSKNRKKADSATTSLLSPYL 240 (475)
T ss_pred CCCCccccCCCccccCChhhcCCCCcccccccccccccCCCccHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCccc
Confidence 23333322211111111223333211000000111234899999999999999999999999999999999999999999
Q ss_pred hCCCCCHHHHHHHHHHHHhhhhhcCCCCCcchHHHHHHHHHHHHHHHHHHHhCCCCCCCcccccccCCCCcCchhHHHHH
Q 005710 248 HFGEVSVRKVFHLVRIKQVSWANEGNKAGDESVNLFLKSIGLREYSRYMSFNHPYSHERPLLGHLKFFSWVVDEGYFKAW 327 (681)
Q Consensus 248 ~fG~LSpReV~~~v~~~~~~~~~~~~~~~~~s~~~fl~eL~WREf~~~l~~~~p~~~~~~~~~~~~~~pW~~d~~~~~aW 327 (681)
+|||||||+||+++..+......++.....++++.|++||+|||||+++++++|.+...++..+++.++|..+++.|++|
T Consensus 241 ~~G~ISpR~v~~~~~~~~~~~~~~~~~~~~~s~~~f~~eL~WRef~~~~~~~~p~~~~~~~~~~~~~~~w~~~~~~f~aW 320 (475)
T TIGR02766 241 HFGEVSVRKVFHLVRMKQIAWANEGNSAGEESVNLFLRSIGLREYSRYISFNHPFSHEKPLLGHLKFFPWAVDENYFKAW 320 (475)
T ss_pred ccCcccHHHHHHHHHhhhhhhhhcccCCCcccHHHHHHHHHHHHHHHHHHHhCCcccccchhhhhhcCCCCCCHHHHHHH
Confidence 99999999999998642211111223344568889999999999999999999987766777777889999999999999
Q ss_pred hcCCCCCHHHHHHHHHHHHhcchhhHHHHHHHHHHhhccCCCchHHHHHHHHhcccccCCCCccchhhhhcCCCCCCCcc
Q 005710 328 RQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVKVLQLPWRWGMKYFWDTLLDADLESDALGWQYISGTIPDGRAFD 407 (681)
Q Consensus 328 ~~G~TG~P~VDAaMRqL~~TGwmHnr~Rm~vAsfl~k~L~idWr~G~~~F~~~LlD~D~a~n~g~Wqw~aG~g~d~~~~~ 407 (681)
++|+|||||||||||||++|||||||+||||||||||+|+||||+|++||+++|||||+|+|+|||||+||+|+|++|||
T Consensus 321 ~~G~TG~P~VDA~MRqL~~TGwmhnR~Rm~vAsfl~k~L~idWr~G~~~F~~~LiD~D~a~N~g~Wqw~Ag~g~d~~~~~ 400 (475)
T TIGR02766 321 RQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVKVLQLPWRWGMKYFWDTLLDADLESDALGWQYISGSLPDGRELD 400 (475)
T ss_pred HcCCCCCcchhHHHHHHHHHCCCcHHHHHHHHHHHHcccCCChHHHHHHHHHHccccchhcccccccccccCCCCCCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCccccccccCCchhhHHhhchhccCCCCCcccCCCCCChhHHHHhCCccCCCCCCCCcCHHHHHHHHHHHH
Q 005710 408 RIDNPQFEGYKFDPNGEYVRRWLPELARLPTEWIHHPWNAPESVLQAAGIELGSNYPFPIVRIDAAKCRLDEAL 481 (681)
Q Consensus 408 RifNP~~q~~k~Dp~G~yIr~wvPeL~~~p~~~ih~pw~~~~~~~~~~g~~~~~~YP~Pivd~~~~~~~~~~~~ 481 (681)
|||||++|++||||+|+|||||||||+++|+++||+||+++..+|+++||.+|.+||.|||||+++|+++++++
T Consensus 401 RifnP~~q~~~~Dp~g~yir~wvPeL~~~p~~~ih~Pw~~~~~~~~~~~~~~g~~YP~PiVd~~~~r~~~~~~~ 474 (475)
T TIGR02766 401 RIDNPQLEGYKFDPNGEYVRRWLPELARLPTEWIHHPWDAPESVLQAAGVELGSNYPLPIVGLDEARARLHEAL 474 (475)
T ss_pred ccCCHHHHHhhcCCCcccHHHhChhhccCCHHHhcCcccCCHHHHHHcCCccCCCCCcccCCHHHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999875
No 2
>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.5e-116 Score=958.15 Aligned_cols=455 Identities=35% Similarity=0.591 Sum_probs=403.1
Q ss_pred CeEEEEEcCCCCCCCCHHHHHHHHcC-C-eEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeCCCh
Q 005710 5 GCSIVWFRRDLRVEDNPALAAGVRAG-A-VIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRSTDS 82 (681)
Q Consensus 5 ~~~LvWFRrDLRl~DN~AL~aA~~~~-~-vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~g~~ 82 (681)
+.+|||||||||++||+||++|++.+ + +++|||++|.+++ ..++.+.+||.+||++|+++|+++|++|++.. +++
T Consensus 2 ~~~l~WfrrDLR~~DN~aL~~A~~~~~~~~~~vfi~~~~~~~--~~~~~~~~Fl~~sL~~L~~~L~~~gi~L~v~~-~~~ 78 (461)
T COG0415 2 STVLVWFRRDLRLTDNAALAAACQSGQPVIIAVFILDPEQLG--HASPRHAAFLLQSLQALQQSLAELGIPLLVRE-GDP 78 (461)
T ss_pred CeEEEEeccccccCChHHHHHHHhcCCCceEEEEEechhhcc--ccCHHHHHHHHHHHHHHHHHHHHcCCceEEEe-CCH
Confidence 57899999999999999999999986 3 6799999999876 34566677999999999999999999999986 789
Q ss_pred HHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecCCeeeCCcccccccCCcccchHHHHHHHHcCC
Q 005710 83 VSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNADLLYEPWDVNDAQGQPFATFAAFWEKCLSMP 162 (681)
Q Consensus 83 ~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~~~L~~p~~i~~~~g~~~~~f~~f~~~~~~~~ 162 (681)
.++|++++++.+++.|++|.+|++.+..||.+|++.|.+.||.+++|++.+|++|+++.+..|++|++||+||++|....
T Consensus 79 ~~~l~~~~~~~~~~~v~~n~~~~~~~~~rD~al~~~l~~~gi~~~~~~d~~l~~p~~~~t~~~~~y~vfT~F~k~~~~~~ 158 (461)
T COG0415 79 EQVLPELAKQLAATTVFWNRDYEEWERQRDAALAQPLTEVGIAVHSFWDALLHEPGEVRTGSGEPYKVFTPFYKAWRDRL 158 (461)
T ss_pred HHHHHHHHHHhCcceEEeeeeechhHHHHHHHHHHHHHhcCceEEEeccccccCHhhccCCCCCCccccchHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998763
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCccccchhchhhhhcCCCCcCHHHHHHHHHHHhcCcCCcccccccCCCCCCCCC
Q 005710 163 FDPDAPLLPPKRINSGDMSRCPSDTLVFEDESEKGSNALLARAWSPGWSNADKALTTFINGPLIEYSKNRRKADSATTSF 242 (681)
Q Consensus 163 ~~p~~p~~~p~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~gGe~~A~~~L~~Fl~~~l~~Y~~~Rn~p~~~~tS~ 242 (681)
. ...+.+.|..+........+.....+.+ .. ......|.+||++|+++|++|+.+++.+|++.||.|..++||+
T Consensus 159 ~-~~~~~~~p~~~~~~~~~~~~~~~~~~P~-~~----~~~~~~~~~Ge~aA~~~l~~F~~~~l~~Y~~~Rd~p~~~~TS~ 232 (461)
T COG0415 159 R-ILRPVPAPDVLDALRDEEPPPEEISLPD-FS----KFDVLLFTGGEKAALARLQDFLAEGLDDYERTRDFPALDGTSR 232 (461)
T ss_pred c-cCCCCCCcchhccccccccCcccccCCc-cc----cccccCCCchHHHHHHHHHHHHHHHHHHHHHhcCCcccccccc
Confidence 2 1123333432221100000000111111 00 0012358999999999999999999999999999999999999
Q ss_pred CchhhhCCCCCHHHHHHHHHHHHhhhhhcCCCCCcchHHHHHHHHHHHHHHHHHHHhCCCC-CCCcccccccCCCCcCch
Q 005710 243 LSPHLHFGEVSVRKVFHLVRIKQVSWANEGNKAGDESVNLFLKSIGLREYSRYMSFNHPYS-HERPLLGHLKFFSWVVDE 321 (681)
Q Consensus 243 LSPyL~fG~LSpReV~~~v~~~~~~~~~~~~~~~~~s~~~fl~eL~WREf~~~l~~~~p~~-~~~~~~~~~~~~pW~~d~ 321 (681)
|||||+||+||||+||+++++... .+.++++.|++||+|||||++++.++|.. ...++......++|.+++
T Consensus 233 LSpyL~~G~IS~r~v~~~~~~~~~--------~~~~~~~~~~~eL~WREFy~h~~~~~p~~~~~~~~~~~~~~~~w~~~~ 304 (461)
T COG0415 233 LSPYLAFGVISPREVYAALLAAES--------DAREGTAALINELIWREFYQHLLYHYPSLSRFEPFAEKTLNIPWEDNP 304 (461)
T ss_pred cCHHHHcCCcCHHHHHHHHHHhhh--------cccchHHHHHHHHHHHHHHHHHHHhCCcccccccccccccCCccccCH
Confidence 999999999999999999987531 14567889999999999999999999988 788888888999999999
Q ss_pred hHHHHHhcCCCCCHHHHHHHHHHHHhcchhhHHHHHHHHHHhhccCCCchHHHHHHHHhcccccCCCCccchhhhhcCCC
Q 005710 322 GYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVKVLQLPWRWGMKYFWDTLLDADLESDALGWQYISGTIP 401 (681)
Q Consensus 322 ~~~~aW~~G~TG~P~VDAaMRqL~~TGwmHnr~Rm~vAsfl~k~L~idWr~G~~~F~~~LlD~D~a~n~g~Wqw~aG~g~ 401 (681)
+.|++|++|+|||||||||||||++||||||||||||||||||+|.||||+|++||+++|||||+|+|+|||||+||+|+
T Consensus 305 ~~f~aW~~G~TGyPIVDA~MRqL~~TG~MHNR~RMivAsFL~k~L~IdWR~GE~~F~~~LiD~D~asN~ggWQW~AstG~ 384 (461)
T COG0415 305 AHFQAWQEGKTGYPIVDAAMRQLNQTGYMHNRMRMIVASFLTKDLLIDWREGEKYFMRQLIDGDPASNNGGWQWAASTGT 384 (461)
T ss_pred HHHHHHhcCCCCCccccHHHHHHHHhCCcchHHHHHHHHHHHHhcCCCHHHHHHHHHHhccCCCcccCCCCeeEEeccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcccccCccccccccCCchhhHHhhchhccCCCCCcccCCCCCChhHHHHhCCccCCCCCCCCcCHHHHHHHHHHHH
Q 005710 402 DGRAFDRIDNPQFEGYKFDPNGEYVRRWLPELARLPTEWIHHPWNAPESVLQAAGIELGSNYPFPIVRIDAAKCRLDEAL 481 (681)
Q Consensus 402 d~~~~~RifNP~~q~~k~Dp~G~yIr~wvPeL~~~p~~~ih~pw~~~~~~~~~~g~~~~~~YP~Pivd~~~~~~~~~~~~ 481 (681)
|+.||||||||++|++||||+|+|||+|||||++||.++||+||.++. +.+|.+||+|||||+++|++++.+|
T Consensus 385 Da~pyfRiFNp~~Q~~kfDp~g~fIr~wvPeL~~~~~~~ih~p~~~~~-------~~~~~~YP~piVd~~~~r~~a~~~y 457 (461)
T COG0415 385 DAAPYFRIFNPVTQAEKFDPDGEFIRRWVPELRNLPDKYIHEPWELSE-------VVLGVDYPKPIVDHKESREQALAAY 457 (461)
T ss_pred CCCcceeccCHHHHHhhcCCCcccHHhhCHHhhCCChhhccChhhccc-------ccccCCCCccccccHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999986 5789999999999999999999988
Q ss_pred HH
Q 005710 482 SE 483 (681)
Q Consensus 482 ~~ 483 (681)
+.
T Consensus 458 ~~ 459 (461)
T COG0415 458 EA 459 (461)
T ss_pred Hh
Confidence 64
No 3
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=100.00 E-value=2.2e-111 Score=944.73 Aligned_cols=459 Identities=32% Similarity=0.525 Sum_probs=389.7
Q ss_pred eEEEEEcCCCCCCCCHHHHHHHHcC--CeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeC---C
Q 005710 6 CSIVWFRRDLRVEDNPALAAGVRAG--AVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRS---T 80 (681)
Q Consensus 6 ~~LvWFRrDLRl~DN~AL~aA~~~~--~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~---g 80 (681)
.+||||||||||+||+||.+|++.+ +|+||||+||........+..+.+||++||.+|+++|+++|++|+++.+ |
T Consensus 3 ~~l~WfRrDLRl~DN~aL~~A~~~~~~~vlpvyv~dp~~~~~~~~~~~r~~Fl~esL~~L~~~L~~~g~~L~v~~g~~~g 82 (472)
T PRK10674 3 THLVWFRNDLRLHDNLALAAACRDPSARVLALFIATPAQWAAHDMAPRQAAFINAQLNALQIALAEKGIPLLFHEVDDFA 82 (472)
T ss_pred ceEEEECCCCCcchHHHHHHHHhCCCCCEEEEEEECchhhccCCCCHHHHHHHHHHHHHHHHHHHHcCCceEEEecCCcC
Confidence 4699999999999999999999874 6999999999865543456677779999999999999999999999863 5
Q ss_pred ChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecCCeeeCCcccccccCCcccchHHHHHHHHc
Q 005710 81 DSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNADLLYEPWDVNDAQGQPFATFAAFWEKCLS 160 (681)
Q Consensus 81 ~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~~~L~~p~~i~~~~g~~~~~f~~f~~~~~~ 160 (681)
++.++|.+|+++++|+.||++++|+++++.||++|++.|. ||.++.|++++|++|+.+.+..|++|++|++|++++..
T Consensus 83 ~~~~vl~~l~~~~~i~~v~~~~~~~~~~~~rd~~v~~~l~--~i~~~~~~~~~l~~~~~i~~~~~~~y~~ft~f~~~~~~ 160 (472)
T PRK10674 83 ASVEWLKQFCQQHQVTHLFYNYQYEVNERQRDAAVERALR--NVVCQGFDDSVLLPPGSVMTGNHEMYKVFTPFKNAFLK 160 (472)
T ss_pred CHHHHHHHHHHHcCCCEEEEecccCHHHHHHHHHHHHHcC--CCEEEEecCceEeCccccccCCCCCCCcccHHHHHHHH
Confidence 7999999999999999999999999999999999999996 89999999999999999998889999999999999876
Q ss_pred CCCCCC-CCCCCCCCCCCCCCCCCCCCCCCccccchhchhhhhcCCCCcCHHHHHHHHHHHhcCcCCcccccccCCCCCC
Q 005710 161 MPFDPD-APLLPPKRINSGDMSRCPSDTLVFEDESEKGSNALLARAWSPGWSNADKALTTFINGPLIEYSKNRRKADSAT 239 (681)
Q Consensus 161 ~~~~p~-~p~~~p~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~gGe~~A~~~L~~Fl~~~l~~Y~~~Rn~p~~~~ 239 (681)
....+. .+.+.|...........++..+++.. . ......|+|||.+|+++|++|+++++.+|++.||.|..++
T Consensus 161 ~~~~~~p~~~~~p~~~~~~~~~~~~~~~~~~~~---~---~~~~~~~~gGe~~A~~~L~~f~~~~l~~Y~~~r~~p~~~~ 234 (472)
T PRK10674 161 RLREGDPECVPAPKVRSSGAIEPLPPIPFNYPQ---Q---SFDTALFPVGEKAAIAQLRQFCQQGAGEYEQQRDFPAVDG 234 (472)
T ss_pred hhcccCCccCCCCccccccccCCCCcccccCcc---c---ccccCCCCCCHHHHHHHHHHHHHHHHHHhccccCCCCccC
Confidence 432211 11222221111001000111111110 0 0011248999999999999999999999999999999999
Q ss_pred CCCCchhhhCCCCCHHHHHHHHHHHHhhhhhcCCCCCcchHHHHHHHHHHHHHHHHHHHhCCCCCC-CcccccccCCCCc
Q 005710 240 TSFLSPHLHFGEVSVRKVFHLVRIKQVSWANEGNKAGDESVNLFLKSIGLREYSRYMSFNHPYSHE-RPLLGHLKFFSWV 318 (681)
Q Consensus 240 tS~LSPyL~fG~LSpReV~~~v~~~~~~~~~~~~~~~~~s~~~fl~eL~WREf~~~l~~~~p~~~~-~~~~~~~~~~pW~ 318 (681)
||+|||||+|||||||+||+++.+... ... ...+.+.|++||+|||||+++++++|.+.. .++.+..+.++|+
T Consensus 235 tS~LSPyL~~G~iS~r~v~~~~~~~~~-----~~~-~~~~~~~fl~eL~WRef~~~~~~~~p~~~~~~~~~~~~~~~~w~ 308 (472)
T PRK10674 235 TSRLSAYLATGVLSPRQCLHRLLAEQP-----QAL-DGGAGSVWLNELIWREFYRHLMVAYPSLCKHRPFIAWTDRVQWQ 308 (472)
T ss_pred CCCcChhhccCcCCHHHHHHHHHHHhh-----hhh-ccCchhHHHHHHHHHHHHHHHHHhCCchhhccCcchhhhccCcc
Confidence 999999999999999999999875321 101 112345799999999999999999998643 3555556678899
Q ss_pred CchhHHHHHhcCCCCCHHHHHHHHHHHHhcchhhHHHHHHHHHHhhccCCCchHHHHHHHHhcccccCCCCccchhhhhc
Q 005710 319 VDEGYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVKVLQLPWRWGMKYFWDTLLDADLESDALGWQYISG 398 (681)
Q Consensus 319 ~d~~~~~aW~~G~TG~P~VDAaMRqL~~TGwmHnr~Rm~vAsfl~k~L~idWr~G~~~F~~~LlD~D~a~n~g~Wqw~aG 398 (681)
++++.|++|++|+|||||||||||||++|||||||+||+|||||||+|+|||++|++||+++|||||+|+|+|||||+||
T Consensus 309 ~~~~~~~~W~~G~TG~P~vDA~mrqL~~tG~mhnr~Rm~vAsfL~k~L~idWr~G~~~F~~~LlD~D~a~N~g~Wqw~ag 388 (472)
T PRK10674 309 SNPAHLQAWQQGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWAAS 388 (472)
T ss_pred cCHHHHHHHHcCCCCCccHHHHHHHHHHHCCccHHHHHHHHHHHHcCcccCCHhHHHHHHHHhhcCCcccchhccceeec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCcccccCccccccccCCchhhHHhhchhccCCCCCcccCCCCCChhHHHHhCCccCCCCCCCCcCHHHHHHHHH
Q 005710 399 TIPDGRAFDRIDNPQFEGYKFDPNGEYVRRWLPELARLPTEWIHHPWNAPESVLQAAGIELGSNYPFPIVRIDAAKCRLD 478 (681)
Q Consensus 399 ~g~d~~~~~RifNP~~q~~k~Dp~G~yIr~wvPeL~~~p~~~ih~pw~~~~~~~~~~g~~~~~~YP~Pivd~~~~~~~~~ 478 (681)
+|+|++||+|||||++|++||||+|+|||+|||||+++|.++||+||+++. .++|.+ +||+|||||+.+|++++
T Consensus 389 ~G~d~~py~R~fnP~~q~~k~Dp~g~yIr~w~PeL~~~p~~~ih~Pw~~~~----~~~~~~--~YP~PiVd~~~~r~~~~ 462 (472)
T PRK10674 389 TGTDAAPYFRIFNPTTQGERFDRDGEFIRRWLPELRDVPGKAIHQPWRWAE----KAGVTL--DYPQPIVDHKQARLATL 462 (472)
T ss_pred CCCCCCcceeecCHHHHHHHhCCCCChHHHhChhhccCCHHhhcCccccch----hcCCCC--CCCcCCcCHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999974 235544 79999999999999999
Q ss_pred HHHHHH
Q 005710 479 EALSEM 484 (681)
Q Consensus 479 ~~~~~~ 484 (681)
++|+.+
T Consensus 463 ~~~~~~ 468 (472)
T PRK10674 463 AAYEAA 468 (472)
T ss_pred HHHHHH
Confidence 999765
No 4
>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type. This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.
Probab=100.00 E-value=4.9e-111 Score=941.74 Aligned_cols=456 Identities=30% Similarity=0.549 Sum_probs=395.0
Q ss_pred eEEEEEcCCCCCCCCHHHHHHHHcC-CeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeCCChHH
Q 005710 6 CSIVWFRRDLRVEDNPALAAGVRAG-AVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRSTDSVS 84 (681)
Q Consensus 6 ~~LvWFRrDLRl~DN~AL~aA~~~~-~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~g~~~~ 84 (681)
.+|||||||||++||+||.+|++.+ +|+||||+||........+..+.+||++||.+|+++|+++|++|+++. |++.+
T Consensus 2 ~vl~WfRrDLRl~DN~AL~~A~~~~~~vl~vfi~dp~~~~~~~~~~~r~~Fl~esL~~L~~~L~~~G~~L~v~~-G~p~~ 80 (471)
T TIGR03556 2 LILFWHRRDLRLSDNIGLAAARQQSAKVVGLFCLDPNILQADDMAPARVAYLIGCLQELQQRYQQAGSQLLILQ-GDPVQ 80 (471)
T ss_pred CEEEEeCCCCCcchHHHHHHHHhcCCCEEEEEEEchhhhccccCCHHHHHHHHHHHHHHHHHHHHCCCCeEEEE-CCHHH
Confidence 6899999999999999999999875 899999999987654445666778999999999999999999999986 89999
Q ss_pred HHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecCCeeeCCcccccccCCcccchHHHHHHHHcCCCC
Q 005710 85 SLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNADLLYEPWDVNDAQGQPFATFAAFWEKCLSMPFD 164 (681)
Q Consensus 85 ~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~~~L~~p~~i~~~~g~~~~~f~~f~~~~~~~~~~ 164 (681)
+|.+|+++++|++||+|++|++++++||++|++.|++.||.|+.+++++|++|+.+.+..|++|++|++|+++++..+..
T Consensus 81 vl~~l~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~~~~~~~~l~~p~~i~~~~~~~y~~ft~f~k~~~~~~~~ 160 (471)
T TIGR03556 81 LIPQLAQQLGAKAVYWNLDVEPYGRKRDRAVAAALKEAGIAVVTLWDQLLHSPDEILTGSGNPYTVYTPFWKNWSSLPKP 160 (471)
T ss_pred HHHHHHHHcCCCEEEEecccCHHHHHHHHHHHHHHHHCCCEEEEeCCcEEECccccccCCCCCCcchhHHHHHHHhcccc
Confidence 99999999999999999999999999999999999999999999999999999999888899999999999998765321
Q ss_pred CCCCCCCCCCCCC---------CCCCC---CCCCCCCccccchhchhhhhcCCCCcCHHHHHHHHHHHhcCcCCcccccc
Q 005710 165 PDAPLLPPKRINS---------GDMSR---CPSDTLVFEDESEKGSNALLARAWSPGWSNADKALTTFINGPLIEYSKNR 232 (681)
Q Consensus 165 p~~p~~~p~~~~~---------~~i~~---~~~~~l~~~~~~~~~~~~~~~~~~~gGe~~A~~~L~~Fl~~~l~~Y~~~R 232 (681)
.+++.|..+.. ..+.. ..++++++.. .. ...|+|||.+|+++|+.|+++++.+|.++|
T Consensus 161 --~~~~~p~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~-----~~---~~~~~gGe~~A~~~L~~f~~~~l~~Y~~~r 230 (471)
T TIGR03556 161 --TPVATPTELEGLTEAELEAAAPLGVIALPTAKDLGFDW-----DG---DLILEPGETAAQARLEEFCDRAIADYQEQR 230 (471)
T ss_pred --CCCCCccccccCCccccccccccccccCCccccccccc-----cc---ccCCCCcHHHHHHHHHHHHHHHHHHhhhcc
Confidence 12222222110 00000 0011111110 00 114899999999999999999999999999
Q ss_pred cCCCCCCCCCCchhhhCCCCCHHHHHHHHHHHHhhhhhcCCCCCcchHHHHHHHHHHHHHHHHHHHhCCCCCCCcccccc
Q 005710 233 RKADSATTSFLSPHLHFGEVSVRKVFHLVRIKQVSWANEGNKAGDESVNLFLKSIGLREYSRYMSFNHPYSHERPLLGHL 312 (681)
Q Consensus 233 n~p~~~~tS~LSPyL~fG~LSpReV~~~v~~~~~~~~~~~~~~~~~s~~~fl~eL~WREf~~~l~~~~p~~~~~~~~~~~ 312 (681)
|.|..++||+|||||+|||||||+||+++.+.... ........+++.|++||+|||||+++++++|.+...++...+
T Consensus 231 ~~p~~~~tS~LSpyL~~G~iS~r~v~~~~~~~~~~---~~~~~~~~~~~~f~~eL~WRef~~~~~~~~p~~~~~~~~~~~ 307 (471)
T TIGR03556 231 NFPALDGTSQLSPALKFGVIGIRTVWQATQEAHEN---SRSEEARNSIRTWQQELAWREFYQHALYHFPELADGPYRSLF 307 (471)
T ss_pred CCCCCCCCCCCChhhcCCcccHHHHHHHHHHHHhh---cccccccccHHHHHHHHHHHHHHHHHHHHCcchhccccchhh
Confidence 99999999999999999999999999999764311 111122447788999999999999999999998777888778
Q ss_pred cCCCCcCchhHHHHHhcCCCCCHHHHHHHHHHHHhcchhhHHHHHHHHHHhhccCCCchHHHHHHHHhcccccCCCCccc
Q 005710 313 KFFSWVVDEGYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVKVLQLPWRWGMKYFWDTLLDADLESDALG 392 (681)
Q Consensus 313 ~~~pW~~d~~~~~aW~~G~TG~P~VDAaMRqL~~TGwmHnr~Rm~vAsfl~k~L~idWr~G~~~F~~~LlD~D~a~n~g~ 392 (681)
..++|..+++.|++|++|+|||||||||||||++|||||||+||+|||||||+|+|||++|++||+++|||||+|+|+||
T Consensus 308 ~~~~w~~~~~~~~~W~~G~TG~P~vDAaMrqL~~tG~mhnr~Rm~vAsfl~k~L~idWr~G~~~F~~~LlD~D~a~N~g~ 387 (471)
T TIGR03556 308 QNFPWENNEAHFQAWCEGRTGYPIVDAAMRQLNETGWMHNRCRMIVASFLTKDLIINWQWGEKYFMQKLIDGDLAANNGG 387 (471)
T ss_pred hcCCCcCCHHHHHHHhcCCCCCCcccHHHHHHHHhCCccHHHHHHHHHHHHcccCCCHHHHHHHHHHHhhhcChhhcccc
Confidence 88899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhcCCCCCCCcccccCccccccccCCchhhHHhhchhccCCCCCcccCCCCCChhHHHHhCCccCCCCCCCCcCHHH
Q 005710 393 WQYISGTIPDGRAFDRIDNPQFEGYKFDPNGEYVRRWLPELARLPTEWIHHPWNAPESVLQAAGIELGSNYPFPIVRIDA 472 (681)
Q Consensus 393 Wqw~aG~g~d~~~~~RifNP~~q~~k~Dp~G~yIr~wvPeL~~~p~~~ih~pw~~~~~~~~~~g~~~~~~YP~Pivd~~~ 472 (681)
|||+||+|+|++| +|||||++|++||||+|+|||||||||+++|+++||+||.++ .+++ ..+||+|||||+.
T Consensus 388 Wqw~a~~G~d~~p-~R~fnp~~q~~k~Dp~G~yIr~w~PeL~~~p~~~ih~p~~~~-~~~~------~~~YP~Pivd~~~ 459 (471)
T TIGR03556 388 WQWSASSGMDPKP-LRIFNPASQAQKFDPEAEYIRRWLPELRSVDTKDLVTGKITP-LERR------AVGYPLPIVDHNQ 459 (471)
T ss_pred ccchhcCCCCCCC-CcccCHHHHHHHhCCCCchHHHhCHhhccCCHhhhcCcccCc-hhhh------ccCCCCCCCCHHH
Confidence 9999999999999 799999999999999999999999999999999999998776 3332 2379999999999
Q ss_pred HHHHHHHHHHH
Q 005710 473 AKCRLDEALSE 483 (681)
Q Consensus 473 ~~~~~~~~~~~ 483 (681)
+|++++.+|+.
T Consensus 460 ~r~~~~~~~~~ 470 (471)
T TIGR03556 460 QQQLFKQLYQQ 470 (471)
T ss_pred HHHHHHHHHhh
Confidence 99999998853
No 5
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=100.00 E-value=5.2e-101 Score=854.11 Aligned_cols=413 Identities=29% Similarity=0.445 Sum_probs=344.9
Q ss_pred CeEEEEEcCCCCCCCCHHHHHHHHcC-CeEEEEEEcCCCCCC------CCCchhhHHHHHHhHHHHHHHHHhCCCceEEE
Q 005710 5 GCSIVWFRRDLRVEDNPALAAGVRAG-AVIAVFIWAPEEEGP------YYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTK 77 (681)
Q Consensus 5 ~~~LvWFRrDLRl~DN~AL~aA~~~~-~vlpVfI~dP~~~~~------~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~ 77 (681)
+++|||||||||++||+||.+|++.+ +||||||+||+++.. ...+..+.+||++||.+|+++|+++|++|+++
T Consensus 1 ~~~l~WfRrDLRl~DN~aL~~A~~~~~~vl~vfi~dp~~~~~~~~~~~~~~~~~r~~Fl~esL~~L~~~L~~~g~~L~v~ 80 (429)
T TIGR02765 1 KVVLYWFRNDLRVHDNPALYKASSSSDTLIPLYCFDPRQFKLTHFFGFPKTGPARGKFLLESLKDLRTSLRKLGSDLLVR 80 (429)
T ss_pred CeEEEEeCCCCccccHHHHHHHHhcCCeEEEEEEECchHhccccccccCCCCHHHHHHHHHHHHHHHHHHHHcCCCeEEE
Confidence 47899999999999999999999875 899999999987652 22466777799999999999999999999998
Q ss_pred eCCChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecCCeeeCCcccccccCCcccchHHHHHH
Q 005710 78 RSTDSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNADLLYEPWDVNDAQGQPFATFAAFWEK 157 (681)
Q Consensus 78 ~~g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~~~L~~p~~i~~~~g~~~~~f~~f~~~ 157 (681)
. |++.++|.+|+++++|++||+|++|+++++.||++|++.|++.||.++.+++++|++|++|....|.+|++|++|+++
T Consensus 81 ~-G~~~~vl~~L~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~~~~~~~~l~~p~~v~~~~~~~~~~ft~f~~~ 159 (429)
T TIGR02765 81 S-GKPEDVLPELIKELGVRTVFLHQEVGSEEKSVERLLQQALARLGIHVEQHWGSTLYHEDDLPFDLEDLPDVFTQFRKQ 159 (429)
T ss_pred e-CCHHHHHHHHHHHhCCCEEEEeccCCHHHHHHHHHHHHHHHhcCceEEEecCCEeECHHhcCCCCCCCCCCchHHHHH
Confidence 6 799999999999999999999999999999999999999999999999999999999999998889999999999999
Q ss_pred HHcCCCCCCCCCCCCCCCCCC-CC---C-CCCCCCCCccccchhchhhhhcCCCCcCHHHHHHHHHHHhc-CcCCccccc
Q 005710 158 CLSMPFDPDAPLLPPKRINSG-DM---S-RCPSDTLVFEDESEKGSNALLARAWSPGWSNADKALTTFIN-GPLIEYSKN 231 (681)
Q Consensus 158 ~~~~~~~p~~p~~~p~~~~~~-~i---~-~~~~~~l~~~~~~~~~~~~~~~~~~~gGe~~A~~~L~~Fl~-~~l~~Y~~~ 231 (681)
+..... +..+.++|..+.+. .. . ..+++++++... .......|+|||.+|+++|++|+. +.+..|++.
T Consensus 160 ~~~~~~-~~~~~~~p~~~~~~~~~~~~~~~~~l~~~~~~~~-----~~~~~~~~~gGe~~A~~~L~~Fl~~~~l~~Y~~~ 233 (429)
T TIGR02765 160 VEAKCS-IRPPLPAPEKLPPLPSVDDPGWIPTLEDLGEESS-----EVDRGLPFVGGETAGLARLKEYFWSKDLKSYKET 233 (429)
T ss_pred HHhhCC-CCCCCCCcccCCCCcccccccCCCChhhcCCCcc-----cccccCCcCchHHHHHHHHHHHHhhccHhhhhhc
Confidence 754221 11222223222110 00 0 001112222110 000122489999999999999997 468999999
Q ss_pred ccCC-CCCCCCCCchhhhCCCCCHHHHHHHHHHHHhhhhhcCCCCCcchHHHHHHHHHHHHHHHHHHHhCCC-CCC-Ccc
Q 005710 232 RRKA-DSATTSFLSPHLHFGEVSVRKVFHLVRIKQVSWANEGNKAGDESVNLFLKSIGLREYSRYMSFNHPY-SHE-RPL 308 (681)
Q Consensus 232 Rn~p-~~~~tS~LSPyL~fG~LSpReV~~~v~~~~~~~~~~~~~~~~~s~~~fl~eL~WREf~~~l~~~~p~-~~~-~~~ 308 (681)
||.| +.++||+|||||+|||||||+|++++.+... . ....++++.|++||+|||||+++++++|. +.. .++
T Consensus 234 R~~~~~~~~tS~LSpyL~~G~iS~r~v~~~~~~~~~-----~-~~~~~~~~~~~~eL~WRef~~~~~~~~~~~~~~~~~~ 307 (429)
T TIGR02765 234 RNGMLGPDYSTKFSPWLALGCVSPRQIYEELQRYET-----E-RGANDSTYWVIFELLWRDYFRFYALKYGNRLFRFGGL 307 (429)
T ss_pred cCcccCCCCcCccCHHHhCCcccHHHHHHHHHHHHh-----h-cccCCCcHHHHHHHHHHHHHHHHHHHcCCcccccCCC
Confidence 9996 4678999999999999999999999866321 1 11123455677899999999998888874 221 222
Q ss_pred cccccCCCCcCchhHHHHHhcCCCCCHHHHHHHHHHHHhcchhhHHHHHHHHHHhhccCCCchHHHHHHHHhcccccCCC
Q 005710 309 LGHLKFFSWVVDEGYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVKVLQLPWRWGMKYFWDTLLDADLES 388 (681)
Q Consensus 309 ~~~~~~~pW~~d~~~~~aW~~G~TG~P~VDAaMRqL~~TGwmHnr~Rm~vAsfl~k~L~idWr~G~~~F~~~LlD~D~a~ 388 (681)
. ...++|..+++.|++|++|+|||||||||||||++|||||||+||+|||||||+|+||||+|++||+++|||||+|+
T Consensus 308 ~--~~~~~w~~~~~~~~~W~~G~TG~PivDAamrqL~~TG~mhnr~Rm~vAsFl~k~L~idWr~G~~~F~~~LiD~D~a~ 385 (429)
T TIGR02765 308 R--GKHPKWSFDAKRFEQWKTGTTGYPLVDANMRELNATGFMSNRGRQNVASFLVKDLGLDWRYGAEWFETQLVDYDVCS 385 (429)
T ss_pred c--cCCCCCccCHHHHHHHhCCCCCChhhhHHHHHHHHhCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHhhccchhc
Confidence 2 23578999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccchhhhhcCCCCCCCcccccCccccccccCCchhhHHhhchhc
Q 005710 389 DALGWQYISGTIPDGRAFDRIDNPQFEGYKFDPNGEYVRRWLPEL 433 (681)
Q Consensus 389 n~g~Wqw~aG~g~d~~~~~RifNP~~q~~k~Dp~G~yIr~wvPeL 433 (681)
|+|||||+||+|+|+.| +|||||++|++||||+|+|||||||||
T Consensus 386 n~g~Wqw~ag~g~d~~~-~Rifnp~~q~~k~Dp~g~yir~wvPeL 429 (429)
T TIGR02765 386 NWGNWQYLAGVGNDPRG-SRQFNIEKQAQDYDPDGEYVATWVPEL 429 (429)
T ss_pred CcccchhhhcCcCCCCc-CccCCHHHHHHhcCCCCCcHHHhcCCC
Confidence 99999999999999999 999999999999999999999999997
No 6
>KOG0133 consensus Deoxyribodipyrimidine photolyase/cryptochrome [Replication, recombination and repair; Signal transduction mechanisms]
Probab=100.00 E-value=8.4e-89 Score=746.33 Aligned_cols=483 Identities=37% Similarity=0.562 Sum_probs=414.8
Q ss_pred CCCCCeEEEEEcCCCCCCCCHHHHHHHHc-CCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeC
Q 005710 1 MSGRGCSIVWFRRDLRVEDNPALAAGVRA-GAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRS 79 (681)
Q Consensus 1 m~~~~~~LvWFRrDLRl~DN~AL~aA~~~-~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~ 79 (681)
|+.+.++|+|||+|||+||||||.+|++. ++|+||||+||+..+.+..|+.+.+||.|+|++|+++|+++|++|.+++
T Consensus 1 ~~~~~~~v~wfr~~lR~~dnpal~~a~~~~~~~~~v~i~d~~~~~~~~~g~~~~~~l~qsL~~ld~sl~~l~~~L~v~~- 79 (531)
T KOG0133|consen 1 MATGSKSVHWFRKGLRLHDNPALLAAAAGKEPVRPVFILDPEEAGSSNVGRNRWRFLLQSLEDLDQSLRELNSRLFVFR- 79 (531)
T ss_pred CCCccceEEecccCcccccChhhHHHhccCCCceeEEEeCHhHhhccccchhHHHHHHHHHHHHHHHHHHhCCceEEEe-
Confidence 67788999999999999999999766655 5999999999999988889999999999999999999999999999987
Q ss_pred CChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecCCeeeCCcccccc-cCCcccchHHHHHHH
Q 005710 80 TDSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNADLLYEPWDVNDA-QGQPFATFAAFWEKC 158 (681)
Q Consensus 80 g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~~~L~~p~~i~~~-~g~~~~~f~~f~~~~ 158 (681)
+.++.+|..+.++++++.|.++.+++|..+.||..++..|.++|+++....+++++.|+.+... .|+++.+|..|+..+
T Consensus 80 ~~p~~vl~~~~~~~~~~~l~~~~~~~p~~~vrD~~~~~~a~~l~i~v~s~~s~~~~~~~~~i~~n~~k~pls~~~~~~~~ 159 (531)
T KOG0133|consen 80 GHPIAVLSRLLEQVGVQKLKFEYDMEPDGKVRDATIKSLATELGLSVVSPVSHTLYLPDKIIEANGGKPPLSYKTFRGVC 159 (531)
T ss_pred CCchHHHhhhhhccceeEEEEEEeccCccccccHHHHHHHHHhhhhhcccCchhhhcHHHHHHhcCCCCccccccccccc
Confidence 4599999999999999999999999999999999999999999999999999999999999887 588999999999877
Q ss_pred HcCCCCCCCCCCCCCCCCC-----CCCC-----CCCCCCCCccccchhchhhhhcCCCCcCHHHHHHHHHHHhcCcCC--
Q 005710 159 LSMPFDPDAPLLPPKRINS-----GDMS-----RCPSDTLVFEDESEKGSNALLARAWSPGWSNADKALTTFINGPLI-- 226 (681)
Q Consensus 159 ~~~~~~p~~p~~~p~~~~~-----~~i~-----~~~~~~l~~~~~~~~~~~~~~~~~~~gGe~~A~~~L~~Fl~~~l~-- 226 (681)
..+.....+..+......+ .... .++++.+++.. .+... ..|++|++.|+++|+.|+...+-
T Consensus 160 ~~~~~~~~p~~v~~~~~~~~~~~~~~~~~~~~~v~~~e~l~~~~-----~~~~~-~~~~~g~s~al~~l~~~l~~~~~~a 233 (531)
T KOG0133|consen 160 QSMSAPKIPALVLSGLAVEKHPNFLANSKASAVVPTLELLRFIP-----SNYGE-VVWRGGESEALKRLDAHLKVPLWVA 233 (531)
T ss_pred cccccccccccccccccCCCChhhhhhcccccccCCchhhccCc-----ccccc-cccCCcccchhHHHHHHhhHHHHHh
Confidence 6653221000000000000 0000 01223333221 12111 23899999999999999987743
Q ss_pred cccccccCC---CCCCCCCCchhhhCCCCCHHHHHHHHHHHHhhhhhcCCCCCcchHHHHHHHHHHHHHHHHHHHhCCCC
Q 005710 227 EYSKNRRKA---DSATTSFLSPHLHFGEVSVRKVFHLVRIKQVSWANEGNKAGDESVNLFLKSIGLREYSRYMSFNHPYS 303 (681)
Q Consensus 227 ~Y~~~Rn~p---~~~~tS~LSPyL~fG~LSpReV~~~v~~~~~~~~~~~~~~~~~s~~~fl~eL~WREf~~~l~~~~p~~ 303 (681)
++......+ ...+++.|||||+|||||+|.+++.....++.|...++..+.++ .|+.||+||||+++++.++|.+
T Consensus 234 n~~~~~~~~~~~~~~s~~~Ls~yL~fg~~svr~~~~~~~~k~V~~~~~~~s~~~es--~~~~qv~Wre~~y~~~~n~p~~ 311 (531)
T KOG0133|consen 234 NLELRYSNANSRVKISTTVLSPYLKFGCLSVRYFYRCVRLKQVKWKAKKNSLPPES--LFLGQVAWREFFYTAAFNTPYF 311 (531)
T ss_pred hhhccccccchhcCCCccccccceeeccceeEeehhHhHHHHHHHhhhcccCCccc--cccceeeeechhhHhhcCCccc
Confidence 333333322 24678899999999999999999766655666666665555554 6999999999999999999999
Q ss_pred CCCcccccccCCCCcCchhHHHHHhcCCCCCHHHHHHHHHHHHhcchhhHHHHHHHHHHhh-ccCCCchHHHHHHHHhcc
Q 005710 304 HERPLLGHLKFFSWVVDEGYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVK-VLQLPWRWGMKYFWDTLL 382 (681)
Q Consensus 304 ~~~~~~~~~~~~pW~~d~~~~~aW~~G~TG~P~VDAaMRqL~~TGwmHnr~Rm~vAsfl~k-~L~idWr~G~~~F~~~Ll 382 (681)
+.++++..+..|||+.|...+++|++|+||||+|||+||||++||||||+.|++||||++| +|+|+|++|+++|+++|+
T Consensus 312 ~~m~~n~~~~~ipw~~n~~~~~aw~~G~tG~P~ida~m~~l~~~gw~h~~~R~~vasf~tr~~L~i~w~eg~~~F~~~ll 391 (531)
T KOG0133|consen 312 DDMPGNKILLQIPWDKNPPKLAAWLEGLTGYPWLDAGMRQLLASGWEHHRSRTIVASFLTRGDLLISWREGLDVFMEYLL 391 (531)
T ss_pred cccccccccccCCcccChhhhHHHHcCCCCCCchhHHHHHHHHHHHHhcccchhhHhHhhccceeeeHHHHHHHHHHHhc
Confidence 8899999999999999999999999999999999999999999999999999999999999 899999999999999999
Q ss_pred cccCCCCccchhhhhcCCCCCCCcccccCccccccccCCchhhHHhhchhccCCCCCcccCCCCCChhHHHHhCCccCCC
Q 005710 383 DADLESDALGWQYISGTIPDGRAFDRIDNPQFEGYKFDPNGEYVRRWLPELARLPTEWIHHPWNAPESVLQAAGIELGSN 462 (681)
Q Consensus 383 D~D~a~n~g~Wqw~aG~g~d~~~~~RifNP~~q~~k~Dp~G~yIr~wvPeL~~~p~~~ih~pw~~~~~~~~~~g~~~~~~ 462 (681)
|+|+..|.|||+|++|+..++.+|+|+|||+.+++++||+|.|||+|||||++.|.++||+||.+|..+|++++|.+|.+
T Consensus 392 D~D~~~~agnW~~~S~~s~f~~~~~~~ysp~~~~kk~dP~g~yir~~lp~l~~~p~~~i~~pW~~p~~~~~~~~~~lg~~ 471 (531)
T KOG0133|consen 392 DADSSKNAGNWMWLSSTSHFFDQFDRVYSPVALGKKLDPDGLYIRQWLPELRSGPMHFIYEPWAAPEGVQTAAGELLGVD 471 (531)
T ss_pred chhhhcCCCccceeccccccccccccccCHHHHhCcCCcchhhHHHHhHHHhcCCcceeccCCCCcHHHhhhhhhhhhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcCHHHHHHHHHHHHHHHHHHHHHHH
Q 005710 463 YPFPIVRIDAAKCRLDEALSEMWQQEAASR 492 (681)
Q Consensus 463 YP~Pivd~~~~~~~~~~~~~~~~~~~~~~~ 492 (681)
||+|||+++.++++.+++++.||+..+..+
T Consensus 472 Yp~~iv~~~~a~k~~~e~~~~~~~~~~~~~ 501 (531)
T KOG0133|consen 472 YPKPIVKLASAAKRNMEAMGCMWSIGAVHD 501 (531)
T ss_pred cchhhhhhHHhhHhHHHHHHHHHhhccccc
Confidence 999999999999999999999998765433
No 7
>TIGR00591 phr2 photolyase PhrII. All proteins in this family for which functions are known are DNA-photolyases used for the direct repair of UV irradiation induced DNA damage. Some repair 6-4 photoproducts while others repair cyclobutane pyrimidine dimers. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.5e-87 Score=750.95 Aligned_cols=392 Identities=20% Similarity=0.252 Sum_probs=321.0
Q ss_pred CCCeEEEEEcCCCCCCCCHHHHHHHH--c--C-CeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEE
Q 005710 3 GRGCSIVWFRRDLRVEDNPALAAGVR--A--G-AVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTK 77 (681)
Q Consensus 3 ~~~~~LvWFRrDLRl~DN~AL~aA~~--~--~-~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~ 77 (681)
++.++|||||||||++||+||.+|++ . + +||||||+||.... .+..+.+||++||.+|+++|+++|++|+++
T Consensus 21 ~~~~vL~WFRrDLRl~DN~aL~~A~~~a~~~~~~vl~vyi~dp~~~~---~~~~r~~Fl~esL~~L~~~L~~~g~~L~v~ 97 (454)
T TIGR00591 21 SSGVVVYWMSRDQRVQDNWALIAAQTLALKKKLPLHVCFCLVDFFLA---ATRRHYFFMLGGLDEVANECERLIIPFHLL 97 (454)
T ss_pred CCCeEEEEecCchhccCCHHHHHHHHHHHHcCCCEEEEEEeCCCccc---ccHHHHHHHHHHHHHHHHHHHHcCCceEEe
Confidence 35679999999999999999999976 2 3 79999999998653 366777899999999999999999999998
Q ss_pred eCCChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecCCeeeCCcccccccCCcccchHHHHHH
Q 005710 78 RSTDSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNADLLYEPWDVNDAQGQPFATFAAFWEK 157 (681)
Q Consensus 78 ~~g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~~~L~~p~~i~~~~g~~~~~f~~f~~~ 157 (681)
. |++.++|.+|+++++|++||+|.+|++++.+||++|++.|++ +|.++.|++++|++|+.+.++ .+|++|++|++.
T Consensus 98 ~-g~~~~~l~~l~~~~~i~~V~~~~~~~~~~~~rd~~v~~~l~~-~i~~~~~~~~~l~p~~~~~~~--~~y~~ft~~~k~ 173 (454)
T TIGR00591 98 D-GPPKELLPYFVDLHAAAAVVTDFSPLRQPEQWDEAVGKLLPK-DVPFQQVDAHNVVPCWAASKK--LEYAARTIRGKI 173 (454)
T ss_pred e-cChHHHHHHHHHHcCCCEEEEecccCcHHHHHHHHHHHHhcC-CCcEEEECCceEeeCcccCCc--eeeeeecHHHHH
Confidence 6 899999999999999999999999999999999999999966 999999999999999888765 588888877764
Q ss_pred HHcCCCCCCCCCCCCCCCC-CCCCCCCCC------CCCCccccchhchhhhhcCCC-CcCHHHHHHHHHHHhcCcCCccc
Q 005710 158 CLSMPFDPDAPLLPPKRIN-SGDMSRCPS------DTLVFEDESEKGSNALLARAW-SPGWSNADKALTTFINGPLIEYS 229 (681)
Q Consensus 158 ~~~~~~~p~~p~~~p~~~~-~~~i~~~~~------~~l~~~~~~~~~~~~~~~~~~-~gGe~~A~~~L~~Fl~~~l~~Y~ 229 (681)
.........+.+.+...+ +..+...+. +.+.+. .......| +|||.+|+++|++|+++++.+|.
T Consensus 174 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~gGe~aA~~~L~~F~~~~l~~Y~ 245 (454)
T TIGR00591 174 -RKLLPEYLTEFPRVLKHPSPLDLEAGPVDWDAVRDSLAVE-------RSVEEVVWAKPGTTAGLIMLESFIEKRLCFFR 245 (454)
T ss_pred -HHhChhhccccCCCccCCcccccccCcCCHHHHHHhccCc-------CCcCCcCCCCCcHHHHHHHHHHHHHHHHHHHH
Confidence 221100000000000000 000000000 000000 00111237 99999999999999999999999
Q ss_pred ccccCCCCCCCCCCchhhhCCCCCHHHHHHHHHHHHhhhhhcCCCCCcchHHHHHHHHHHH-HHHHHHHHhCCCCCCCcc
Q 005710 230 KNRRKADSATTSFLSPHLHFGEVSVRKVFHLVRIKQVSWANEGNKAGDESVNLFLKSIGLR-EYSRYMSFNHPYSHERPL 308 (681)
Q Consensus 230 ~~Rn~p~~~~tS~LSPyL~fG~LSpReV~~~v~~~~~~~~~~~~~~~~~s~~~fl~eL~WR-Ef~~~l~~~~p~~~~~~~ 308 (681)
++||.|+.++||+|||||+||+||||+|++++.+.. . ....+++.|++||+|| ||++++++++|.+.. +
T Consensus 246 ~~Rn~p~~~~tS~LSPyL~~G~IS~R~i~~~~~~~~------~--~~~~~~~~fl~EL~WR~ef~~~~~~~~p~~~~--~ 315 (454)
T TIGR00591 246 TRRNDPNNDALSMLSPWLHFGQLSAQRAARAVERAR------G--NAGESVEFFEEELVVRRELADNFCFYNPYYDS--L 315 (454)
T ss_pred HhcCCcccccccccchHHhcCcccHHHHHHHHHHhc------c--CCchHHHHHHHHHHHHHHHHhHhhhcCCCccc--c
Confidence 999999999999999999999999999999985421 1 1123567899999999 899999999998753 2
Q ss_pred cccccCCCCc--------Cch-h---HHHHHhcCCCCCHHHHHHHHHHHHhcchhhHHHHHHHHHHhhccCCCchHHHHH
Q 005710 309 LGHLKFFSWV--------VDE-G---YFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVKVLQLPWRWGMKY 376 (681)
Q Consensus 309 ~~~~~~~pW~--------~d~-~---~~~aW~~G~TG~P~VDAaMRqL~~TGwmHnr~Rm~vAsfl~k~L~idWr~G~~~ 376 (681)
.. ...|. .|. + .|++|++|+|||||||||||||++|||||||+||+|| |+| |||++|++|
T Consensus 316 ~~---~~~w~~~~l~~~~~d~r~~~~~~~~W~~G~Tg~pivdA~MrqL~~TG~MHNr~RMi~a----K~l-i~W~~g~~~ 387 (454)
T TIGR00591 316 CG---AYWWARTTLDDHAKDKREHLYSLEQLEKSTTHDYLWNAAQEQLVTEGKMHGFLRMYWA----KKI-LEWTHSPEE 387 (454)
T ss_pred cc---chHHHHHHHHHHhcCCccccCCHHHHHhcCcCcHhHhHHHHHHHHhCccccceeeeee----eeh-hhcCCCHHH
Confidence 21 22365 343 3 6999999999999999999999999999999999999 888 999999999
Q ss_pred HHH--------hcccccCCCCccchhhhhcCCCCCCCc-----c---cccCccccccccCCchhhHHhh
Q 005710 377 FWD--------TLLDADLESDALGWQYISGTIPDGRAF-----D---RIDNPQFEGYKFDPNGEYVRRW 429 (681)
Q Consensus 377 F~~--------~LlD~D~a~n~g~Wqw~aG~g~d~~~~-----~---RifNP~~q~~k~Dp~G~yIr~w 429 (681)
|++ +|||||+|+|+|||||+ |+|+|.+|| | |+|||.+|++||||+| |||+|
T Consensus 388 f~~~~~~ln~~~lvDgd~a~n~~~wqW~-~~G~d~~p~~~~~~fg~iR~~np~~q~~kfd~~~-yi~~~ 454 (454)
T TIGR00591 388 ALSIAIYLNDKYILDGRDPNGYVGCMWS-ICGIHDQGWAERIVFGKIRYMNYAGCRRKFNVAY-FERKY 454 (454)
T ss_pred HHHHHHHhhhhhhccCCCCCccceeeeE-eccccCCCCCCCccceeeeecChhhhhccCCHHH-HHhhC
Confidence 999 89999999999999999 999999999 9 9999999999999999 99998
No 8
>PF03441 FAD_binding_7: FAD binding domain of DNA photolyase from Prosite.; InterPro: IPR005101 This entry represents a multi-helical domain composed of two all-alpha subdomains that is found as the C-terminal domain in cryptochrome proteins, as well as at the N-terminal of DNA photolyase where it acts as a FAD-binding domain (the N-terminal of DNA photolyase binds a light-harvesting cofactor). Photolyases and cryptochromes are related flavoproteins that bind FAD. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes (CRY1 and CRY2) are blue light photoreceptors that mediate blue light-induced gene expression [, ]. DNA photolyases are DNA repair enzymes that repair mismatched pyrimidine dimers induced by exposure to ultra-violet light. They bind to UV-damaged DNA containing pyrimidine dimers and, upon absorbing a near-UV photon (300 to 500 nm), they catalyse dimer splitting, breaking the cyclobutane ring joining the two pyrimidines of the dimer so as to split them into the constituent monomers; this process is called photoreactivation. DNA photolyases require two choromophore-cofactors for their activity. All monomers contain a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm [, ].; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 3ZXS_A 1DNP_A 2XRZ_B 2XRY_A 2VTB_A 2J4D_B 2IJG_X 3TVS_A 2E0I_D ....
Probab=100.00 E-value=2.2e-84 Score=679.94 Aligned_cols=272 Identities=41% Similarity=0.727 Sum_probs=244.7
Q ss_pred cCHHHHHHHHHHHhcCcCCcccccccCCCCCCCCCCchhhhCCCCCHHHHHHHHHHHHhhhhhcCCCCCcchHHHHHHHH
Q 005710 208 PGWSNADKALTTFINGPLIEYSKNRRKADSATTSFLSPHLHFGEVSVRKVFHLVRIKQVSWANEGNKAGDESVNLFLKSI 287 (681)
Q Consensus 208 gGe~~A~~~L~~Fl~~~l~~Y~~~Rn~p~~~~tS~LSPyL~fG~LSpReV~~~v~~~~~~~~~~~~~~~~~s~~~fl~eL 287 (681)
|||++|+++|+.|++++|.+|++.||.|..++||+|||||+|||||||+|++++.+... ......++++.|++||
T Consensus 1 GGe~~A~~~L~~Fl~~~l~~Y~~~r~~p~~~~~S~LSpyL~~G~lS~r~v~~~~~~~~~-----~~~~~~~~~~~f~~eL 75 (277)
T PF03441_consen 1 GGETAALKRLEEFLKERLADYGEQRDDPAADGTSRLSPYLNFGCLSPREVYRAVKKAQE-----ANDAHSESAEKFIREL 75 (277)
T ss_dssp SSHHHHHHHHHHHHHHCGGGHHHHTT-TTSTTS---HHHHHTTSS-HHHHHHHHHHHHH-----CHTCHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHHHHhhchhccCCCcCCcCcccHHHhCCCcCHHHHHHHHHHHhh-----hcccccchHHHHHHHH
Confidence 79999999999999999999999999999999999999999999999999999987642 1111236889999999
Q ss_pred HHHHHHHHHHHhCCCCC-CCcccccccCCCCc---CchhHHHHHhcCCCCCHHHHHHHHHHHHhcchhhHHHHHHHHHHh
Q 005710 288 GLREYSRYMSFNHPYSH-ERPLLGHLKFFSWV---VDEGYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFV 363 (681)
Q Consensus 288 ~WREf~~~l~~~~p~~~-~~~~~~~~~~~pW~---~d~~~~~aW~~G~TG~P~VDAaMRqL~~TGwmHnr~Rm~vAsfl~ 363 (681)
+||||++++++++|.+. ..++.+.++.++|. .+.+.|++|++|+|||||||||||||++|||||||+|||||||||
T Consensus 76 ~WRef~~~~~~~~p~~~~~~~~~~~~~~~~w~~~~~~~~~~~~w~~G~TG~p~vDAamrqL~~tG~mHn~~R~~vasfl~ 155 (277)
T PF03441_consen 76 IWREFYRQLLYHNPNLDMFENFNPKFRQIPWEDDRENPELFEAWCEGRTGYPLVDAAMRQLRQTGWMHNRLRMIVASFLT 155 (277)
T ss_dssp HHHHHHHHHHHHSGGCTCSSTSSTTCCCSHCBTSBSTHHHHHHHHTT-SS-HHHHHHHHHHHHHS---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCcchhhhhccHHHHhhhhcccccCHHHHHHHHcCCCCChHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence 99999999999999877 77888888889995 577899999999999999999999999999999999999999999
Q ss_pred hccCCCchHHHHHHHHhcccccCCCCccchhhhhcCCCCCCCcccccCccccccccCCchhhHHhhchhccCCCCCcccC
Q 005710 364 KVLQLPWRWGMKYFWDTLLDADLESDALGWQYISGTIPDGRAFDRIDNPQFEGYKFDPNGEYVRRWLPELARLPTEWIHH 443 (681)
Q Consensus 364 k~L~idWr~G~~~F~~~LlD~D~a~n~g~Wqw~aG~g~d~~~~~RifNP~~q~~k~Dp~G~yIr~wvPeL~~~p~~~ih~ 443 (681)
|+|+|||+.|++||+++|||||+|+|+|||||+||+|+|++||+|+|||++|++||||+|+|||||||||+++|.++||+
T Consensus 156 k~l~i~W~~g~~~f~~~liD~d~a~n~~~wqw~ag~g~d~~~~~r~~np~~q~~~~Dp~g~~ir~w~PeL~~~~~~~ih~ 235 (277)
T PF03441_consen 156 KDLLIDWREGAEWFAEHLIDYDPASNYGNWQWAAGTGTDAKPYFRIFNPVKQSKKFDPDGEYIRRWVPELADLPDEYIHE 235 (277)
T ss_dssp HTSHBHHHHHHHHHHHHHTT--HHHHHHHHHHHTTSSSTGCSTTTHHHHHHHHHHHSTTSHHHHHHSGGGTTSTHHHHTS
T ss_pred HhccCCccccHHHHHHHhhccCcchHHHHHHHHHhhccccCccccccCchHHHHhhCcHHHHHHHHHHHHhcCChhheeC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCChhHHHHhCCccCCCCCCCCcCHHHHHHHHHHHHHHH
Q 005710 444 PWNAPESVLQAAGIELGSNYPFPIVRIDAAKCRLDEALSEM 484 (681)
Q Consensus 444 pw~~~~~~~~~~g~~~~~~YP~Pivd~~~~~~~~~~~~~~~ 484 (681)
||+++..+|+++||.+|.+||+|||||+++|++++++|+++
T Consensus 236 p~~~~~~~~~~~~~~~~~~YP~pivd~~~~r~~~~~~~~~~ 276 (277)
T PF03441_consen 236 PWKAPPAVQKAAGCVLGNDYPKPIVDHKEARKRALKRYKAA 276 (277)
T ss_dssp CHGSHHHHHHHCT-CTTTSSBTSSSHHHHHHHHHHHHHHHH
T ss_pred hhccChHHHHHhCCccCCCCCcccCCHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999876
No 9
>COG3046 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]
Probab=100.00 E-value=3.6e-38 Score=329.16 Aligned_cols=383 Identities=17% Similarity=0.201 Sum_probs=293.9
Q ss_pred eEEEEEcCCCCCCCCHHHHHHHHcCCeEEEEEEcCCCCC-CCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeCCC--h
Q 005710 6 CSIVWFRRDLRVEDNPALAAGVRAGAVIAVFIWAPEEEG-PYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRSTD--S 82 (681)
Q Consensus 6 ~~LvWFRrDLRl~DN~AL~aA~~~~~vlpVfI~dP~~~~-~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~g~--~ 82 (681)
.+++|.--|.-.++++||.. ..+. .+|.+.+-..+. ....++.+..+++.+|+++.+.|+..|.++.+....+ .
T Consensus 3 ~~~~lvLgdQL~~~~~al~~--d~~~-~~vllvE~~~~a~~~r~HkqKl~lv~aAMR~Fad~LraeG~~V~Y~~~~~~~~ 79 (505)
T COG3046 3 SSVVLVLGDQLSEDHSALGD--DRSQ-DGVLLVESAAEARYRRHHKQKLVLVFAAMRHFADELRAEGLKVRYERADDNSF 79 (505)
T ss_pred ceEEEEeccccccccchhcc--Cccc-CcEEEehhHhHhhhhhcchhhhHHHHHHHHHHHHHHhhCCceeEEEEcCCccc
Confidence 56899999999999999965 1122 234444433221 1112333444889999999999999999986655433 5
Q ss_pred HHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecCC-eeeCCccccccc-CCcccchHHHHHHHHc
Q 005710 83 VSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNAD-LLYEPWDVNDAQ-GQPFATFAAFWEKCLS 160 (681)
Q Consensus 83 ~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~~-~L~~p~~i~~~~-g~~~~~f~~f~~~~~~ 160 (681)
...|...++.++.++|++. +|.+...+.+++++.-..||++..+++. .|.++.++...- +.+.-.+..||+++.+
T Consensus 80 ~~~l~~~l~~~~~d~~~~~---~p~~~~l~~~m~~L~~~~g~~i~~~~~~~Fl~s~a~f~~w~~~~k~~lme~FYr~mRk 156 (505)
T COG3046 80 GGELRRALEAYPGDRVQVQ---EPGDHRLEARMKSLSMALGIEITEVENPHFLCSRAEFDAWAGDRKPLLMESFYRRMRK 156 (505)
T ss_pred chHHHHHHHhcCCCeEEEe---cCcchhHHHHHHhhhhhcCceeEEecCcceecCHHHhhhhhccCcchhhHHHHHHHHH
Confidence 6678899999999999998 7888888888888777899999999876 788888887763 3444579999988765
Q ss_pred C---CCCCCCCCCCCCCCC--------CCCCCC----CCCCCC------CccccchhchhhhhcCCCCcCHHHHHHHHHH
Q 005710 161 M---PFDPDAPLLPPKRIN--------SGDMSR----CPSDTL------VFEDESEKGSNALLARAWSPGWSNADKALTT 219 (681)
Q Consensus 161 ~---~~~p~~p~~~p~~~~--------~~~i~~----~~~~~l------~~~~~~~~~~~~~~~~~~~gGe~~A~~~L~~ 219 (681)
. .|+...|...-+.+. ++-.++ .+.++. -++..+..+.+.+..+.|+.++++|...|+.
T Consensus 157 r~g~LM~~dqP~GGrWnFDaeNR~~~~pdL~~P~pl~fppd~~vq~v~e~Ve~~f~~~~G~~e~F~wpvtr~~A~~~L~~ 236 (505)
T COG3046 157 RTGILMEDDQPEGGRWNFDAENRKKLPPDLLPPKPLKFPPDEIVQEVKERVERLFPDNFGQVEGFGWPVTRTQALRALKH 236 (505)
T ss_pred hhceeccCCCCCCCcCCcCcccccCCCCcCCCCCCCCCCCcchhHHHHHHHHhhCCCCCCccccCCCCCCHHHHHHHHHH
Confidence 4 233323333222111 100000 000110 0111122334445567899999999999999
Q ss_pred HhcCcCCcccccccCCCCC----CCCCCchhhhCCCCCHHHHHHHHHHHHhhhhhcCCCCCcchHHHHHHHH-HHHHHHH
Q 005710 220 FINGPLIEYSKNRRKADSA----TTSFLSPHLHFGEVSVRKVFHLVRIKQVSWANEGNKAGDESVNLFLKSI-GLREYSR 294 (681)
Q Consensus 220 Fl~~~l~~Y~~~Rn~p~~~----~tS~LSPyL~fG~LSpReV~~~v~~~~~~~~~~~~~~~~~s~~~fl~eL-~WREf~~ 294 (681)
|+..+|.+|+..+|++..+ .+|.|||||+.|+|+|+||+.++.+++. ...++.+++|+||||| +||||++
T Consensus 237 Fi~~~L~nFG~yQDam~~d~~~L~HSllS~alNigLL~PleVi~Aa~~Ay~-----~g~ipLN~VEGFvRQiiGWREfmR 311 (505)
T COG3046 237 FIADRLPNFGSYQDAMSADDPHLWHSLLSFALNIGLLTPLEVIRAALKAYR-----EGDIPLNSVEGFVRQIIGWREFMR 311 (505)
T ss_pred HHHHhhhcCCcHHHHHhcCCchhHHHHHHHHhhccCCCHHHHHHHHHHhhc-----cCCCchHHHHHHHHHHhhHHHHHH
Confidence 9999999999999998654 5899999999999999999999988752 3467788999999999 5999999
Q ss_pred HHHHhC-CCCCCCcccccccCCCCcCchhHHHHHhcCCCCCHHHHHHHHHHHHhcchhhHHHHHHHHHHhhccCCCchHH
Q 005710 295 YMSFNH-PYSHERPLLGHLKFFSWVVDEGYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVKVLQLPWRWG 373 (681)
Q Consensus 295 ~l~~~~-p~~~~~~~~~~~~~~pW~~d~~~~~aW~~G~TG~P~VDAaMRqL~~TGwmHnr~Rm~vAsfl~k~L~idWr~G 373 (681)
.+|+.. |.+.++|++++...+| ...+.|+|++.|++-+..+...+||.||+.|.||.++|+..+++|+...
T Consensus 312 giY~~~~P~y~trN~f~~d~~Lp--------~~yw~g~T~M~cl~~av~~v~d~gYAHHIqRLMV~gNfALl~G~dPd~v 383 (505)
T COG3046 312 GIYWLKMPDYATRNFFNADRKLP--------PFYWTGQTKMACLAIAVGRVLDHGYAHHIQRLMVTGNFALLLGVDPDAV 383 (505)
T ss_pred HhhhhcCCchhhhhhhccCCCCC--------CccccCCcCchHHHHHHHHHhhhhHHHHHHHHHHHhhHHHHhCCCHHHH
Confidence 999876 8899999887766666 4457899999999999999999999999999999999999999999999
Q ss_pred HHHHHHhccc-ccC---CCCccchhhhhcCCCCCCCcc
Q 005710 374 MKYFWDTLLD-ADL---ESDALGWQYISGTIPDGRAFD 407 (681)
Q Consensus 374 ~~~F~~~LlD-~D~---a~n~g~Wqw~aG~g~d~~~~~ 407 (681)
.+||+..+|| ||| ++.+|+-|++.|....++||.
T Consensus 384 ~~Wf~~~fiDAYdWV~~PNv~GM~qFADGG~iatKPYa 421 (505)
T COG3046 384 DRWFMEVFIDAYDWVELPNVRGMSQFADGGLIATKPYA 421 (505)
T ss_pred HHHHHHHHhhHhhheecccccchhhcccCceeecCccc
Confidence 9999999999 577 677888899999877778874
No 10
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=100.00 E-value=8.5e-34 Score=275.55 Aligned_cols=156 Identities=41% Similarity=0.698 Sum_probs=133.8
Q ss_pred EEEEEcCCCCCCCCHHHHHHHHcC-CeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeCCChHHH
Q 005710 7 SIVWFRRDLRVEDNPALAAGVRAG-AVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRSTDSVSS 85 (681)
Q Consensus 7 ~LvWFRrDLRl~DN~AL~aA~~~~-~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~g~~~~~ 85 (681)
+|||||||||++||+||++|++.+ +|+||||+||........+..+++||++||.+|+++|+++|++|+++. |++.++
T Consensus 1 ~l~Wfr~DLRl~DN~aL~~A~~~~~~v~~vfv~d~~~~~~~~~~~~r~~Fl~~sL~~L~~~L~~~g~~L~v~~-g~~~~~ 79 (165)
T PF00875_consen 1 VLVWFRRDLRLHDNPALHAAAQNGDPVLPVFVFDPEEFHPYRIGPRRRRFLLESLADLQESLRKLGIPLLVLR-GDPEEV 79 (165)
T ss_dssp EEEEESS--SSTT-HHHHHHHHTTSEEEEEEEE-HHGGTTCSSCHHHHHHHHHHHHHHHHHHHHTTS-EEEEE-SSHHHH
T ss_pred CEEEEcCCCchhhhHHHHHHHHcCCCeEEEEEecccccccccCcchHHHHHHHHHHHHHHHHHhcCcceEEEe-cchHHH
Confidence 699999999999999999999884 899999999983222234777788999999999999999999999986 789999
Q ss_pred HHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecCCeeeCCcccccccCCcccchHHHHHHHHcCCC
Q 005710 86 LLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNADLLYEPWDVNDAQGQPFATFAAFWEKCLSMPF 163 (681)
Q Consensus 86 L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~~~L~~p~~i~~~~g~~~~~f~~f~~~~~~~~~ 163 (681)
|.+|+++++|++||++++|+++++.||++|++.|.+.||.++.+++++|++|+.+.++.|.+|++|+||+++|++...
T Consensus 80 l~~l~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~~~~~~~~L~~~~~i~~~~~~~~~vFtpf~k~~~~~~~ 157 (165)
T PF00875_consen 80 LPELAKEYGATAVYFNEEYTPYERRRDERVRKALKKHGIKVHTFDDHTLVPPDDIPKKDGEPYKVFTPFRKKWEKQLL 157 (165)
T ss_dssp HHHHHHHHTESEEEEE---SHHHHHHHHHHHHHHHHTTSEEEEE--SSSS-HHHCHSTTSSSHSSHHHHHHHHHCHCS
T ss_pred HHHHHHhcCcCeeEeccccCHHHHHHHHHHHHHHHhcceEEEEECCcEEEeccccccCCCCCcccHHHHHHHHHhcCC
Confidence 999999999999999999999999999999999999999999999999999999988899999999999999998764
No 11
>PF12546 Cryptochrome_C: Blue/Ultraviolet sensing protein C terminal; InterPro: IPR020978 Cryptochromes are blue/ultraviolet-A light sensing photoreceptors involved in regulating various growth and developmental responses in plants []. This signature is found in eukaryotic proteins at the C-terminal end and are typically between 113 and 125 amino acids in length. The family is found in association with PF03441 from PFAM and PF00875 from PFAM.
Probab=99.78 E-value=5.9e-20 Score=165.81 Aligned_cols=117 Identities=62% Similarity=0.863 Sum_probs=95.3
Q ss_pred CCCCCCCCCCcccCCCCCCCCCCCc-cccccccCCCCccccCcch-hhhhhhHhhhcccccccccccCCccCCC-CCccc
Q 005710 510 APIAFPPDIQMEEIPEPARNNLPTT-ARRYEDQMVPSMTTSLVRV-EEEESSLELRNSAEESRAEVPRNANVNQ-EPRRD 586 (681)
Q Consensus 510 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~-~~~~~~~d~~~~~~~~~~~~~~~~~~~~-~~~~~ 586 (681)
.+|+||+++|||+++++++.+++.+ +|++.|||||+|+++++|+ +|+|.|.|++|+++++|+|||+++++.. ..+.+
T Consensus 1 ~piaFPq~~qMEv~repvr~n~~~~~~Rr~~DQMVPsmTsSl~Ra~~e~e~S~d~~ns~~~sRAEVP~~~~~~~~~~~~~ 80 (121)
T PF12546_consen 1 APIAFPQDLQMEVDREPVRNNPPATITRRYEDQMVPSMTSSLIRAVEEEETSADLRNSSEDSRAEVPSNTHFQPQAERRE 80 (121)
T ss_pred CCcCCccceecccccccccCCCCccccccccccccccccHHHHHhhcccccchhhhcccccccccCCccccccchhhhhh
Confidence 3689999999999999999888553 5999999999999999996 5568999999989999999999987644 44444
Q ss_pred ccc-cccccccccchhhhhhhHHHHHhhcCCCccccccccc
Q 005710 587 TLN-QGVLQTVHNNNAFQQFNAAIVLANAEDSTAESSSTSR 626 (681)
Q Consensus 587 v~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~ 626 (681)
.-+ +.+....+++..+|++++.+.+.+.+|||||||||.+
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~STAESSSs~~ 121 (121)
T PF12546_consen 81 TVDQGGGQNVNHNQNNFQQFNHRVRRRNEEDSTAESSSSTR 121 (121)
T ss_pred hhhcccccccccccccccchhHHhhccccCCCchhhccccC
Confidence 333 4444456677789999998777778899999998864
No 12
>PF04244 DPRP: Deoxyribodipyrimidine photo-lyase-related protein; InterPro: IPR007357 This family appears to be related to DNA photolyases.; PDB: 3ZXS_A.
Probab=98.44 E-value=7.7e-07 Score=90.78 Aligned_cols=147 Identities=17% Similarity=0.168 Sum_probs=87.2
Q ss_pred EEEEcCCCCCCCCHHHHHHHHcCCeEEEEEEcCCCC-CCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeCC------
Q 005710 8 IVWFRRDLRVEDNPALAAGVRAGAVIAVFIWAPEEE-GPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRST------ 80 (681)
Q Consensus 8 LvWFRrDLRl~DN~AL~aA~~~~~vlpVfI~dP~~~-~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~g------ 80 (681)
|+|.--|.-..++++|.. . ..-..|++++-..+ .....++.+..+++.||+++++.|++.|.++.++..+
T Consensus 1 L~lIlgdQL~~~~~~l~~-~--~~~~~v~mvE~~~~~~~~~~HkqKl~l~~saMRhfa~~L~~~G~~V~Y~~~~~~~~~~ 77 (224)
T PF04244_consen 1 LRLILGDQLFEDHPALRD-D--PADDRVLMVEVPEEFTYVPHHKQKLVLFFSAMRHFADELRAKGFRVHYIELDDPENTQ 77 (224)
T ss_dssp EEE--TT---TT-HHHHT----TTT-EEEEE--HHHHHSS---HHHHHHHHHHHHHHHHHHHHTT--EEEE-TT-TT--S
T ss_pred CeEeccCCCCCccccccc-C--CCCCEEEEEEchHHhCcCcccHHHHHHHHHHHHHHHHHHHhCCCEEEEEeCCCccccc
Confidence 567778888899999966 2 22345666553322 2333455666699999999999999999999887654
Q ss_pred ChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecCC-eeeCCcccccc-cCCcccchHHHHHHH
Q 005710 81 DSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNAD-LLYEPWDVNDA-QGQPFATFAAFWEKC 158 (681)
Q Consensus 81 ~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~~-~L~~p~~i~~~-~g~~~~~f~~f~~~~ 158 (681)
...+.|.+++++++++.|.+. +|.+...+++++++|++.||++..+++. .|.++.++... .|+....+..||+.+
T Consensus 78 s~~~~L~~~~~~~~~~~~~~~---~P~d~~l~~~l~~~~~~~~i~~~~~~~~~Fl~s~~~f~~~~~~~k~~~Me~FYR~m 154 (224)
T PF04244_consen 78 SFEDALARALKQHGIDRLHVM---EPGDYRLEQRLESLAQQLGIPLEVLEDPHFLTSREEFAEWFEGRKRLRMEYFYREM 154 (224)
T ss_dssp SHHHHHHHHHHHH----EEEE-----S-HHHHHHHHH----SSS-EEEE--TTSSS-HHHHHHHHTT-SS--HHHHHHHH
T ss_pred cHHHHHHHHHHHcCCCEEEEE---CCCCHHHHHHHHhhhcccCCceEEeCCCCccCCHHHHHHHHccCCceeHHHHHHHH
Confidence 346789899999999999987 8999999999999999999999999887 46677777664 455556799999876
Q ss_pred Hc
Q 005710 159 LS 160 (681)
Q Consensus 159 ~~ 160 (681)
++
T Consensus 155 Rk 156 (224)
T PF04244_consen 155 RK 156 (224)
T ss_dssp HH
T ss_pred HH
Confidence 55
No 13
>TIGR00289 conserved hypothetical protein TIGR00289. Homologous proteins related to MJ0570 of Methanococcus jannaschii include both the apparent orthologs found by this model above the trusted cutoff, the much longer protein YLR143W from Saccharomyces cerevisiae, and second homologous proteins from Archaeoglobus fulgidus and Pyrococcus horikoshii that appear to represent a second orthologous group.
Probab=83.83 E-value=18 Score=37.18 Aligned_cols=97 Identities=16% Similarity=0.181 Sum_probs=60.0
Q ss_pred HHHHHHHcCCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeC-C---ChHHHHHHHHHHcCCCE
Q 005710 22 ALAAGVRAGAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRS-T---DSVSSLLEVVKATGATQ 97 (681)
Q Consensus 22 AL~aA~~~~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~-g---~~~~~L~~L~~~~~~~~ 97 (681)
||+.|.+...|..|+..-|.....+ .|-...+..++..-+.+|++|+.... + +..+.|.+.+++.|++.
T Consensus 16 Al~~~~~~~~V~~L~~~~~~~~~s~-------~~h~~~~~~~~~qA~algiPl~~~~~~~~~e~~~~~l~~~l~~~gv~~ 88 (222)
T TIGR00289 16 ALYKALEEHEVISLVGVFSENEESY-------MFHSPNLHLTDLVAEAVGIPLIKLYTSGEEEKEVEDLAGQLGELDVEA 88 (222)
T ss_pred HHHHHHHcCeeEEEEEEcCCCCCcc-------ccccCCHHHHHHHHHHcCCCeEEEEcCCchhHHHHHHHHHHHHcCCCE
Confidence 5666665545777777766532211 12233556666667788999976542 2 24455666677789999
Q ss_pred EEEecccChhhHHHHHHHHHHHHhCCeEEEE
Q 005710 98 LFFNHLYDPLSLVRDHRAKEALTAQGIAVRS 128 (681)
Q Consensus 98 V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~ 128 (681)
|++-.-...+.+ .++.+.|.+.|+....
T Consensus 89 vv~GdI~s~~qr---~~~e~vc~~~gl~~~~ 116 (222)
T TIGR00289 89 LCIGAIESNYQK---SRIDKVCRELGLKSIA 116 (222)
T ss_pred EEECccccHHHH---HHHHHHHHHcCCEEec
Confidence 998744433333 3566678888886654
No 14
>COG2102 Predicted ATPases of PP-loop superfamily [General function prediction only]
Probab=79.19 E-value=24 Score=36.14 Aligned_cols=99 Identities=18% Similarity=0.220 Sum_probs=62.3
Q ss_pred CHHHHHHHHcC-CeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeC-C---ChHHHHHHHHHHcC
Q 005710 20 NPALAAGVRAG-AVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRS-T---DSVSSLLEVVKATG 94 (681)
Q Consensus 20 N~AL~aA~~~~-~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~-g---~~~~~L~~L~~~~~ 94 (681)
+-||+.|.+.+ .|..+.++-|+....+..+... +.-....=+.+|++++.... + .-++.|.++++..+
T Consensus 14 ~~Al~~a~~~G~eV~~Ll~~~p~~~dS~m~H~~n-------~~~~~~~Ae~~gi~l~~~~~~g~~e~eve~L~~~l~~l~ 86 (223)
T COG2102 14 FYALYLALEEGHEVVYLLTVKPENGDSYMFHTPN-------LELAELQAEAMGIPLVTFDTSGEEEREVEELKEALRRLK 86 (223)
T ss_pred HHHHHHHHHcCCeeEEEEEEecCCCCeeeeeccc-------hHHHHHHHHhcCCceEEEecCccchhhHHHHHHHHHhCc
Confidence 56888899887 7888888877643221111111 22222222446999876542 2 25667888888889
Q ss_pred CCEEEEecccChhhHHHHHHHHHHHHhCCeEEEE
Q 005710 95 ATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRS 128 (681)
Q Consensus 95 ~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~ 128 (681)
++.|+.-.-+.-+.+ .++..+|.+.|+.+..
T Consensus 87 ~d~iv~GaI~s~yqk---~rve~lc~~lGl~~~~ 117 (223)
T COG2102 87 VDGIVAGAIASEYQK---ERVERLCEELGLKVYA 117 (223)
T ss_pred ccEEEEchhhhHHHH---HHHHHHHHHhCCEEee
Confidence 999988744444443 3566778888987654
No 15
>cd01994 Alpha_ANH_like_IV This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily of proteins is predicted to bind ATP. This domainhas a strongly conserved motif SGGKD at the N terminus.
Probab=76.54 E-value=34 Score=34.21 Aligned_cols=96 Identities=19% Similarity=0.303 Sum_probs=55.7
Q ss_pred HHHHHHHcC-CeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeC----CChHH----HHHHHHHH
Q 005710 22 ALAAGVRAG-AVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRS----TDSVS----SLLEVVKA 92 (681)
Q Consensus 22 AL~aA~~~~-~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~----g~~~~----~L~~L~~~ 92 (681)
+|+.|.+.+ .|++|++..|...... .|-...+..++...+++|+++++... .+..+ .|.++.++
T Consensus 15 al~~a~~~G~~v~~l~~~~~~~~~~~-------~~h~~~~e~~~~~A~~lgipl~~i~~~~~~e~~~~~l~~~l~~~~~~ 87 (194)
T cd01994 15 ALYRALEEGHEVVALLNLTPEEGSSM-------MYHTVNHELLELQAEAMGIPLIRIEISGEEEDEVEDLKELLRKLKEE 87 (194)
T ss_pred HHHHHHHcCCEEEEEEEEecCCCCcc-------cccccCHHHHHHHHHHcCCcEEEEeCCCCchHHHHHHHHHHHHHHHc
Confidence 455666666 6889988766532111 11123455666666778999977642 11222 34444444
Q ss_pred cCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEE
Q 005710 93 TGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRS 128 (681)
Q Consensus 93 ~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~ 128 (681)
|++.|++=....-+.+ ..+++.|.+.|+....
T Consensus 88 -g~~~vv~G~i~sd~~~---~~~e~~~~~~gl~~~~ 119 (194)
T cd01994 88 -GVDAVVFGAILSEYQR---TRVERVCERLGLEPLA 119 (194)
T ss_pred -CCCEEEECccccHHHH---HHHHHHHHHcCCEEEe
Confidence 6888887643433333 3566678888886654
No 16
>cd01989 STK_N The N-terminal domain of Eukaryotic Serine Threonine kinases. The Serine Threonine kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. The N-terminal domain is homologous to the USP family which has a ATP binding fold. The N-terminal domain is predicted to be involved in ATP binding.
Probab=75.18 E-value=41 Score=31.00 Aligned_cols=84 Identities=19% Similarity=0.207 Sum_probs=49.7
Q ss_pred CCCHHHHHHHHc-----CCeEEEEEEcCCCCCCCCCc------hhhH---HHHHHhHHHHHHHHHhCCCce--EEEeCCC
Q 005710 18 EDNPALAAGVRA-----GAVIAVFIWAPEEEGPYYPG------RVSR---WWLKHSLSHLDSSLRSLGTSL--VTKRSTD 81 (681)
Q Consensus 18 ~DN~AL~aA~~~-----~~vlpVfI~dP~~~~~~~~~------r~~r---~FL~esL~dL~~~L~~~G~~L--~v~~~g~ 81 (681)
.-..||..|++. ..+.-|+|.+|........+ .... .-..+-|..+.+.+++.|.+. ++..+++
T Consensus 11 ~s~~al~~a~~~a~~~~~~l~ll~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~g~~ 90 (146)
T cd01989 11 KSKNALKWALDNLATKGQTIVLVHVHPPITSIPSSSGKLEVASAYKQEEDKEAKELLLPYRCFCSRKGVQCEDVVLEDDD 90 (146)
T ss_pred ccHHHHHHHHHhccCCCCcEEEEEeccCcccCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCeEEEEEEeCCc
Confidence 344677777643 37888899876422111111 0000 012334445555565667654 4444457
Q ss_pred hHHHHHHHHHHcCCCEEEEe
Q 005710 82 SVSSLLEVVKATGATQLFFN 101 (681)
Q Consensus 82 ~~~~L~~L~~~~~~~~V~~n 101 (681)
+.+.|.+.+++++++.|+.-
T Consensus 91 ~~~~I~~~a~~~~~dlIV~G 110 (146)
T cd01989 91 VAKAIVEYVADHGITKLVMG 110 (146)
T ss_pred HHHHHHHHHHHcCCCEEEEe
Confidence 88899999999999999886
No 17
>TIGR00290 MJ0570_dom MJ0570-related uncharacterized domain. Proteins with this uncharacterized domain include two apparent ortholog families in the Archaea, one of which is universal among the first four completed archaeal genomes, and YLR143W, a much longer protein from Saccharomyces cerevisiae. The domain comprises the full length of the archaeal proteins and the first third of the yeast protein.
Probab=72.16 E-value=51 Score=33.88 Aligned_cols=98 Identities=19% Similarity=0.293 Sum_probs=56.7
Q ss_pred HHHHHHHHcCCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeC----CChHHHHHHHHHHcCCC
Q 005710 21 PALAAGVRAGAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRS----TDSVSSLLEVVKATGAT 96 (681)
Q Consensus 21 ~AL~aA~~~~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~----g~~~~~L~~L~~~~~~~ 96 (681)
-||+.|.+.-.|..|..+-|.....+. |-.-.+.-++.+-+.+|++|+.... ++..+.|.+++++.|++
T Consensus 15 ~al~~a~~~~~v~~L~t~~~~~~~s~~-------~H~~~~~~~~~qA~algipl~~~~~~~~~e~~~e~l~~~l~~~gv~ 87 (223)
T TIGR00290 15 LALYHALKEHEVISLVNIMPENEESYM-------FHGVNAHLTDLQAESIGIPLIKLYTEGTEEDEVEELKGILHTLDVE 87 (223)
T ss_pred HHHHHHHHhCeeEEEEEEecCCCCccc-------ccccCHHHHHHHHHHcCCCeEEeecCCCccHHHHHHHHHHHHcCCC
Confidence 467777765446666666665321111 1111233333444567999875431 23566677778888999
Q ss_pred EEEEecccChhhHHHHHHHHHHHHhCCeEEEE
Q 005710 97 QLFFNHLYDPLSLVRDHRAKEALTAQGIAVRS 128 (681)
Q Consensus 97 ~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~ 128 (681)
.|++-.-..-+.+. .+++.|.+.|+....
T Consensus 88 ~vv~GdI~s~~qr~---~~e~v~~~lgl~~~~ 116 (223)
T TIGR00290 88 AVVFGAIYSEYQKT---RIERVCRELGLKSFA 116 (223)
T ss_pred EEEECCcccHHHHH---HHHHHHHhcCCEEec
Confidence 99987444333333 456678888886543
No 18
>cd01988 Na_H_Antiporter_C The C-terminal domain of a subfamily of Na+ /H+ antiporter existed in bacteria and archea . Na+/H+ exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolising cells. Na+ /H+ exchange activity is also crucial for the regulation of cell volume, and for the reabsorption of NaCl across renal, intestinal, and other epithelia. These antiports exchange Na+ for H+ in an electroneutral manner, and this activity is carried out by a family of Na+ /H+ exchangers, or NHEs, which are known to be present in both prokaryotic and eukaryotic cells. These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N-terminus and a large cytoplasmic region at the C-terminus. The transmembrane regions M3-M12 share identity wit h other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the regio
Probab=70.99 E-value=52 Score=29.36 Aligned_cols=83 Identities=17% Similarity=0.166 Sum_probs=51.7
Q ss_pred HHHHHHHH----c-CCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEE--EeCCChHHHHHHHHHHc
Q 005710 21 PALAAGVR----A-GAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVT--KRSTDSVSSLLEVVKAT 93 (681)
Q Consensus 21 ~AL~aA~~----~-~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v--~~~g~~~~~L~~L~~~~ 93 (681)
.+|..|.. . ..+..++++++..............-..+.+..+.+.+++.|++... ..++++.+.|.++++++
T Consensus 14 ~~l~~a~~la~~~~~~v~ll~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~~~a~~~ 93 (132)
T cd01988 14 DLLELAAALARAQNGEIIPLNVIEVPNHSSPSQLEVNVQRARKLLRQAERIAASLGVPVHTIIRIDHDIASGILRTAKER 93 (132)
T ss_pred HHHHHHHHHhhcCCCeEEEEEEEecCCCCCcchhHHHHHHHHHHHHHHHHHhhhcCCceEEEEEecCCHHHHHHHHHHhc
Confidence 45655543 1 37888999886422110000111113456677777778888888532 23467888999999999
Q ss_pred CCCEEEEecc
Q 005710 94 GATQLFFNHL 103 (681)
Q Consensus 94 ~~~~V~~n~~ 103 (681)
+++-|++-..
T Consensus 94 ~~dlIV~G~~ 103 (132)
T cd01988 94 QADLIIMGWH 103 (132)
T ss_pred CCCEEEEecC
Confidence 9999988643
No 19
>PF01902 ATP_bind_4: ATP-binding region; InterPro: IPR002761 This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N-terminal. The structure of Q8U2K6 from SWISSPROT from Pyrococcus furiosus has been resolved to 2.7A and is suggested to be a putative N-type pytophosphatase. In some members of the family e.g. Q12429 from SWISSPROT, this domain is associated with IPR006175 from INTERPRO, another domain of unknown function. Proteins with this uncharacterised domain include two apparent ortholog families in the archaea, one of which is universal among the first four completed archaeal genomes. The domain comprises the full length of the archaeal proteins and the first third of fungal proteins.; PDB: 3RK0_A 3RK1_A 3RJZ_A 2D13_D.
Probab=70.75 E-value=19 Score=36.78 Aligned_cols=98 Identities=21% Similarity=0.327 Sum_probs=49.1
Q ss_pred HHHHHHHHcCCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeC----CChHHHHHHHHHHcCCC
Q 005710 21 PALAAGVRAGAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRS----TDSVSSLLEVVKATGAT 96 (681)
Q Consensus 21 ~AL~aA~~~~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~----g~~~~~L~~L~~~~~~~ 96 (681)
-||+.|.+.-.|..+..+-|+....+..+... +.-+..+-+.+|+||+.... .+..+.|.+.+++.+++
T Consensus 15 lAl~~a~~~~~v~~L~t~~~~~~~s~~~H~~~-------~~~~~~qA~algipl~~~~~~g~~~~~~~~l~~~l~~~~v~ 87 (218)
T PF01902_consen 15 LALYRALRQHEVVCLLTMVPEEEDSYMFHGVN-------IELIEAQAEALGIPLIEIPTSGDEEDYVEDLKEALKELKVE 87 (218)
T ss_dssp HHHHHHHHT-EEEEEEEEEESTTT-SSS-STT-------GTCHHHHHHHHT--EEEEEE---CCCHHHHHHHHHCTC--S
T ss_pred HHHHHHHHhCCccEEEEeccCCCCcccccccC-------HHHHHHHHHHCCCCEEEEEccCccchhhHHHHHHHHHcCCC
Confidence 36777777645666666655533221112111 11222223456999976542 34566788888889999
Q ss_pred EEEEecccChhhHHHHHHHHHHHHhCCeEEEE
Q 005710 97 QLFFNHLYDPLSLVRDHRAKEALTAQGIAVRS 128 (681)
Q Consensus 97 ~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~ 128 (681)
.|++-.-..- ..|. .+++.|.+.|+....
T Consensus 88 ~vv~GdI~~~--~~r~-~~e~vc~~lGl~~~~ 116 (218)
T PF01902_consen 88 AVVFGDIDSE--YQRN-WVERVCERLGLEAVF 116 (218)
T ss_dssp EEE--TTS-H--HHHH-HHHHHHHHCT-EEE-
T ss_pred EEEECcCCcH--HHHH-HHHHHHHHcCCEEEe
Confidence 9988633322 2333 567778888887654
No 20
>cd00293 USP_Like Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae Usp reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, athough Usp lacks ATP-binding activity.
Probab=70.27 E-value=54 Score=28.59 Aligned_cols=73 Identities=15% Similarity=0.192 Sum_probs=45.3
Q ss_pred CCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEE-eCCChHHHHHHHHHHcCCCEEEEec
Q 005710 30 GAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTK-RSTDSVSSLLEVVKATGATQLFFNH 102 (681)
Q Consensus 30 ~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~-~~g~~~~~L~~L~~~~~~~~V~~n~ 102 (681)
..+..|+|.++..............-..+.|..+...+...|+++... ..+++...|.+.+++.+++.|+.-.
T Consensus 28 ~~i~~l~v~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~dlvvig~ 101 (130)
T cd00293 28 AELVLLHVVDPPPSSAAELAELLEEEARALLEALREALAEAGVKVETVVLEGDPAEAILEAAEELGADLIVMGS 101 (130)
T ss_pred CEEEEEEEecCCCCcchhHHHHHHHHHHHHHHHHHHHHhcCCCceEEEEecCCCHHHHHHHHHHcCCCEEEEcC
Confidence 378888887654221100001111234566777777666778886332 2366688999999999999998863
No 21
>TIGR03679 arCOG00187 arCOG00187 universal archaeal metal-binding-domain/4Fe-4S-binding-domain containing ABC transporter, ATP-binding protein. This model has the same scope as an archaeal COG (arCOG00187) and is found in all completely sequenced archaea and does not recognize any known non-archaeal genes.
Probab=70.25 E-value=62 Score=32.93 Aligned_cols=96 Identities=20% Similarity=0.284 Sum_probs=51.4
Q ss_pred HHHHHHHcC-CeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeCC----ChH----HHHHHHHHH
Q 005710 22 ALAAGVRAG-AVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRST----DSV----SSLLEVVKA 92 (681)
Q Consensus 22 AL~aA~~~~-~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~g----~~~----~~L~~L~~~ 92 (681)
+|..|.+.+ .|.+++++.+.....+... ...+..++...+.+|+++++.... ... ..|.++.++
T Consensus 13 al~~a~~~G~~v~~l~~~~~~~~~~~~~~-------~~~~~~~~~~A~~lgip~~~i~~~~~~~~~~~~l~~~l~~~~~~ 85 (218)
T TIGR03679 13 ALYKALEEGHEVRCLITVVPENEESYMFH-------TPNIELTRLQAEALGIPLVKIETSGEKEKEVEDLKGALKELKRE 85 (218)
T ss_pred HHHHHHHcCCEEEEEEEeccCCCCccccC-------CCCHHHHHHHHHHhCCCEEEEECCCCChHHHHHHHHHHHHHHHc
Confidence 455566666 5667766665421111101 123444555556779998776422 112 234444443
Q ss_pred cCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEE
Q 005710 93 TGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRS 128 (681)
Q Consensus 93 ~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~ 128 (681)
|++.|++-...+.+. +.++.+.|.+.|+++..
T Consensus 86 -g~~~vv~G~i~sd~~---~~~~e~v~~~~gl~~~~ 117 (218)
T TIGR03679 86 -GVEGIVTGAIASRYQ---KSRIERICEELGLKVFA 117 (218)
T ss_pred -CCCEEEECCcccHhH---HHHHHHHHHhCCCeEEe
Confidence 899988854333332 44555677777776543
No 22
>PF08218 Citrate_ly_lig: Citrate lyase ligase C-terminal domain; InterPro: IPR013166 [Citrate (pro-3S)-lyase] ligase (6.2.1.22 from EC), also known as citrate lyase ligase, is responsible for acetylation of the prosthetic group (2-(5''-phosphoribosyl)-3'-dephosphocoenzyme-A) of the gamma subunit of citrate lyase. It converts the inactive thiol form of the enzyme to the active form. In Clostridium sphenoides, citrate lyase ligase actively degrades citrate. In Clostridium sporosphaeroides and Lactococcus lactis, however, the enzyme is under stringent regulatory control. The enzyme's activity in anaerobic bacteria is modulated by phosphorylation and dephosphorylation []. The proteins in this entry represent the C-terminal domain of citrate lyase ligase.; GO: 0008771 [citrate (pro-3S)-lyase] ligase activity
Probab=69.57 E-value=20 Score=35.39 Aligned_cols=107 Identities=18% Similarity=0.273 Sum_probs=71.6
Q ss_pred HH-HHHHHcCCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeC---------CC---------h
Q 005710 22 AL-AAGVRAGAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRS---------TD---------S 82 (681)
Q Consensus 22 AL-~aA~~~~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~---------g~---------~ 82 (681)
-| ..|++.+..+-|||+.... ...+-..|...+.++.+||..=.---|++.+|-.. .+ .
T Consensus 17 yLiE~Aa~~~d~l~vFVV~eD~--S~Fpf~~R~~LVk~G~~~L~NV~V~~~g~YiIS~aTFPsYFlK~~~~~~~~~~~lD 94 (182)
T PF08218_consen 17 YLIEQAAKECDWLHVFVVSEDR--SLFPFADRYELVKEGTADLPNVTVHPGGDYIISSATFPSYFLKDEDDVIKAQAELD 94 (182)
T ss_pred HHHHHHHHhCCEEEEEEEcccc--CcCCHHHHHHHHHHHhCcCCCEEEEcCCCeeeecccChhhhccchhHHHHHHHHHH
Confidence 44 3466667888999987543 23344455558889998886644444666555321 01 1
Q ss_pred HHHHHH-HHHHcCCCEEEEecc-cChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 83 VSSLLE-VVKATGATQLFFNHL-YDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 83 ~~~L~~-L~~~~~~~~V~~n~~-y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
..++.+ ++...||++-|+-.| +++....--+.++++|...||+|....
T Consensus 95 ~~iF~~~IAp~L~It~RfVG~EP~~~vT~~YN~~M~~~Lp~~gi~v~ei~ 144 (182)
T PF08218_consen 95 ATIFKKYIAPALGITKRFVGEEPFSPVTRIYNEAMKEILPPYGIEVVEIP 144 (182)
T ss_pred HHHHHHHhhHhcCcccceeCCCCCCHHHHHHHHHHHHhccccCCEEEEEe
Confidence 223444 778889998887644 667777778899999999999998764
No 23
>cd01987 USP_OKCHK USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium transport. The USP domain is homologous to the universal stress protein Usp Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity.
Probab=65.17 E-value=60 Score=28.95 Aligned_cols=78 Identities=15% Similarity=0.222 Sum_probs=50.3
Q ss_pred CCHHHHHHHHc-----CCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeCCChHHHHHHHHHHc
Q 005710 19 DNPALAAGVRA-----GAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKAT 93 (681)
Q Consensus 19 DN~AL~aA~~~-----~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~~ 93 (681)
...+|..|+.. ..+.-|+|.++... ...... .+-|..+.+.+++.|.+..+..++++.+.|.+.++++
T Consensus 12 s~~al~~a~~la~~~~~~l~ll~v~~~~~~--~~~~~~-----~~~l~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~ 84 (124)
T cd01987 12 AERLIRRAARLADRLKAPWYVVYVETPRLN--RLSEAE-----RRRLAEALRLAEELGAEVVTLPGDDVAEAIVEFAREH 84 (124)
T ss_pred hHHHHHHHHHHHHHhCCCEEEEEEecCccc--cCCHHH-----HHHHHHHHHHHHHcCCEEEEEeCCcHHHHHHHHHHHc
Confidence 34566555432 37888888876421 011111 2335555566667788765555677889999999999
Q ss_pred CCCEEEEecc
Q 005710 94 GATQLFFNHL 103 (681)
Q Consensus 94 ~~~~V~~n~~ 103 (681)
+++.|+.-..
T Consensus 85 ~~dllviG~~ 94 (124)
T cd01987 85 NVTQIVVGKS 94 (124)
T ss_pred CCCEEEeCCC
Confidence 9999988643
No 24
>PRK12652 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=63.56 E-value=56 Score=36.03 Aligned_cols=96 Identities=14% Similarity=0.129 Sum_probs=57.4
Q ss_pred CeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHh------CCCceE--EEe-------CCChHHHHHHHHHHcCC
Q 005710 31 AVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRS------LGTSLV--TKR-------STDSVSSLLEVVKATGA 95 (681)
Q Consensus 31 ~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~------~G~~L~--v~~-------~g~~~~~L~~L~~~~~~ 95 (681)
.|..|+|.++..... .......--.+-|..+.+.+++ .|++.. +.. .|++.+.|.+.++++++
T Consensus 37 eL~lL~Vv~~~~~~~--~~~~~~~~~eelle~~~~~~~~~l~~~~~gV~ve~~vv~~~~~~~~~G~pae~Iv~~Aee~~a 114 (357)
T PRK12652 37 TVHLVAAASGRAVDP--EGQDELAAAEELLERVEVWATEDLGDDASSVTIETALLGTDEYLFGPGDYAEVLIAYAEEHGI 114 (357)
T ss_pred EEEEEEEecCccccc--chhHHHHHHHHHHHHHHHHHHHhhhcccCCCceEEEEEeccccccCCCCHHHHHHHHHHHcCC
Confidence 688889887642211 1100000111234444444443 477752 222 27899999999999999
Q ss_pred CEEEEecccChhhHH-HHHHHHHHHHhCCeEEEE
Q 005710 96 TQLFFNHLYDPLSLV-RDHRAKEALTAQGIAVRS 128 (681)
Q Consensus 96 ~~V~~n~~y~p~~~~-rD~~v~~~l~~~gI~v~~ 128 (681)
+.|+...+|.|.... .=+-++..|.+.||.++.
T Consensus 115 DLIVm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 148 (357)
T PRK12652 115 DRVVLDPEYNPGGTAPMLQPLERELARAGITYEE 148 (357)
T ss_pred CEEEECCCCCCCCCCcccchHHHHHHhcCCceec
Confidence 999999999887532 122344456667776655
No 25
>PRK09982 universal stress protein UspD; Provisional
Probab=60.19 E-value=1.4e+02 Score=27.55 Aligned_cols=108 Identities=13% Similarity=0.124 Sum_probs=58.6
Q ss_pred CHHHHHHHHc-----CCeEEEEEEcCCCCC---CCCCc--hhhH---HHHHHhHHHHHHHHHhCCCceEEEeCCChHHHH
Q 005710 20 NPALAAGVRA-----GAVIAVFIWAPEEEG---PYYPG--RVSR---WWLKHSLSHLDSSLRSLGTSLVTKRSTDSVSSL 86 (681)
Q Consensus 20 N~AL~aA~~~-----~~vlpVfI~dP~~~~---~~~~~--r~~r---~FL~esL~dL~~~L~~~G~~L~v~~~g~~~~~L 86 (681)
..||..|++. ..+..|+|.++.... ..... .... ....+.|.++.+.+...+....+.. |++.+.|
T Consensus 17 ~~al~~A~~lA~~~~a~l~llhV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~v~~-G~p~~~I 95 (142)
T PRK09982 17 ALLVNKALELARHNDAHLTLIHIDDGLSELYPGIYFPATEDILQLLKNKSDNKLYKLTKNIQWPKTKLRIER-GEMPETL 95 (142)
T ss_pred HHHHHHHHHHHHHhCCeEEEEEEccCcchhchhhhccchHHHHHHHHHHHHHHHHHHHHhcCCCcceEEEEe-cCHHHHH
Confidence 4666666532 378888998753211 00011 1000 1222234444444433344455554 8999999
Q ss_pred HHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEe
Q 005710 87 LEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSF 129 (681)
Q Consensus 87 ~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~ 129 (681)
.+++++.+++-|+.-..-........ .-.+.++...|+|-.+
T Consensus 96 ~~~A~~~~aDLIVmG~~~~~~~~~~~-va~~V~~~s~~pVLvv 137 (142)
T PRK09982 96 LEIMQKEQCDLLVCGHHHSFINRLMP-AYRGMINKMSADLLIV 137 (142)
T ss_pred HHHHHHcCCCEEEEeCChhHHHHHHH-HHHHHHhcCCCCEEEe
Confidence 99999999999998643222222222 3344566667777654
No 26
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=58.12 E-value=46 Score=29.15 Aligned_cols=69 Identities=19% Similarity=0.172 Sum_probs=46.9
Q ss_pred HHHHHHHHHhCCCceEEE--eCCChHH--HHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecCC
Q 005710 60 LSHLDSSLRSLGTSLVTK--RSTDSVS--SLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNAD 132 (681)
Q Consensus 60 L~dL~~~L~~~G~~L~v~--~~g~~~~--~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~~ 132 (681)
...+++.+++.|..+.+. ..+.... .|+..++ .++.|++--++ ..-.--..+++.|++.|+++....+.
T Consensus 12 ~~~~~~~~~~~G~~~~~hg~~~~~~~~~~~l~~~i~--~aD~VIv~t~~--vsH~~~~~vk~~akk~~ip~~~~~~~ 84 (97)
T PF10087_consen 12 ERRYKRILEKYGGKLIHHGRDGGDEKKASRLPSKIK--KADLVIVFTDY--VSHNAMWKVKKAAKKYGIPIIYSRSR 84 (97)
T ss_pred HHHHHHHHHHcCCEEEEEecCCCCccchhHHHHhcC--CCCEEEEEeCC--cChHHHHHHHHHHHHcCCcEEEECCC
Confidence 567778899999999877 2232222 3666555 56777776433 33344457888999999999887643
No 27
>PRK10116 universal stress protein UspC; Provisional
Probab=53.55 E-value=1.8e+02 Score=26.52 Aligned_cols=116 Identities=13% Similarity=0.100 Sum_probs=61.5
Q ss_pred CCCCCCCHHHHHHHHc----C-CeEEEEEEcCCCCCCCCCc----hhhHHHHHHhHHHHHHHHHhCCCce--EEEeCCCh
Q 005710 14 DLRVEDNPALAAGVRA----G-AVIAVFIWAPEEEGPYYPG----RVSRWWLKHSLSHLDSSLRSLGTSL--VTKRSTDS 82 (681)
Q Consensus 14 DLRl~DN~AL~aA~~~----~-~vlpVfI~dP~~~~~~~~~----r~~r~FL~esL~dL~~~L~~~G~~L--~v~~~g~~ 82 (681)
|.--+...||..|+.. + .+.-|+++++......... ........+..+.|++...+.|++. .+...|++
T Consensus 11 D~s~~s~~al~~A~~lA~~~~a~l~ll~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~G~~ 90 (142)
T PRK10116 11 AVTPESQQLLAKAVSIARPVNGKISLITLASDPEMYNQFAAPMLEDLRSVMQEETQSFLDKLIQDADYPIEKTFIAYGEL 90 (142)
T ss_pred cCCcchHHHHHHHHHHHHHhCCEEEEEEEccCcccchhhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEEEEEecCCH
Confidence 4444556888877642 3 6667777754311000001 0111111122233333344556543 22335888
Q ss_pred HHHHHHHHHHcCCCEEEEecc-cChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 83 VSSLLEVVKATGATQLFFNHL-YDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 83 ~~~L~~L~~~~~~~~V~~n~~-y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
.+.|.+.+++.+++-|+.-.. ........ ....+.+...+|+|-.+.
T Consensus 91 ~~~I~~~a~~~~~DLiV~g~~~~~~~~~~~-s~a~~v~~~~~~pVLvv~ 138 (142)
T PRK10116 91 SEHILEVCRKHHFDLVICGNHNHSFFSRAS-CSAKRVIASSEVDVLLVP 138 (142)
T ss_pred HHHHHHHHHHhCCCEEEEcCCcchHHHHHH-HHHHHHHhcCCCCEEEEe
Confidence 999999999999999998533 22222222 123456777788776653
No 28
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=51.59 E-value=1.6e+02 Score=35.89 Aligned_cols=107 Identities=20% Similarity=0.181 Sum_probs=64.9
Q ss_pred CCHHHHHHH-H----c-CCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeCCChHHHHHHHHHH
Q 005710 19 DNPALAAGV-R----A-GAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKA 92 (681)
Q Consensus 19 DN~AL~aA~-~----~-~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~ 92 (681)
.|+.|...+ + . ++...|||-.|+.... ....+.- ++....|.++| |..++...+++....|.++|+.
T Consensus 260 ~~e~liR~a~RlA~~~~a~~~av~v~~~~~~~~---~~~~~~~-l~~~~~Lae~l---Gae~~~l~~~dv~~~i~~ya~~ 332 (890)
T COG2205 260 GSEKLIRRAARLASRLHAKWTAVYVETPELHRL---SEKEARR-LHENLRLAEEL---GAEIVTLYGGDVAKAIARYARE 332 (890)
T ss_pred chHHHHHHHHHHHHHhCCCeEEEEEeccccccc---cHHHHHH-HHHHHHHHHHh---CCeEEEEeCCcHHHHHHHHHHH
Confidence 366665432 2 2 4889999988874322 1122212 34455666666 9999888778888999999999
Q ss_pred cCCCEEEEecccChhhHH-HHHHHHHHH--HhCCeEEEEecCC
Q 005710 93 TGATQLFFNHLYDPLSLV-RDHRAKEAL--TAQGIAVRSFNAD 132 (681)
Q Consensus 93 ~~~~~V~~n~~y~p~~~~-rD~~v~~~l--~~~gI~v~~~~~~ 132 (681)
+++|+|+.-+.-...... ....+...+ ...+|+++.+..+
T Consensus 333 ~~~TkiViG~~~~~rw~~~~~~~l~~~L~~~~~~idv~ii~~~ 375 (890)
T COG2205 333 HNATKIVIGRSRRSRWRRLFKGSLADRLAREAPGIDVHIVALD 375 (890)
T ss_pred cCCeeEEeCCCcchHHHHHhcccHHHHHHhcCCCceEEEeeCC
Confidence 999999987543322211 112222222 2346777766543
No 29
>PRK10490 sensor protein KdpD; Provisional
Probab=51.24 E-value=85 Score=38.95 Aligned_cols=94 Identities=13% Similarity=0.112 Sum_probs=57.3
Q ss_pred CCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeCCChHHHHHHHHHHcCCCEEEEecccChhhH
Q 005710 30 GAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKATGATQLFFNHLYDPLSL 109 (681)
Q Consensus 30 ~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~ 109 (681)
++++.|||-.|.... .....+.-+.+.+ .|.++| |..++...+++..+.|.+++++.++++|+.-+......+
T Consensus 279 a~~~~l~V~~~~~~~---~~~~~~~~l~~~~-~lA~~l---Ga~~~~~~~~dva~~i~~~A~~~~vt~IViG~s~~~~~~ 351 (895)
T PRK10490 279 SVWHAVYVETPRLHR---LPEKKRRAILSAL-RLAQEL---GAETATLSDPAEEKAVLRYAREHNLGKIIIGRRASRRWW 351 (895)
T ss_pred CCEEEEEEecCCcCc---CCHHHHHHHHHHH-HHHHHc---CCEEEEEeCCCHHHHHHHHHHHhCCCEEEECCCCCCCCc
Confidence 489999998764211 1111222344555 255555 999877777788999999999999999999765332112
Q ss_pred HHHHHHHHHHH-hCCeEEEEec
Q 005710 110 VRDHRAKEALT-AQGIAVRSFN 130 (681)
Q Consensus 110 ~rD~~v~~~l~-~~gI~v~~~~ 130 (681)
.+..-+.++++ ..+|+++.+.
T Consensus 352 ~~~s~~~~l~r~~~~idi~iv~ 373 (895)
T PRK10490 352 RRESFADRLARLGPDLDLVIVA 373 (895)
T ss_pred cCCCHHHHHHHhCCCCCEEEEe
Confidence 11111222222 3467777774
No 30
>cd00466 DHQase_II Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway and the catabolic quinate pathway. There are two types of DHQases, which are distinct from each other in amino acid sequence and three-dimensional structure. Type I enzymes usually catalyze the biosynthetic reaction using a syn elimination mechanism. In contrast, type II enzymes, found in the quinate pathway of fungi and in the shikimate pathway of many bacteria, are dodecameric enzymes that employ an anti elimination reaction mechanism.
Probab=49.19 E-value=1.1e+02 Score=29.13 Aligned_cols=77 Identities=22% Similarity=0.332 Sum_probs=46.4
Q ss_pred hHHHHHHHHH----hCCCceEEEeCCChHHHHHHHHHHc--CCCEEEEecc-cChhhHHHHHHHHHHHHhCCeEEEEecC
Q 005710 59 SLSHLDSSLR----SLGTSLVTKRSTDSVSSLLEVVKAT--GATQLFFNHL-YDPLSLVRDHRAKEALTAQGIAVRSFNA 131 (681)
Q Consensus 59 sL~dL~~~L~----~~G~~L~v~~~g~~~~~L~~L~~~~--~~~~V~~n~~-y~p~~~~rD~~v~~~l~~~gI~v~~~~~ 131 (681)
+|.++.+.|+ ++|+.+.++.. +.+..|.+.+++. +++.|+.|.. |+-.+. +++++++..++++..++-
T Consensus 25 tl~~i~~~l~~~a~~~g~~v~~~QS-N~Egelid~I~~a~~~~dgiIINpga~THtSv----Ai~DAl~~~~~P~VEVHi 99 (140)
T cd00466 25 TLADIEALLRELAAELGVEVEFFQS-NHEGELIDWIHEARDGADGIIINPGAYTHTSI----ALRDALAAVSIPVIEVHI 99 (140)
T ss_pred CHHHHHHHHHHHHHHcCCEEEEEee-CcHHHHHHHHHHhhccCcEEEEcchHHHHHHH----HHHHHHHcCCCCEEEEec
Confidence 3444444443 45899988764 3444444444432 4788998833 333333 566777888999999886
Q ss_pred CeeeCCccc
Q 005710 132 DLLYEPWDV 140 (681)
Q Consensus 132 ~~L~~p~~i 140 (681)
+.++..+++
T Consensus 100 SNi~aRE~f 108 (140)
T cd00466 100 SNIHAREEF 108 (140)
T ss_pred CCccccccc
Confidence 666554433
No 31
>PF06574 FAD_syn: FAD synthetase; InterPro: IPR015864 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents prokaryotic-type FAD synthetase, which occurs primarily as part of a bifunctional enzyme.; GO: 0003919 FMN adenylyltransferase activity, 0009231 riboflavin biosynthetic process; PDB: 2X0K_B 3OP1_B 1T6Z_A 2I1L_A 1T6Y_B 1T6X_B 1S4M_A 1MRZ_A.
Probab=47.91 E-value=17 Score=35.08 Aligned_cols=104 Identities=16% Similarity=0.118 Sum_probs=59.1
Q ss_pred HHHcCCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEe-------CCChHHHHHHHHH-HcCCCE
Q 005710 26 GVRAGAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKR-------STDSVSSLLEVVK-ATGATQ 97 (681)
Q Consensus 26 A~~~~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~-------~g~~~~~L~~L~~-~~~~~~ 97 (681)
|.+.+....|+.|+|.-..-..+.... +++-++.+=.+.|+++|++.++.- .-++.+-+..++. ..++..
T Consensus 32 a~~~~~~~~v~tF~~~P~~~~~~~~~~--~~l~s~~ek~~~l~~~Gvd~~~~~~F~~~~~~ls~~~Fi~~iL~~~l~~~~ 109 (157)
T PF06574_consen 32 AKEKGLKSVVLTFDPHPKEVLNPDKPP--KLLTSLEEKLELLESLGVDYVIVIPFTEEFANLSPEDFIEKILKEKLNVKH 109 (157)
T ss_dssp HHHCT-EEEEEEESS-CHHHHSCTCCG--GBSS-HHHHHHHHHHTTESEEEEE-CCCHHCCS-HHHHHHHHCCCHCTEEE
T ss_pred hhhcccceEEEEcccCHHHHhcCCCcc--cCCCCHHHHHHHHHHcCCCEEEEecchHHHHcCCHHHHHHHHHHhcCCccE
Confidence 334455667888987521100111111 346778888888999999965432 1245556666555 889999
Q ss_pred EEEecccChhh--HHHHHHHHHHHHhCCeEEEEecC
Q 005710 98 LFFNHLYDPLS--LVRDHRAKEALTAQGIAVRSFNA 131 (681)
Q Consensus 98 V~~n~~y~p~~--~~rD~~v~~~l~~~gI~v~~~~~ 131 (681)
|++-.++.... .---+.+++.+++.|+.|..++.
T Consensus 110 ivvG~DfrFG~~~~G~~~~L~~~~~~~g~~v~~v~~ 145 (157)
T PF06574_consen 110 IVVGEDFRFGKNRSGDVELLKELGKEYGFEVEVVPP 145 (157)
T ss_dssp EEEETT-EESGGGEEEHHHHHHCTTTT-SEEEEE--
T ss_pred EEEccCccCCCCCCCCHHHHHHhcccCceEEEEECC
Confidence 99987753221 11123577788888999988753
No 32
>COG1139 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]
Probab=47.27 E-value=53 Score=36.87 Aligned_cols=68 Identities=15% Similarity=0.183 Sum_probs=51.9
Q ss_pred HhHHHHHHHHHhCCCceEEEeC-CChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEe
Q 005710 58 HSLSHLDSSLRSLGTSLVTKRS-TDSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSF 129 (681)
Q Consensus 58 esL~dL~~~L~~~G~~L~v~~~-g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~ 129 (681)
+=|..+.+++.++|+.+++-.. .++.+++.+++++.+++.|+-.+...-++. .+.+.|++.|+.|..-
T Consensus 65 ~~l~~~~~~v~~~Gg~vy~A~~aedA~~ii~~iv~~k~~k~vVKsKSmvseEI----gln~~Le~~G~ev~ET 133 (459)
T COG1139 65 EYLEQLEENVTRNGGHVYFAKDAEDAREIIGEIVGEKNGKKVVKSKSMVSEEI----GLNHYLEEKGIEVWET 133 (459)
T ss_pred HHHHHHHHHHHHcCCEEEEeCCHHHHHHHHHHHHhhccCcEEEEecchhHHHh----hhHHHHHHcCCeEEEc
Confidence 3355677888899999988653 356677889999999999999877655555 4667788889988654
No 33
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=46.53 E-value=1.5e+02 Score=26.27 Aligned_cols=64 Identities=20% Similarity=0.360 Sum_probs=44.1
Q ss_pred HHhHHHHHHHHHhCCCceEE---Ee----------CCChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCC
Q 005710 57 KHSLSHLDSSLRSLGTSLVT---KR----------STDSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQG 123 (681)
Q Consensus 57 ~esL~dL~~~L~~~G~~L~v---~~----------~g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~g 123 (681)
-++|.+|.+=.+..|+..+- .. +.--++.|.++++..+++.|+++.+.+|...+ .+.+. .|
T Consensus 7 ~~~l~El~~L~~t~g~~vv~~~~q~~~~~~p~~~iG~GK~eei~~~~~~~~~d~vvfd~~Lsp~Q~r---NLe~~---~~ 80 (95)
T PF13167_consen 7 EESLEELEELAETAGYEVVGTVVQKRRKPDPKTYIGSGKVEEIKELIEELDADLVVFDNELSPSQQR---NLEKA---LG 80 (95)
T ss_pred HHHHHHHHHHHHHCCCeEEEEEEecCCCCCcceeechhHHHHHHHHHhhcCCCEEEECCCCCHHHHH---HHHHH---HC
Confidence 57888888888888977532 11 01136678889999999999999888886433 34433 36
Q ss_pred eEE
Q 005710 124 IAV 126 (681)
Q Consensus 124 I~v 126 (681)
++|
T Consensus 81 ~~V 83 (95)
T PF13167_consen 81 VKV 83 (95)
T ss_pred Cee
Confidence 655
No 34
>PRK05395 3-dehydroquinate dehydratase; Provisional
Probab=46.45 E-value=1.2e+02 Score=29.11 Aligned_cols=77 Identities=22% Similarity=0.318 Sum_probs=47.2
Q ss_pred HhHHHHHHHHH----hCCCceEEEeCCChHHHHHHHHHHc--CCCEEEEecc-cChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 58 HSLSHLDSSLR----SLGTSLVTKRSTDSVSSLLEVVKAT--GATQLFFNHL-YDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 58 esL~dL~~~L~----~~G~~L~v~~~g~~~~~L~~L~~~~--~~~~V~~n~~-y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
.+|.++.+.|+ ++|+.+.++.. +.+..|.+.+++. +++.|+.|.. |+-++. +++++++..++++..++
T Consensus 26 ~tl~~i~~~~~~~a~~~g~~v~~~QS-N~EGelId~I~~a~~~~dgiiINpga~THtSi----Al~DAl~~~~~P~VEVH 100 (146)
T PRK05395 26 TTLADIEALLEEEAAELGVELEFFQS-NHEGELIDRIHEARDGADGIIINPGAYTHTSV----ALRDALAAVSIPVIEVH 100 (146)
T ss_pred CCHHHHHHHHHHHHHHcCCEEEEEee-CcHHHHHHHHHhcccCCcEEEECchHHHHHHH----HHHHHHHcCCCCEEEEe
Confidence 33445444444 45888988764 4444454444443 5788999833 333333 56667778899999988
Q ss_pred CCeeeCCcc
Q 005710 131 ADLLYEPWD 139 (681)
Q Consensus 131 ~~~L~~p~~ 139 (681)
-..++.+++
T Consensus 101 iSNi~aRE~ 109 (146)
T PRK05395 101 LSNIHAREE 109 (146)
T ss_pred cCCcccccc
Confidence 666655443
No 35
>PRK13015 3-dehydroquinate dehydratase; Reviewed
Probab=44.79 E-value=1.2e+02 Score=29.11 Aligned_cols=75 Identities=17% Similarity=0.258 Sum_probs=45.2
Q ss_pred HHHHHHHHH----hCCCceEEEeCCChHHHHHHHHHHc--CCCEEEEecc-cChhhHHHHHHHHHHHHhCCeEEEEecCC
Q 005710 60 LSHLDSSLR----SLGTSLVTKRSTDSVSSLLEVVKAT--GATQLFFNHL-YDPLSLVRDHRAKEALTAQGIAVRSFNAD 132 (681)
Q Consensus 60 L~dL~~~L~----~~G~~L~v~~~g~~~~~L~~L~~~~--~~~~V~~n~~-y~p~~~~rD~~v~~~l~~~gI~v~~~~~~ 132 (681)
|.++.+.|+ ++|+.|.++.. +.+..|.+.+++. +++.|+.|.. |+-++. .++++++..++++..++-.
T Consensus 28 l~~i~~~~~~~a~~~g~~~~~~QS-N~EGelId~i~~a~~~~dgiIINpga~THtSi----Al~DAl~~~~~P~VEVHiS 102 (146)
T PRK13015 28 LADVEALCRAAAEALGLEVEFRQS-NHEGELIDWIHEARGDVAGIVINPGAYTHTSV----AIRDALAALELPVIEVHIS 102 (146)
T ss_pred HHHHHHHHHHHHHHcCCEEEEEee-CcHHHHHHHHHHhhhcCCEEEEcchHHhhhHH----HHHHHHHcCCCCEEEEEcC
Confidence 444444443 45888988764 4444444444432 4678998833 333333 4666777889999998866
Q ss_pred eeeCCcc
Q 005710 133 LLYEPWD 139 (681)
Q Consensus 133 ~L~~p~~ 139 (681)
.++..++
T Consensus 103 Ni~aRE~ 109 (146)
T PRK13015 103 NVHAREA 109 (146)
T ss_pred Ccccccc
Confidence 5554433
No 36
>COG3053 CitC Citrate lyase synthetase [Energy production and conversion]
Probab=44.45 E-value=1e+02 Score=33.04 Aligned_cols=98 Identities=12% Similarity=0.172 Sum_probs=65.4
Q ss_pred HHHHHcCCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeCC------------------ChHHH
Q 005710 24 AAGVRAGAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRST------------------DSVSS 85 (681)
Q Consensus 24 ~aA~~~~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~g------------------~~~~~ 85 (681)
..|++.+..+-|||+..... ..+-..|...+.+++.+|..----.|++.+|.+.. -...+
T Consensus 166 EqAaaqcDwlHLFvV~eD~S--~f~y~~R~~Lv~~G~~~l~Nvt~HsgsdYiISrATFP~YFiKeq~vv~~s~t~iDl~i 243 (352)
T COG3053 166 EQAAAQCDWLHLFVVKEDSS--LFPYEDRLDLVKKGTADLPNVTVHSGSDYIISRATFPAYFIKEQSVVNDSQTEIDLKI 243 (352)
T ss_pred HHHHhhCCEEEEEEEecccc--cCCHHHHHHHHHHhhccCCceEEecCCCeEEEecccchhhhhhHHHHHHHHHHHHHHH
Confidence 45776778899999864422 22333444488999999987666678887775431 02334
Q ss_pred HHH-HHHHcCCCEEEEecc-cChhhHHHHHHHHHHHHhCC
Q 005710 86 LLE-VVKATGATQLFFNHL-YDPLSLVRDHRAKEALTAQG 123 (681)
Q Consensus 86 L~~-L~~~~~~~~V~~n~~-y~p~~~~rD~~v~~~l~~~g 123 (681)
+.+ +++..||++=|+-.| .++....-.+.+..+|.+.+
T Consensus 244 Fr~~iA~aLgIThRfVG~EP~c~vT~~YNq~M~~~L~~~~ 283 (352)
T COG3053 244 FRKYIAPALGITHRFVGTEPFCRVTAIYNQQMRYWLEDPT 283 (352)
T ss_pred HHHHHHHHhCcceeeecCCCCcHHHHHHHHHHHHHHhccC
Confidence 555 788889998887643 34555566777888888776
No 37
>TIGR01088 aroQ 3-dehydroquinate dehydratase, type II. This model specifies the type II enzyme. The type I enzyme, often found as part of a multifunctional protein, is described by TIGR01093.
Probab=44.37 E-value=1.3e+02 Score=28.79 Aligned_cols=76 Identities=16% Similarity=0.176 Sum_probs=46.4
Q ss_pred hHHHHHHHHH----hCCCceEEEeCCChHHHHHHHHHHc--CCCEEEEecc-cChhhHHHHHHHHHHHHhCCeEEEEecC
Q 005710 59 SLSHLDSSLR----SLGTSLVTKRSTDSVSSLLEVVKAT--GATQLFFNHL-YDPLSLVRDHRAKEALTAQGIAVRSFNA 131 (681)
Q Consensus 59 sL~dL~~~L~----~~G~~L~v~~~g~~~~~L~~L~~~~--~~~~V~~n~~-y~p~~~~rD~~v~~~l~~~gI~v~~~~~ 131 (681)
+|.++.+.|+ ++|+.+.++.. +.+..|.+.+++. .++.|+.|.. |+-.+. +++++++..++++..++-
T Consensus 25 tl~di~~~~~~~a~~~g~~v~~~QS-N~EGelId~i~~a~~~~dgiIINpga~THtSi----Al~DAl~~~~~P~vEVHi 99 (141)
T TIGR01088 25 TLEEIVEIIETFAAQLNVELEFFQS-NSEGQLIDKIHEAEGQYDGIIINPGALTHTSV----ALRDALAAVSLPVVEVHL 99 (141)
T ss_pred CHHHHHHHHHHHHHHcCCEEEEEee-CcHHHHHHHHHhccccCCEEEEcChHHhhhHH----HHHHHHHcCCCCEEEEEc
Confidence 3444444444 45888888764 4444555444443 3678998843 333333 466667788999999886
Q ss_pred CeeeCCcc
Q 005710 132 DLLYEPWD 139 (681)
Q Consensus 132 ~~L~~p~~ 139 (681)
..++..++
T Consensus 100 SNi~aRE~ 107 (141)
T TIGR01088 100 SNVHAREE 107 (141)
T ss_pred CCcccccc
Confidence 66655443
No 38
>PRK15005 universal stress protein F; Provisional
Probab=41.47 E-value=2.2e+02 Score=25.88 Aligned_cols=44 Identities=11% Similarity=0.161 Sum_probs=30.2
Q ss_pred HhHHHHHHHHHhCCC--ceEEEeCCChHHHHHHHHHHcCCCEEEEec
Q 005710 58 HSLSHLDSSLRSLGT--SLVTKRSTDSVSSLLEVVKATGATQLFFNH 102 (681)
Q Consensus 58 esL~dL~~~L~~~G~--~L~v~~~g~~~~~L~~L~~~~~~~~V~~n~ 102 (681)
+.|..+.+.+...|. ..++. .|++.+.|.+++++.+++-|+.-.
T Consensus 70 ~~l~~~~~~~~~~~~~~~~~v~-~G~p~~~I~~~a~~~~~DLIV~Gs 115 (144)
T PRK15005 70 SQLEEIIKKFKLPTDRVHVHVE-EGSPKDRILELAKKIPADMIIIAS 115 (144)
T ss_pred HHHHHHHHHhCCCCCceEEEEe-CCCHHHHHHHHHHHcCCCEEEEeC
Confidence 344444444444443 34554 488999999999999999988863
No 39
>PRK15456 universal stress protein UspG; Provisional
Probab=38.99 E-value=2.4e+02 Score=25.75 Aligned_cols=80 Identities=10% Similarity=0.042 Sum_probs=44.9
Q ss_pred HHHHHHHHc----CCeEEEEEEcCCCCCCC---CC--chhhHH---HHHHhHHHHHHHHHhCCCc--eEEEeCCChHHHH
Q 005710 21 PALAAGVRA----GAVIAVFIWAPEEEGPY---YP--GRVSRW---WLKHSLSHLDSSLRSLGTS--LVTKRSTDSVSSL 86 (681)
Q Consensus 21 ~AL~aA~~~----~~vlpVfI~dP~~~~~~---~~--~r~~r~---FL~esL~dL~~~L~~~G~~--L~v~~~g~~~~~L 86 (681)
.||.+|+.. +.+.-|+|+++...... .. ...... -..+.|..+.+.+...|.+ .++. .|++.+.|
T Consensus 19 ~al~~A~~la~~~~~l~llhv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~~v~-~G~~~~~I 97 (142)
T PRK15456 19 KAVRHAEFLAQDDGVIHLLHVLPGSASLSLHRFAADVRRFEEHLQHEAEERLQTMVSHFTIDPSRIKQHVR-FGSVRDEV 97 (142)
T ss_pred HHHHHHHHHHhcCCeEEEEEEecCcccccccccccchhhHHHHHHHHHHHHHHHHHHHhCCCCcceEEEEc-CCChHHHH
Confidence 455555432 46778888876421100 00 001111 2234455555555444443 3444 47899999
Q ss_pred HHHHHHcCCCEEEEe
Q 005710 87 LEVVKATGATQLFFN 101 (681)
Q Consensus 87 ~~L~~~~~~~~V~~n 101 (681)
.+++++++++-|+.-
T Consensus 98 ~~~a~~~~~DLIVmG 112 (142)
T PRK15456 98 NELAEELGADVVVIG 112 (142)
T ss_pred HHHHhhcCCCEEEEc
Confidence 999999999999885
No 40
>TIGR00273 iron-sulfur cluster-binding protein. Members of this family have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4fe-4S iron-sulfur clusters.
Probab=38.96 E-value=58 Score=36.84 Aligned_cols=68 Identities=13% Similarity=0.156 Sum_probs=48.9
Q ss_pred HHhHHHHHHHHHhCCCceEEEeC-CChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEE
Q 005710 57 KHSLSHLDSSLRSLGTSLVTKRS-TDSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRS 128 (681)
Q Consensus 57 ~esL~dL~~~L~~~G~~L~v~~~-g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~ 128 (681)
-+=|..+.+++++.|..+++... .+..+.+.+++++.+++.|+........+ -.+.+.|.+.|+.+..
T Consensus 50 d~~l~~~~~~~~~~g~~v~~a~t~~eA~~~v~~i~~~~~~~~vv~~kS~~~ee----igl~~~L~~~g~~~~e 118 (432)
T TIGR00273 50 DFYLDQLKENVTQRGGHVYYAKTAEEARKIIGKVAQEKNGKKVVKSKSMVSEE----IGLNEVLEKIGIEVWE 118 (432)
T ss_pred HHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHHHhCCCEEEEcCchHHHH----hCCHHHHHhCCCeeee
Confidence 34456677888899999988754 45667788999999999999875433333 3466677778887543
No 41
>TIGR00268 conserved hypothetical protein TIGR00268. The N-terminal region of the model shows similarity to Argininosuccinate synthase proteins using PSI-blast and using the recognize protein identification server.
Probab=38.54 E-value=1.5e+02 Score=30.78 Aligned_cols=72 Identities=15% Similarity=0.064 Sum_probs=46.1
Q ss_pred HHHHHHHHHhCCCceEEEeCCChHHHHHHHHHHcCCC--EEEEecccChhhHHHHHHHHHHHHhCCeEEEEecCCe
Q 005710 60 LSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKATGAT--QLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNADL 133 (681)
Q Consensus 60 L~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~~~~~--~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~~~ 133 (681)
+..|++-|++.+.-++.+.+|-...++..++.+.|.. .|+++....+. .-.+.+++.|+..||+.+.++-+.
T Consensus 2 ~~~l~~~l~~~~~vlVa~SGGvDSs~ll~la~~~g~~v~av~~~~~~~~~--~e~~~a~~~a~~lgi~~~ii~~~~ 75 (252)
T TIGR00268 2 LENLRNFLKEFKKVLIAYSGGVDSSLLAAVCSDAGTEVLAITVVSPSISP--RELEDAIIIAKEIGVNHEFVKIDK 75 (252)
T ss_pred hHHHHHHHHhcCCEEEEecCcHHHHHHHHHHHHhCCCEEEEEecCCCCCH--HHHHHHHHHHHHcCCCEEEEEcHH
Confidence 3567777888776666666676666777888777544 44444322221 112456778999999988876543
No 42
>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
Probab=36.82 E-value=84 Score=34.70 Aligned_cols=61 Identities=20% Similarity=0.286 Sum_probs=39.5
Q ss_pred HHHhCCCc--eEEEeCCChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEE
Q 005710 66 SLRSLGTS--LVTKRSTDSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVR 127 (681)
Q Consensus 66 ~L~~~G~~--L~v~~~g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~ 127 (681)
+|+++|++ .++.. ..+.....+.+-+.|+.+|++-.|.+|....--+++.+.|++.||+|.
T Consensus 37 ~l~~lgi~g~~i~~s-~~p~~~cad~ii~~gi~rVVi~~D~d~~G~~~~~~~~~~L~~aGi~V~ 99 (360)
T PRK14719 37 SLKNLKINANFITVS-NTPVFQIADDLIAENISEVILLTDFDRAGRVYAKNIMEEFQSRGIKVN 99 (360)
T ss_pred HHHHcCCCCcEEEEe-CCchHHHHHHHHHcCCCEEEEEECCCCCCCccchHHHHHHHHCCCEEE
Confidence 57888885 44333 444444554455569999988766666433333456778999999994
No 43
>PRK08057 cobalt-precorrin-6x reductase; Reviewed
Probab=35.24 E-value=2.1e+02 Score=29.83 Aligned_cols=47 Identities=17% Similarity=0.225 Sum_probs=39.2
Q ss_pred hHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 82 SVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 82 ~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
..+.+.+++++++++.|+ +. .-|++..--+.+.++|++.||++.-|.
T Consensus 53 ~~~~l~~~l~~~~i~~VI-DA-THPfA~~is~~a~~ac~~~~ipyiR~e 99 (248)
T PRK08057 53 GAEGLAAYLREEGIDLVI-DA-THPYAAQISANAAAACRALGIPYLRLE 99 (248)
T ss_pred CHHHHHHHHHHCCCCEEE-EC-CCccHHHHHHHHHHHHHHhCCcEEEEe
Confidence 467899999999999876 32 358888888899999999999998775
No 44
>PF00582 Usp: Universal stress protein family; InterPro: IPR006016 The universal stress protein UspA P28242 from SWISSPROT [] is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA [] reveals an alpha/beta fold similar to that of the Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0577 protein, which binds ATP [], though UspA lacks ATP-binding activity.; GO: 0006950 response to stress; PDB: 3DLO_C 3QTB_A 2PFS_A 3TNJ_A 1JMV_D 3FH0_B 3FDX_B 3AB7_A 3AB8_A 2GM3_F ....
Probab=35.13 E-value=2.7e+02 Score=24.23 Aligned_cols=52 Identities=17% Similarity=0.161 Sum_probs=35.6
Q ss_pred eCCChHHHHHHHHHHcCCCEEEEeccc-Chhh-HHHHHHHHHHHHhCCeEEEEe
Q 005710 78 RSTDSVSSLLEVVKATGATQLFFNHLY-DPLS-LVRDHRAKEALTAQGIAVRSF 129 (681)
Q Consensus 78 ~~g~~~~~L~~L~~~~~~~~V~~n~~y-~p~~-~~rD~~v~~~l~~~gI~v~~~ 129 (681)
..++..+.+.+++++.+++.|+.-..- .... ...-....+++....|+|..+
T Consensus 86 ~~~~~~~~i~~~~~~~~~dliv~G~~~~~~~~~~~~gs~~~~l~~~~~~pVlvv 139 (140)
T PF00582_consen 86 ESGDVADAIIEFAEEHNADLIVMGSRGRSGLERLLFGSVAEKLLRHAPCPVLVV 139 (140)
T ss_dssp EESSHHHHHHHHHHHTTCSEEEEESSSTTSTTTSSSHHHHHHHHHHTSSEEEEE
T ss_pred EeeccchhhhhccccccceeEEEeccCCCCccCCCcCCHHHHHHHcCCCCEEEe
Confidence 357889999999999999999997543 2222 122334555667777877654
No 45
>COG3590 PepO Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]
Probab=35.05 E-value=21 Score=41.15 Aligned_cols=44 Identities=30% Similarity=0.440 Sum_probs=34.3
Q ss_pred ccccCCCCccchhhhhcCCCCCCCcccccCccccccccCCchhhHHhhchh
Q 005710 382 LDADLESDALGWQYISGTIPDGRAFDRIDNPQFEGYKFDPNGEYVRRWLPE 432 (681)
Q Consensus 382 lD~D~a~n~g~Wqw~aG~g~d~~~~~RifNP~~q~~k~Dp~G~yIr~wvPe 432 (681)
+|+|.+.||||..-+.|--. ++.| -.|+.|||++|....=|.+|
T Consensus 476 ~ea~~a~NYGgIGaVIgHEI-~HgF------DdqGakfD~~GnL~dWWT~e 519 (654)
T COG3590 476 PEADSAANYGGIGAVIGHEI-GHGF------DDQGAKFDGDGNLNDWWTDE 519 (654)
T ss_pred CCcchhhcccCccceehhhh-cccc------cCCccccCCCCcHHhhcCHH
Confidence 67899999999988776422 2333 26999999999999888775
No 46
>PF05889 SLA_LP_auto_ag: Soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen); InterPro: IPR008829 This family consists of several eukaryotic and archaeal proteins which are related to the Homo sapiens soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen). Autoantibodies are a hallmark of autoimmune hepatitis, but most are not disease specific. Autoantibodies to soluble liver antigen (SLA) and to liver and pancreas antigen (LP) have been described as disease specific, occurring in about 30% of all patients with autoimmune hepatitis []. The function of SLA/LP is unknown, however, it has been suggested that the protein may function as a serine hydroxymethyltransferase and may be an important enzyme in the thus far poorly understood selenocysteine pathway []. The archaeal sequences Q8TXK0 from SWISSPROT and Q8TYR3 from SWISSPROT are annotated as being pyridoxal phosphate-dependent enzymes.; GO: 0016740 transferase activity; PDB: 2E7J_B 2E7I_B 2Z67_C 3HL2_D 3BC8_A 3BCA_A 3BCB_A.
Probab=32.72 E-value=75 Score=35.33 Aligned_cols=120 Identities=21% Similarity=0.283 Sum_probs=65.8
Q ss_pred CCCeEEEEEcCCCCCCCCHHHHHHHHcCCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCc--eEEEeC-
Q 005710 3 GRGCSIVWFRRDLRVEDNPALAAGVRAGAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTS--LVTKRS- 79 (681)
Q Consensus 3 ~~~~~LvWFRrDLRl~DN~AL~aA~~~~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~--L~v~~~- 79 (681)
+....++|-|-|. +..+.++...+ +-|+.| +....+.. +.--+..+++.+++.|.. |.+...
T Consensus 99 ~~a~~Viw~ridq----kSc~kai~~AG-l~~~vV-~~~~~~d~---------l~td~~~ie~~i~~~G~~~iLcvlttt 163 (389)
T PF05889_consen 99 PKAKYVIWPRIDQ----KSCFKAIERAG-LEPVVV-ENVLEGDE---------LITDLEAIEAKIEELGADNILCVLTTT 163 (389)
T ss_dssp CT--EEEEEEEET----HHHHHHHHHTT--EEEEE--EEEETTE---------EEEHHHHHHHHHHHHCGGGEEEEEEES
T ss_pred cCCceEEEeeccc----cchHHHHHhcC-CeEEEe-eccCCCCe---------eeccHHHHHHHHHHhCCCCeEEEEEec
Confidence 3456688887554 47887776665 223322 11111111 111134444555555655 433321
Q ss_pred -------CChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHh--CCeEEEEecCCeeeCCc
Q 005710 80 -------TDSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTA--QGIAVRSFNADLLYEPW 138 (681)
Q Consensus 80 -------g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~--~gI~v~~~~~~~L~~p~ 138 (681)
.+.+..+.++|++++|-+|+ |--|..-...--+.|+++++. ..+.++..+-+.|++.+
T Consensus 164 scfapr~~D~i~~IakiC~~~~IPhlv-NnAYgvQ~~~~~~~i~~a~~~GRvda~vqS~dkNF~VPvG 230 (389)
T PF05889_consen 164 SCFAPRLPDDIEEIAKICKEYDIPHLV-NNAYGVQSSKCMHLIQQAWRVGRVDAFVQSTDKNFMVPVG 230 (389)
T ss_dssp STTTTB----HHHHHHHHHHHT--EEE-EGTTTTT-HHHHHHHHHHHHHSTCSEEEEEHHHHHCEESS
T ss_pred CccCCCCCccHHHHHHHHHHcCCceEE-ccchhhhHHHHHHHHHHHHhcCCcceeeeecCCCEEecCC
Confidence 34577899999999999987 656877666666777777653 34556777777888865
No 47
>PLN02347 GMP synthetase
Probab=32.49 E-value=1.7e+02 Score=34.22 Aligned_cols=77 Identities=6% Similarity=0.038 Sum_probs=51.0
Q ss_pred HHHHhHHHHHHHHHhCCCceEEEeCCChHHHHHHHHHH-c--CCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecC
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKA-T--GATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNA 131 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~-~--~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~ 131 (681)
|+.+.++++++.+.+.+.-++-+.+|-.-.++..++.+ . ++..|+++....+.. ..++.++.++++.||+++.++-
T Consensus 214 ~~~~~i~~i~~~~~~~~~vvvalSGGVDSsvla~l~~~alG~~v~av~id~g~~~~~-E~~~~~~~~a~~lgi~~~vvd~ 292 (536)
T PLN02347 214 VLEEQIELIKATVGPDEHVICALSGGVDSTVAATLVHKAIGDRLHCVFVDNGLLRYK-EQERVMETFKRDLHLPVTCVDA 292 (536)
T ss_pred HHHHHHHHHHHHhccCCeEEEEecCChhHHHHHHHHHHHhCCcEEEEEEeCCCCChh-HHHHHHHHHHHHcCCcEEEEeC
Confidence 56678888888877555445555667666677778777 3 456777774443332 2344446677889999988765
Q ss_pred C
Q 005710 132 D 132 (681)
Q Consensus 132 ~ 132 (681)
.
T Consensus 293 ~ 293 (536)
T PLN02347 293 S 293 (536)
T ss_pred c
Confidence 4
No 48
>PF13911 AhpC-TSA_2: AhpC/TSA antioxidant enzyme
Probab=32.03 E-value=89 Score=27.92 Aligned_cols=42 Identities=21% Similarity=0.301 Sum_probs=30.7
Q ss_pred HHHHHHHHHhCCCceEEEeCCChHHHHHHHHHHcCCC-EEEEec
Q 005710 60 LSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKATGAT-QLFFNH 102 (681)
Q Consensus 60 L~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~~~~~-~V~~n~ 102 (681)
|.....+|++.|++|+++..|+... +.++++..+.. .||++.
T Consensus 2 L~~~~~~l~~~gv~lv~I~~g~~~~-~~~f~~~~~~p~~ly~D~ 44 (115)
T PF13911_consen 2 LSRRKPELEAAGVKLVVIGCGSPEG-IEKFCELTGFPFPLYVDP 44 (115)
T ss_pred hhHhHHHHHHcCCeEEEEEcCCHHH-HHHHHhccCCCCcEEEeC
Confidence 6677888999999998886666544 88888765542 377663
No 49
>TIGR00884 guaA_Cterm GMP synthase (glutamine-hydrolyzing), C-terminal domain or B subunit. This protein of purine de novo biosynthesis is well-conserved. However, it appears to split into two separate polypeptide chains in most of the Archaea. This C-terminal region would be the larger subunit
Probab=31.21 E-value=2.2e+02 Score=30.71 Aligned_cols=74 Identities=8% Similarity=0.135 Sum_probs=46.3
Q ss_pred HHHHhHHHHHHHHHhCCCce-EEEeCCChHHHHHHHHHHc---CCCEEEEecccChhhHHHHHHHHHHH-HhCCeEEEEe
Q 005710 55 WLKHSLSHLDSSLRSLGTSL-VTKRSTDSVSSLLEVVKAT---GATQLFFNHLYDPLSLVRDHRAKEAL-TAQGIAVRSF 129 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L-~v~~~g~~~~~L~~L~~~~---~~~~V~~n~~y~p~~~~rD~~v~~~l-~~~gI~v~~~ 129 (681)
|+-+.+..|++.+.+ .++ +.+.+|-...++..++.+. ++..|+++....+. .-...+++.+ +..||+++.+
T Consensus 2 ~~~~~~~~l~~~v~~--~kVvValSGGVDSsvla~ll~~~~G~~v~av~vd~G~~~~--~E~e~~~~~~~~~lgi~~~vv 77 (311)
T TIGR00884 2 FIEEAVEEIREQVGD--AKVIIALSGGVDSSVAAVLAHRAIGDRLTCVFVDHGLLRK--GEAEQVVKTFGDRLGLNLVYV 77 (311)
T ss_pred hHHHHHHHHHHHhCC--CcEEEEecCChHHHHHHHHHHHHhCCCEEEEEEeCCCCCh--HHHHHHHHHHHHHcCCcEEEE
Confidence 677888999988865 344 4455565555666666553 45677777554332 2223444444 4799999887
Q ss_pred cCC
Q 005710 130 NAD 132 (681)
Q Consensus 130 ~~~ 132 (681)
+-+
T Consensus 78 d~~ 80 (311)
T TIGR00884 78 DAK 80 (311)
T ss_pred eCc
Confidence 654
No 50
>PF04104 DNA_primase_lrg: Eukaryotic and archaeal DNA primase, large subunit; InterPro: IPR007238 DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 (58 kDa in the yeast Saccharomyces cerevisiae) []. Both subunits participate in the formation of the active site, but the ATP binding site is located on the small subunit []. Primase function has also been demonstrated for human and mouse primase subunits [].; GO: 0003896 DNA primase activity, 0006269 DNA replication, synthesis of RNA primer; PDB: 1ZT2_B 3Q36_A 3L9Q_B 2DLA_B 3LGB_B.
Probab=29.98 E-value=45 Score=34.99 Aligned_cols=48 Identities=15% Similarity=0.193 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHhcchhhHHHHHHHHHHhhccCCCchHHHHHHHHhccc
Q 005710 335 PLVDAGMRELWATGWLHDRIRVVVSSFFVKVLQLPWRWGMKYFWDTLLD 383 (681)
Q Consensus 335 P~VDAaMRqL~~TGwmHnr~Rm~vAsfl~k~L~idWr~G~~~F~~~LlD 383 (681)
||+-+.+..|+..+-+.|..|+.+++|| |.++++-.+...+|...+-.
T Consensus 110 pCMr~l~~~L~~~~hL~h~~R~ql~lFL-k~iGl~~ee~l~f~~~~f~~ 157 (260)
T PF04104_consen 110 PCMRNLHERLRKGHHLKHSGRFQLGLFL-KGIGLSLEEALEFWRSEFSK 157 (260)
T ss_dssp HHHHHHHHHHHHHS---HHHHHHHHHHH-HHTTEECCCHHHCCHHHCCT
T ss_pred hHHHHHHHHHhhCCCCCchhHhhHHHHH-HhcCCCHHHHHHHHHHHhcc
Confidence 6788888888999999999999999999 57788877776666655433
No 51
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=29.81 E-value=1.3e+02 Score=36.44 Aligned_cols=64 Identities=19% Similarity=0.209 Sum_probs=45.7
Q ss_pred HHHHHHHHHhCCCceEEEeCCChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEe
Q 005710 60 LSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSF 129 (681)
Q Consensus 60 L~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~ 129 (681)
-.+.=+.|+++|+++++.. ||....-.+++++.||++|+.+ .-|.+.. +.|+ .+++.|-.|-.+
T Consensus 542 a~~aI~~L~~~Gi~~~mLT-GDn~~~A~~iA~~lGId~v~Ae--llPedK~--~~V~-~l~~~g~~VamV 605 (713)
T COG2217 542 AKEAIAALKALGIKVVMLT-GDNRRTAEAIAKELGIDEVRAE--LLPEDKA--EIVR-ELQAEGRKVAMV 605 (713)
T ss_pred HHHHHHHHHHCCCeEEEEc-CCCHHHHHHHHHHcChHhhecc--CCcHHHH--HHHH-HHHhcCCEEEEE
Confidence 3344456888999988874 8889999999999999999877 5777654 2333 455666444443
No 52
>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A ....
Probab=29.44 E-value=2.3e+02 Score=28.39 Aligned_cols=73 Identities=18% Similarity=0.341 Sum_probs=46.7
Q ss_pred HHHHhHHHHHHHHHhCCCceEEE-eCC-Ch---HHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEe
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTK-RST-DS---VSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSF 129 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~-~~g-~~---~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~ 129 (681)
|..+-..-+++.++++|..+.+. ... +. .+.+..+++ .+++.|++..- ++.... ..++ .|.+.||+|..+
T Consensus 12 ~~~~~~~g~~~~a~~~g~~~~~~~~~~~d~~~q~~~i~~~i~-~~~d~Iiv~~~-~~~~~~--~~l~-~~~~~gIpvv~~ 86 (257)
T PF13407_consen 12 FWQQVIKGAKAAAKELGYEVEIVFDAQNDPEEQIEQIEQAIS-QGVDGIIVSPV-DPDSLA--PFLE-KAKAAGIPVVTV 86 (257)
T ss_dssp HHHHHHHHHHHHHHHHTCEEEEEEESTTTHHHHHHHHHHHHH-TTESEEEEESS-STTTTH--HHHH-HHHHTTSEEEEE
T ss_pred HHHHHHHHHHHHHHHcCCEEEEeCCCCCCHHHHHHHHHHHHH-hcCCEEEecCC-CHHHHH--HHHH-HHhhcCceEEEE
Confidence 66677788888888899998774 432 22 223444443 37999887632 222222 2343 467789999998
Q ss_pred cCC
Q 005710 130 NAD 132 (681)
Q Consensus 130 ~~~ 132 (681)
+..
T Consensus 87 d~~ 89 (257)
T PF13407_consen 87 DSD 89 (257)
T ss_dssp SST
T ss_pred ecc
Confidence 876
No 53
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=29.17 E-value=94 Score=29.28 Aligned_cols=45 Identities=20% Similarity=0.218 Sum_probs=30.0
Q ss_pred HHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEe
Q 005710 83 VSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSF 129 (681)
Q Consensus 83 ~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~ 129 (681)
.+.+.+++++++++.|++.-. ..+..+-+++-+.|++.||++...
T Consensus 130 ~~~l~~~~~~~~id~v~ial~--~~~~~~i~~ii~~~~~~~v~v~~v 174 (175)
T PF13727_consen 130 LDDLPELVREHDIDEVIIALP--WSEEEQIKRIIEELENHGVRVRVV 174 (175)
T ss_dssp GGGHHHHHHHHT--EEEE--T--TS-HHHHHHHHHHHHTTT-EEEE-
T ss_pred HHHHHHHHHhCCCCEEEEEcC--ccCHHHHHHHHHHHHhCCCEEEEe
Confidence 467899999999999999832 234455667788899999998864
No 54
>cd06313 PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=29.17 E-value=3.7e+02 Score=27.45 Aligned_cols=73 Identities=16% Similarity=0.211 Sum_probs=46.5
Q ss_pred HHHHhHHHHHHHHHhCCCceEEEeCC-Ch---HHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTKRST-DS---VSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~~~g-~~---~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
|..+-+..+.+.+++.|..+.+.... +. .+.+..+. ..+++.|++... ++ -..+..++ .+.+.||++..++
T Consensus 13 f~~~~~~gi~~~~~~~G~~~~~~~~~~d~~~~~~~i~~~~-~~~vdgiii~~~-~~--~~~~~~i~-~~~~~~iPvV~~~ 87 (272)
T cd06313 13 WCAQGKQAADEAGKLLGVDVTWYGGALDAVKQVAAIENMA-SQGWDFIAVDPL-GI--GTLTEAVQ-KAIARGIPVIDMG 87 (272)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEecCCCCHHHHHHHHHHHH-HcCCCEEEEcCC-Ch--HHhHHHHH-HHHHCCCcEEEeC
Confidence 67778888999999999999876432 22 23344444 468998888521 11 11223343 4566799999987
Q ss_pred CC
Q 005710 131 AD 132 (681)
Q Consensus 131 ~~ 132 (681)
..
T Consensus 88 ~~ 89 (272)
T cd06313 88 TL 89 (272)
T ss_pred CC
Confidence 54
No 55
>TIGR01490 HAD-SF-IB-hyp1 HAD-superfamily subfamily IB hydrolase, TIGR01490. A subset of these sequences, including the Caulobacter crescentus CicA protein, cluster together and may represent a separate equivalog.
Probab=28.96 E-value=2.2e+02 Score=27.73 Aligned_cols=44 Identities=9% Similarity=0.010 Sum_probs=33.4
Q ss_pred HHhHHHHHHHHHhCCCceEEEeCCChHHHHHHHHHHcCCCEEEEe
Q 005710 57 KHSLSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKATGATQLFFN 101 (681)
Q Consensus 57 ~esL~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~~~~~~V~~n 101 (681)
...+.++-+.|++.|.++.+.. +.+...+..+++..|++.++.+
T Consensus 89 ~~~~~~~l~~l~~~g~~v~ivS-~s~~~~v~~~~~~lg~~~~~~~ 132 (202)
T TIGR01490 89 YPEARDLIRWHKAEGHTIVLVS-ASLTILVKPLARILGIDNAIGT 132 (202)
T ss_pred cHHHHHHHHHHHHCCCEEEEEe-CCcHHHHHHHHHHcCCcceEec
Confidence 4466666677888999998875 5566778888888899887755
No 56
>PF02571 CbiJ: Precorrin-6x reductase CbiJ/CobK; InterPro: IPR003723 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CobK and CbiJ precorrin-6x reductase (1.3.1.54 from EC). In the aerobic pathway, CobK catalyses the reduction of the macrocycle of precorrin-6X to produce precorrin-6Y; while in the anaerobic pathway CbiJ catalyses the reduction of the macrocycle of cobalt-precorrin-6X into cobalt-precorrin-6Y [, ].; GO: 0016994 precorrin-6A reductase activity, 0009236 cobalamin biosynthetic process, 0055114 oxidation-reduction process
Probab=28.52 E-value=2.3e+02 Score=29.55 Aligned_cols=56 Identities=20% Similarity=0.220 Sum_probs=43.8
Q ss_pred eEEEeCCC-hHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecC
Q 005710 74 LVTKRSTD-SVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNA 131 (681)
Q Consensus 74 L~v~~~g~-~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~ 131 (681)
+.++.++- ..+.+.+++++++++.|+=. .-|++..--+.+.++|++.||++.-|.=
T Consensus 45 ~~v~~G~lg~~~~l~~~l~~~~i~~vIDA--THPfA~~is~na~~a~~~~~ipylR~eR 101 (249)
T PF02571_consen 45 LEVRVGRLGDEEGLAEFLRENGIDAVIDA--THPFAAEISQNAIEACRELGIPYLRFER 101 (249)
T ss_pred ceEEECCCCCHHHHHHHHHhCCCcEEEEC--CCchHHHHHHHHHHHHhhcCcceEEEEc
Confidence 33443333 57889999999999988722 3599999999999999999999987753
No 57
>PRK14010 potassium-transporting ATPase subunit B; Provisional
Probab=27.58 E-value=2.2e+02 Score=34.23 Aligned_cols=63 Identities=19% Similarity=0.226 Sum_probs=45.3
Q ss_pred HhHHHHHHHHHhCCCceEEEeCCChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEE
Q 005710 58 HSLSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAV 126 (681)
Q Consensus 58 esL~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v 126 (681)
....+.=++|++.|++.++.. ||....-..++++.|++.++.. ..|.... ++-+.+++.|-.|
T Consensus 444 ~~a~e~I~~Lr~~GI~vvMiT-GDn~~TA~aIA~elGI~~v~A~--~~PedK~---~iV~~lQ~~G~~V 506 (673)
T PRK14010 444 DGLVERFRELREMGIETVMCT-GDNELTAATIAKEAGVDRFVAE--CKPEDKI---NVIREEQAKGHIV 506 (673)
T ss_pred HHHHHHHHHHHHCCCeEEEEC-CCCHHHHHHHHHHcCCceEEcC--CCHHHHH---HHHHHHHhCCCEE
Confidence 445555567888999998875 7778888899999999998865 5777654 2334456666433
No 58
>PRK08535 translation initiation factor IF-2B subunit delta; Provisional
Probab=27.03 E-value=3.7e+02 Score=28.96 Aligned_cols=93 Identities=13% Similarity=0.131 Sum_probs=50.2
Q ss_pred HHHHHHcCCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeCCChHHHHHHHHHH--cCCCEEEE
Q 005710 23 LAAGVRAGAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKA--TGATQLFF 100 (681)
Q Consensus 23 L~aA~~~~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~--~~~~~V~~ 100 (681)
|..|.+.+.-+-|||.+.+ + ..|+ +.+..+|.+.|++..+.- +.....+..-+.. .|++.|+.
T Consensus 137 l~~A~~~~k~~~V~v~Esr---P----------~~~G-~~~a~~L~~~GI~vtlI~-Dsav~~~m~~vd~VivGAd~v~~ 201 (310)
T PRK08535 137 IKTAHEQGKDIEVIATETR---P----------RNQG-HITAKELAEYGIPVTLIV-DSAVRYFMKDVDKVVVGADAITA 201 (310)
T ss_pred HHHHHHCCCeEEEEEecCC---c----------hhhH-HHHHHHHHHCCCCEEEEe-hhHHHHHHHhCCEEEECccEEec
Confidence 3445555555778887643 1 1255 567788999999987764 3333333211111 13444443
Q ss_pred ecccChhhHHHHHHHHHHHHhCCeEEEEecCC
Q 005710 101 NHLYDPLSLVRDHRAKEALTAQGIAVRSFNAD 132 (681)
Q Consensus 101 n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~~ 132 (681)
|- +.....=-..+.-+++..+++|..+-..
T Consensus 202 nG--~v~nkiGT~~~A~~Ak~~~vPv~V~a~~ 231 (310)
T PRK08535 202 NG--AVINKIGTSQIALAAHEARVPFMVAAET 231 (310)
T ss_pred CC--CEEeHHhHHHHHHHHHHhCCCEEEeccc
Confidence 41 1222222234555778889999876443
No 59
>PRK09590 celB cellobiose phosphotransferase system IIB component; Reviewed
Probab=26.88 E-value=3.8e+02 Score=24.08 Aligned_cols=67 Identities=12% Similarity=0.103 Sum_probs=45.5
Q ss_pred HHHHhHHHHHHHHHhCCCceEEEeCCChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
++.+.+ ++.++++|+++.+... +...+.......+++-|+. .|.-.-+...+++.+...|++|...+
T Consensus 16 lla~k~---k~~~~e~gi~~~i~a~--~~~e~~~~~~~~~~DvIll----~PQi~~~~~~i~~~~~~~~ipv~~I~ 82 (104)
T PRK09590 16 MMAKKT---TEYLKEQGKDIEVDAI--TATEGEKAIAAAEYDLYLV----SPQTKMYFKQFEEAGAKVGKPVVQIP 82 (104)
T ss_pred HHHHHH---HHHHHHCCCceEEEEe--cHHHHHHhhccCCCCEEEE----ChHHHHHHHHHHHHhhhcCCCEEEeC
Confidence 665555 6667889999887542 3444555444445665554 56666667789999988999988764
No 60
>PRK01122 potassium-transporting ATPase subunit B; Provisional
Probab=26.47 E-value=2.3e+02 Score=34.06 Aligned_cols=61 Identities=15% Similarity=0.177 Sum_probs=44.2
Q ss_pred HhHHHHHHHHHhCCCceEEEeCCChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCe
Q 005710 58 HSLSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGI 124 (681)
Q Consensus 58 esL~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI 124 (681)
....+.=++|++.|++.++.. ||....-..++++.|++.++.+ ..|.+.. ++-+.+++.|-
T Consensus 448 ~~~~eai~~Lr~~GI~vvMiT-GDn~~TA~aIA~elGId~v~A~--~~PedK~---~iV~~lQ~~G~ 508 (679)
T PRK01122 448 PGIKERFAELRKMGIKTVMIT-GDNPLTAAAIAAEAGVDDFLAE--ATPEDKL---ALIRQEQAEGR 508 (679)
T ss_pred hhHHHHHHHHHHCCCeEEEEC-CCCHHHHHHHHHHcCCcEEEcc--CCHHHHH---HHHHHHHHcCC
Confidence 445555667889999998875 7778888899999999998766 5777654 22334556663
No 61
>cd06295 PBP1_CelR Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn chang
Probab=26.37 E-value=4.1e+02 Score=26.87 Aligned_cols=71 Identities=15% Similarity=0.179 Sum_probs=45.3
Q ss_pred HHHHhHHHHHHHHHhCCCceEEEeCCC-hHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecC
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTKRSTD-SVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNA 131 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~~~g~-~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~ 131 (681)
|..+-++.+.+.+++.|..+.+...+. ....+.+.+.+.+++.|++.-.... +..+ +.+.+.||++..++.
T Consensus 24 ~~~~~~~gi~~~~~~~g~~~~v~~~~~~~~~~~~~~l~~~~~dgiii~~~~~~-----~~~~-~~~~~~~ipvV~~~~ 95 (275)
T cd06295 24 FFLSLLGGIADALAERGYDLLLSFVSSPDRDWLARYLASGRADGVILIGQHDQ-----DPLP-ERLAETGLPFVVWGR 95 (275)
T ss_pred hHHHHHHHHHHHHHHcCCEEEEEeCCchhHHHHHHHHHhCCCCEEEEeCCCCC-----hHHH-HHHHhCCCCEEEECC
Confidence 555666777888999999987764322 2345556666678998876521111 1223 345678999998864
No 62
>TIGR02990 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.
Probab=26.35 E-value=2.8e+02 Score=28.71 Aligned_cols=50 Identities=14% Similarity=0.221 Sum_probs=42.5
Q ss_pred hHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecCCee
Q 005710 82 SVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNADLL 134 (681)
Q Consensus 82 ~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~~~L 134 (681)
+...+.+.++..|+++|..- +||.....+.+++.+.+.|++|..+.+..+
T Consensus 107 ~~~A~~~AL~alg~~RIalv---TPY~~~v~~~~~~~l~~~G~eV~~~~~~~~ 156 (239)
T TIGR02990 107 PSSAAVDGLAALGVRRISLL---TPYTPETSRPMAQYFAVRGFEIVNFTCLGL 156 (239)
T ss_pred HHHHHHHHHHHcCCCEEEEE---CCCcHHHHHHHHHHHHhCCcEEeeeeccCC
Confidence 56677788888999999887 899999999999999999999988765433
No 63
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=26.11 E-value=4.7e+02 Score=26.44 Aligned_cols=73 Identities=21% Similarity=0.253 Sum_probs=45.5
Q ss_pred HHHHhHHHHHHHHHhCCCceEEEeCC--ChH---HHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEe
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTKRST--DSV---SSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSF 129 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~~~g--~~~---~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~ 129 (681)
|+.+-+..+.+.+++.|..+.+.... +.. +.+..+.. .+++.|+.... .+. .-...++ .+.+.||++..+
T Consensus 14 ~~~~~~~g~~~~~~~~g~~v~~~~~~~~~~~~~~~~i~~l~~-~~vdgiii~~~-~~~--~~~~~l~-~~~~~~ipvV~~ 88 (271)
T cd06312 14 FWTVVKNGAEDAAKDLGVDVEYRGPETFDVADMARLIEAAIA-AKPDGIVVTIP-DPD--ALDPAIK-RAVAAGIPVISF 88 (271)
T ss_pred HHHHHHHHHHHHHHHhCCEEEEECCCCCCHHHHHHHHHHHHH-hCCCEEEEeCC-ChH--HhHHHHH-HHHHCCCeEEEe
Confidence 66778888888899999999876433 222 23334443 48998887521 111 1122343 456789999998
Q ss_pred cCC
Q 005710 130 NAD 132 (681)
Q Consensus 130 ~~~ 132 (681)
+..
T Consensus 89 ~~~ 91 (271)
T cd06312 89 NAG 91 (271)
T ss_pred CCC
Confidence 643
No 64
>PF01220 DHquinase_II: Dehydroquinase class II; InterPro: IPR001874 3-dehydroquinate dehydratase (4.2.1.10 from EC), or dehydroquinase, catalyzes the conversion of 3-dehydroquinate into 3-dehydroshikimate. It is the third step in the shikimate pathway for the biosynthesis of aromatic amino acids from chorismate. Two classes of dehydroquinases exist, known as types I and II. Class-II enzymes are homododecameric enzymes of about 17 kDa. They are found in some bacteria such as actinomycetales [, ] and some fungi where they act in a catabolic pathway that allows the use of quinic acid as a carbon source.; GO: 0003855 3-dehydroquinate dehydratase activity; PDB: 3N8K_J 3N7A_I 3N87_F 3N8N_H 3N86_N 1H0S_A 3N59_J 1H05_A 1H0R_A 2Y71_A ....
Probab=25.95 E-value=5.3e+02 Score=24.65 Aligned_cols=69 Identities=17% Similarity=0.221 Sum_probs=41.7
Q ss_pred HHhCCCceEEEeCCChHHHHHHHHHHc--CCCEEEEecc-cChhhHHHHHHHHHHHHhCCeEEEEecCCeeeCCccc
Q 005710 67 LRSLGTSLVTKRSTDSVSSLLEVVKAT--GATQLFFNHL-YDPLSLVRDHRAKEALTAQGIAVRSFNADLLYEPWDV 140 (681)
Q Consensus 67 L~~~G~~L~v~~~g~~~~~L~~L~~~~--~~~~V~~n~~-y~p~~~~rD~~v~~~l~~~gI~v~~~~~~~L~~p~~i 140 (681)
-+++|+.+.++.. +.+..|.+.+++. .++.|+.|.. |+-.+. ++.++++..++++..++-..++.++++
T Consensus 38 a~~~g~~v~~~QS-N~EGelid~I~~a~~~~dgiIINpga~thtS~----Ai~DAl~~~~~P~vEVHiSNi~~RE~f 109 (140)
T PF01220_consen 38 AAELGVEVEFFQS-NHEGELIDWIHEARDDVDGIIINPGAYTHTSI----AIRDALKAISIPVVEVHISNIHAREEF 109 (140)
T ss_dssp HHHTTEEEEEEE--SSHHHHHHHHHHHTCTTSEEEEE-GGGGHT-H----HHHHHHHCCTS-EEEEESS-GGGS-GG
T ss_pred HHHCCCeEEEEec-CCHHHHHHHHHHHHhhCCEEEEccchhccccH----HHHHHHHcCCCCEEEEEcCCccccccc
Confidence 3456888888864 4455555444443 3789999943 333444 466677888999999987766665444
No 65
>TIGR00715 precor6x_red precorrin-6x reductase. This enzyme was found to be a monomer by gel filtration.
Probab=25.57 E-value=4e+02 Score=27.87 Aligned_cols=46 Identities=20% Similarity=0.179 Sum_probs=37.6
Q ss_pred HHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 83 VSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 83 ~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
.+.+.+++++.+++.|+-. .-|++..--+.+.++|++.||++.-|.
T Consensus 54 ~~~l~~~l~~~~i~~VIDA--tHPfA~~is~~a~~a~~~~~ipylR~e 99 (256)
T TIGR00715 54 PQELREFLKRHSIDILVDA--THPFAAQITTNATAVCKELGIPYVRFE 99 (256)
T ss_pred HHHHHHHHHhcCCCEEEEc--CCHHHHHHHHHHHHHHHHhCCcEEEEE
Confidence 3458889999999977644 468888888889999999999998874
No 66
>PF03392 OS-D: Insect pheromone-binding family, A10/OS-D; InterPro: IPR005055 A class of small (14-20 Kd) water-soluble proteins, called odorant binding proteins (OBPs), first discovered in the insect sensillar lymph but also in the mucus of vertebrates, is postulated to mediate the solubilisation of hydrophobic odorant molecules, and thereby to facilitate their transport to the receptor neurons. The product of a gene expressed in the olfactory system of Drosophila melanogaster (Fruit fly), OS-D, shares features common to vertebrate odorant-binding proteins, but has a primary structure unlike odorant-binding proteins []. OS-D derivatives have subsequently been found in chemosensory organs of phylogenetically distinct insects, including cockroaches, phasmids and moths, suggesting that OS-D-like proteins seem to be conserved in the insect phylum.; PDB: 1KX9_A 1N8U_A 1KX8_A 1K19_A 1N8V_A 2GVS_A 2JNT_A.
Probab=24.56 E-value=27 Score=30.98 Aligned_cols=13 Identities=38% Similarity=1.089 Sum_probs=9.5
Q ss_pred cccCCchhhHHhh
Q 005710 417 YKFDPNGEYVRRW 429 (681)
Q Consensus 417 ~k~Dp~G~yIr~w 429 (681)
.||||+|+|.++|
T Consensus 83 ~KyDp~~~y~~ky 95 (95)
T PF03392_consen 83 KKYDPEGKYRKKY 95 (95)
T ss_dssp HHHTTT-TTHHHH
T ss_pred HHHCCCcchhhcC
Confidence 4788999888775
No 67
>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein. Members of this family are periplasmic (when in Gram-negative bacteria) binding proteins for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter.
Probab=24.23 E-value=5.2e+02 Score=27.00 Aligned_cols=73 Identities=15% Similarity=0.219 Sum_probs=47.3
Q ss_pred HHHHhHHHHHHHHHhCCCceEEEeCC-Ch---HHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTKRST-DS---VSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~~~g-~~---~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
|+.+...-+++.+++.|..+++...+ +. .+.+.. +...+++.|+... .....-+..++ .+.+.||+|..++
T Consensus 12 ~~~~~~~~i~~~a~~~g~~v~~~~~~~~~~~q~~~i~~-l~~~~vDgIIi~~---~~~~~~~~~l~-~~~~~~iPvV~~d 86 (302)
T TIGR02634 12 RWQKDRDIFVAAAESLGAKVFVQSANGNEAKQISQIEN-LIARGVDVLVIIP---QNGQVLSNAVQ-EAKDEGIKVVAYD 86 (302)
T ss_pred hHHHHHHHHHHHHHhcCCEEEEEeCCCCHHHHHHHHHH-HHHcCCCEEEEeC---CChhHHHHHHH-HHHHCCCeEEEec
Confidence 77788889999999999998776432 21 123333 4456899888762 22122233343 4577899999986
Q ss_pred CC
Q 005710 131 AD 132 (681)
Q Consensus 131 ~~ 132 (681)
..
T Consensus 87 ~~ 88 (302)
T TIGR02634 87 RL 88 (302)
T ss_pred Cc
Confidence 53
No 68
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=23.98 E-value=4.6e+02 Score=26.33 Aligned_cols=73 Identities=18% Similarity=0.235 Sum_probs=45.2
Q ss_pred HHHHhHHHHHHHHHhCCCceEEEeCC-Ch---HHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTKRST-DS---VSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~~~g-~~---~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
|..+-+..+.+.++++|..+.+.... ++ .+.+..+.. .+++.|++... ++. .-+..++ .+++.||++..++
T Consensus 13 ~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~l~~~~~-~~vdgii~~~~-~~~--~~~~~i~-~~~~~~ipvV~~~ 87 (273)
T cd06305 13 FDQAYLAGTKAEAEALGGDLRVYDAGGDDAKQADQIDQAIA-QKVDAIIIQHG-RAE--VLKPWVK-RALDAGIPVVAFD 87 (273)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHHH-cCCCEEEEecC-Chh--hhHHHHH-HHHHcCCCEEEec
Confidence 55677788888999999998776432 22 234444444 48999888521 111 1122233 4567899988886
Q ss_pred CC
Q 005710 131 AD 132 (681)
Q Consensus 131 ~~ 132 (681)
..
T Consensus 88 ~~ 89 (273)
T cd06305 88 VD 89 (273)
T ss_pred CC
Confidence 53
No 69
>cd06811 PLPDE_III_yhfX_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX. This subfamily is composed of the uncharacterized protein yhfX from Escherichia coli K-12 and similar bacterial proteins. These proteins are homologous to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.
Probab=23.69 E-value=3.3e+02 Score=30.15 Aligned_cols=71 Identities=15% Similarity=0.218 Sum_probs=46.1
Q ss_pred CCCCHHHHHHHH----cCCeEE-EEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEE-EeCC-ChHHHHHHH
Q 005710 17 VEDNPALAAGVR----AGAVIA-VFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVT-KRST-DSVSSLLEV 89 (681)
Q Consensus 17 l~DN~AL~aA~~----~~~vlp-VfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v-~~~g-~~~~~L~~L 89 (681)
..-||+|..|+- +|.+.| +|++|.. -|.+.++.|++.+.+.|++|.. .+.. ... .+.++
T Consensus 7 ~~~n~~~~~~a~~~~~~g~~~~~~yvIDl~-------------~I~~N~~~l~~~~~~~~~~l~~vvKAna~~~-~ia~~ 72 (382)
T cd06811 7 LKRNPALIEAALTLHQSGAIPPDTYVIDLD-------------QIEENARLLAETAEKYGIELYFMTKQFGRNP-FLARA 72 (382)
T ss_pred hhhCHHHHHHHHHHHHcCCCCCCEEEecHH-------------HHHHHHHHHHHHHhhCCCEEEEEEccCCCCH-HHHHH
Confidence 467999988763 366554 7777742 3567788888888877888744 3322 233 44456
Q ss_pred HHHcCCCEEEEe
Q 005710 90 VKATGATQLFFN 101 (681)
Q Consensus 90 ~~~~~~~~V~~n 101 (681)
+.+.|++.+.+.
T Consensus 73 l~~~G~~g~~va 84 (382)
T cd06811 73 LLEAGIPGAVAV 84 (382)
T ss_pred HHHcCCCeEeEe
Confidence 667788766554
No 70
>PRK13384 delta-aminolevulinic acid dehydratase; Provisional
Probab=23.46 E-value=5.7e+02 Score=27.77 Aligned_cols=65 Identities=23% Similarity=0.229 Sum_probs=45.9
Q ss_pred cCCCCCCCCHHHHHHHHc------CCeEEEEEEcCCCC-C--CCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEe
Q 005710 12 RRDLRVEDNPALAAGVRA------GAVIAVFIWAPEEE-G--PYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKR 78 (681)
Q Consensus 12 RrDLRl~DN~AL~aA~~~------~~vlpVfI~dP~~~-~--~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~ 78 (681)
+|=-|+.-|+++-.-.++ +.++||||.+.... . ..-+|-.+ |=.+.|...-++|.++|++-+++.
T Consensus 8 ~R~RRlR~~~~~R~lv~Et~l~~~dLI~PlFV~eg~~~~~~I~smPg~~r--~sid~l~~~~~~~~~~Gi~~v~lF 81 (322)
T PRK13384 8 RRLRRLRRSEAMRDLVRETEVSLSDLIYPIFIEEHITDAVPISTLPGISR--LPESALADEIERLYALGIRYVMPF 81 (322)
T ss_pred cCCCcCCCCHHHHHHHhcCCCCHHHceeeEEEecCCCCceecCCCCCcce--ECHHHHHHHHHHHHHcCCCEEEEe
Confidence 577788889998777654 26899999875421 1 22355433 556788888888999999976655
No 71
>PF06415 iPGM_N: BPG-independent PGAM N-terminus (iPGM_N); InterPro: IPR011258 This family represents the N-terminal region of the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (or phosphoglyceromutase or BPG-independent PGAM) protein (5.4.2.1 from EC). The family is found in conjunction with Metalloenzyme (located in the C-terminal region of the protein). ; GO: 0004619 phosphoglycerate mutase activity, 0030145 manganese ion binding, 0006007 glucose catabolic process, 0005737 cytoplasm; PDB: 1EQJ_A 1EJJ_A 1O99_A 1O98_A 3IGZ_B 3IGY_B 3NVL_A 2IFY_A.
Probab=23.38 E-value=2.6e+02 Score=28.77 Aligned_cols=75 Identities=20% Similarity=0.230 Sum_probs=36.9
Q ss_pred HhHHHHHHHHHhCCCceEEEe---CC------ChHHHHHHHHHHcCCCEEEEe-----cccChhh-HHHHHHHHHHHHhC
Q 005710 58 HSLSHLDSSLRSLGTSLVTKR---ST------DSVSSLLEVVKATGATQLFFN-----HLYDPLS-LVRDHRAKEALTAQ 122 (681)
Q Consensus 58 esL~dL~~~L~~~G~~L~v~~---~g------~~~~~L~~L~~~~~~~~V~~n-----~~y~p~~-~~rD~~v~~~l~~~ 122 (681)
+.|.++-+.+++.|..|++.- .| +-.-.|.+++++.|+..|+++ ++..|.+ ..--+++.+.|++.
T Consensus 14 ~~l~~~~~~~k~~~~~lHl~GLlSdGGVHSh~~Hl~al~~~a~~~gv~~V~vH~f~DGRDt~P~S~~~yl~~l~~~l~~~ 93 (223)
T PF06415_consen 14 PVLLEAIEHAKKNGGRLHLMGLLSDGGVHSHIDHLFALIKLAKKQGVKKVYVHAFTDGRDTPPKSALKYLEELEEKLAEI 93 (223)
T ss_dssp HHHHHHHHHHCCTT--EEEEEEESS-SSS--HHHHHHHHHHHHHTT-SEEEEEEEE-SSSS-TTTHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCCeEEEEEEecCCCccccHHHHHHHHHHHHHcCCCEEEEEEecCCCCCCcchHHHHHHHHHHHHHhh
Confidence 445555666666666666642 01 234456666777777766554 3334442 23334555556655
Q ss_pred Ce-EEEEecCC
Q 005710 123 GI-AVRSFNAD 132 (681)
Q Consensus 123 gI-~v~~~~~~ 132 (681)
|+ .+-++-+.
T Consensus 94 ~~g~IAsv~GR 104 (223)
T PF06415_consen 94 GIGRIASVSGR 104 (223)
T ss_dssp TCTEEEEEEEC
T ss_pred CCceEEEEece
Confidence 44 55555444
No 72
>PF07476 MAAL_C: Methylaspartate ammonia-lyase C-terminus; InterPro: IPR022662 Methylaspartate ammonia-lyase 4.3.1.2 from EC catalyses the second step of fermentation of glutamate. It is a homodimer. This domain represents the C-terminal region of methylaspartate ammonia-lyase and contains a TIM barrel fold similar to the PF01188 from PFAM. This domain represents the catalytic domain and contains a metal binding site []. ; PDB: 1KKO_B 1KKR_A 3ZVI_A 1KD0_B 1KCZ_B 3ZVH_A.
Probab=22.85 E-value=4.3e+02 Score=27.35 Aligned_cols=89 Identities=16% Similarity=0.147 Sum_probs=47.7
Q ss_pred eEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeC--CChHHHHHHHHHHcCCCEEEEecccChhhH
Q 005710 32 VIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRS--TDSVSSLLEVVKATGATQLFFNHLYDPLSL 109 (681)
Q Consensus 32 vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~--g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~ 109 (681)
=++|+|=.|-..+ ++.. =++.|..|++.|+++|+++-+.-. -++.+-+..++.. ++.+++--+-.+-...
T Consensus 104 P~~L~iEgP~d~g----~r~~---QI~~l~~Lr~~L~~~g~~v~iVADEWCNT~eDI~~F~da-~A~dmVQIKtPDLGgi 175 (248)
T PF07476_consen 104 PFKLRIEGPMDAG----SREA---QIEALAELREELDRRGINVEIVADEWCNTLEDIREFADA-KAADMVQIKTPDLGGI 175 (248)
T ss_dssp TS-EEEE-SB--S----SHHH---HHHHHHHHHHHHHHCT--EEEEE-TT--SHHHHHHHHHT-T-SSEEEE-GGGGSST
T ss_pred CCeeeeeCCcCCC----ChHH---HHHHHHHHHHHHHhcCCCCeEEeehhcCCHHHHHHHHhc-CCcCEEEecCCCccch
Confidence 3688887775322 2222 269999999999999999976642 3567777777765 5555544332222233
Q ss_pred HHHHHHHHHHHhCCeEEEE
Q 005710 110 VRDHRAKEALTAQGIAVRS 128 (681)
Q Consensus 110 ~rD~~v~~~l~~~gI~v~~ 128 (681)
..--...--|++.|+-...
T Consensus 176 ~ntieAvlyCk~~gvgaY~ 194 (248)
T PF07476_consen 176 NNTIEAVLYCKEHGVGAYL 194 (248)
T ss_dssp HHHHHHHHHHHHTT-EEEE
T ss_pred hhHHHHHHHHHhcCCceee
Confidence 3222222368898886654
No 73
>TIGR01497 kdpB K+-transporting ATPase, B subunit. One sequence is apparently mis-annotated in the primary literature, but properly annotated by TIGR.
Probab=22.79 E-value=3.9e+02 Score=32.18 Aligned_cols=62 Identities=15% Similarity=0.228 Sum_probs=44.0
Q ss_pred HHhHHHHHHHHHhCCCceEEEeCCChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCe
Q 005710 57 KHSLSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGI 124 (681)
Q Consensus 57 ~esL~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI 124 (681)
.....+.=+.|++.|+++++.. |+.......++++.|++.++.+ ..|.... ..|+++ ++.|-
T Consensus 448 Rp~a~eaI~~l~~~Gi~v~miT-GD~~~ta~~iA~~lGI~~v~a~--~~PedK~--~~v~~l-q~~g~ 509 (675)
T TIGR01497 448 KGGIKERFAQLRKMGIKTIMIT-GDNRLTAAAIAAEAGVDDFIAE--ATPEDKI--ALIRQE-QAEGK 509 (675)
T ss_pred hhHHHHHHHHHHHCCCEEEEEc-CCCHHHHHHHHHHcCCCEEEcC--CCHHHHH--HHHHHH-HHcCC
Confidence 3556666677888999998875 7778888899999999998865 5676543 234443 34443
No 74
>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=22.75 E-value=5.3e+02 Score=25.78 Aligned_cols=72 Identities=10% Similarity=0.166 Sum_probs=45.5
Q ss_pred HHHHhHHHHHHHHHhCCCceEEEeCC-Ch---HHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTKRST-DS---VSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~~~g-~~---~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
|..+-+..+.+.+++.|..+.+.... +. .+.+..+. ..+++.|++.-. .+ ..-+..+.. +.+.||++..++
T Consensus 13 ~~~~~~~~i~~~~~~~g~~~~i~~~~~~~~~~~~~~~~~~-~~~vdgiii~~~-~~--~~~~~~~~~-~~~~~ipvV~~~ 87 (267)
T cd06322 13 FYIELANAMKEEAKKQKVNLIVSIANQDLNKQLSDVEDFI-TKKVDAIVLSPV-DS--KGIRAAIAK-AKKAGIPVITVD 87 (267)
T ss_pred HHHHHHHHHHHHHHhcCCEEEEecCCCCHHHHHHHHHHHH-HcCCCEEEEcCC-Ch--hhhHHHHHH-HHHCCCCEEEEc
Confidence 66788888999999999998776432 22 23344443 568998888521 11 111223443 567899998886
Q ss_pred C
Q 005710 131 A 131 (681)
Q Consensus 131 ~ 131 (681)
.
T Consensus 88 ~ 88 (267)
T cd06322 88 I 88 (267)
T ss_pred c
Confidence 4
No 75
>PRK00074 guaA GMP synthase; Reviewed
Probab=22.67 E-value=3.1e+02 Score=31.78 Aligned_cols=75 Identities=8% Similarity=0.084 Sum_probs=45.4
Q ss_pred HHHHhHHHHHHHHHhCCCce-EEEeCCChHHHHHHHHHHc---CCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 55 WLKHSLSHLDSSLRSLGTSL-VTKRSTDSVSSLLEVVKAT---GATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L-~v~~~g~~~~~L~~L~~~~---~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
|+.+.++.|++.++. .++ +-+.+|-...++..++.+. ++..|++++...+. ...+...+.+|+..||+++.++
T Consensus 201 ~~~~~~~~l~~~v~~--~~vlva~SGGvDS~vll~ll~~~lg~~v~av~vd~g~~~~-~e~~~~~~~~a~~lgi~~~vvd 277 (511)
T PRK00074 201 FIEEAIEEIREQVGD--KKVILGLSGGVDSSVAAVLLHKAIGDQLTCVFVDHGLLRK-NEAEQVMEMFREHFGLNLIHVD 277 (511)
T ss_pred HHHHHHHHHHHhcCC--CcEEEEeCCCccHHHHHHHHHHHhCCceEEEEEeCCCCCH-HHHHHHHHHHHHHcCCcEEEEc
Confidence 555667777777764 333 3344565556666666554 46677777554332 2334444446789999998876
Q ss_pred CC
Q 005710 131 AD 132 (681)
Q Consensus 131 ~~ 132 (681)
-.
T Consensus 278 ~~ 279 (511)
T PRK00074 278 AS 279 (511)
T ss_pred cH
Confidence 44
No 76
>PF00702 Hydrolase: haloacid dehalogenase-like hydrolase; InterPro: IPR005834 This group of hydrolase enzymes is structurally different from the alpha/beta hydrolase family (abhydrolase). This group includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of HAD1_PSESP. The rest of the fold is composed of the core alpha/beta domain.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1TE2_A 3NAL_A 3NAM_A 3NAN_A 3A1D_B 3J09_A 3J08_A 2B8E_C 3A1E_A 2VOY_J ....
Probab=22.61 E-value=2.2e+02 Score=27.67 Aligned_cols=41 Identities=17% Similarity=0.195 Sum_probs=33.5
Q ss_pred HHHhHHHHHHHHHhCCCceEEEeCCChHHHHHHHHHHcCCCE
Q 005710 56 LKHSLSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKATGATQ 97 (681)
Q Consensus 56 L~esL~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~~~~~~ 97 (681)
++..+.++=+.|++.|+++.+.. |+.......++++.|+..
T Consensus 128 ~~~~~~~~l~~L~~~Gi~~~i~T-GD~~~~a~~~~~~lgi~~ 168 (215)
T PF00702_consen 128 LRPGAKEALQELKEAGIKVAILT-GDNESTASAIAKQLGIFD 168 (215)
T ss_dssp BHTTHHHHHHHHHHTTEEEEEEE-SSEHHHHHHHHHHTTSCS
T ss_pred chhhhhhhhhhhhccCcceeeee-cccccccccccccccccc
Confidence 34566777777899999998885 788888999999999954
No 77
>PRK15118 universal stress global response regulator UspA; Provisional
Probab=22.57 E-value=5.9e+02 Score=23.12 Aligned_cols=68 Identities=15% Similarity=0.100 Sum_probs=40.5
Q ss_pred HHHHHHHHhCCCce--EEEeCCChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEe
Q 005710 61 SHLDSSLRSLGTSL--VTKRSTDSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSF 129 (681)
Q Consensus 61 ~dL~~~L~~~G~~L--~v~~~g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~ 129 (681)
..|++-+++.|+.. .+...|++.+.|.+.+++++++-|+.-........ .--...+.+....|+|-.+
T Consensus 68 ~~l~~~~~~~~~~~~~~~~~~G~p~~~I~~~a~~~~~DLIV~Gs~~~~~~~-lgSva~~v~~~a~~pVLvv 137 (144)
T PRK15118 68 HALTELSTNAGYPITETLSGSGDLGQVLVDAIKKYDMDLVVCGHHQDFWSK-LMSSARQLINTVHVDMLIV 137 (144)
T ss_pred HHHHHHHHhCCCCceEEEEEecCHHHHHHHHHHHhCCCEEEEeCcccHHHH-HHHHHHHHHhhCCCCEEEe
Confidence 33444445567664 22234889999999999999999998543322111 1122334556666766654
No 78
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=22.55 E-value=3.4e+02 Score=27.19 Aligned_cols=73 Identities=8% Similarity=0.115 Sum_probs=46.0
Q ss_pred HHHHhHHHHHHHHHhCCCceEEEeCCC----hHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTKRSTD----SVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~~~g~----~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
|..+-+.-+++.+++.|..+.+..... ....+.+++...+++.|+..-.... . . .+.+.+.+.||++..++
T Consensus 13 ~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~-~---~-~~~~~~~~~~ipvv~i~ 87 (270)
T cd01545 13 YVSEIQLGALDACRDTGYQLVIEPCDSGSPDLAERVRALLQRSRVDGVILTPPLSD-N---P-ELLDLLDEAGVPYVRIA 87 (270)
T ss_pred cHHHHHHHHHHHHHhCCCeEEEEeCCCCchHHHHHHHHHHHHCCCCEEEEeCCCCC-c---c-HHHHHHHhcCCCEEEEe
Confidence 556667777788889999987754321 2334556666789999887621111 1 1 22234567899998886
Q ss_pred CC
Q 005710 131 AD 132 (681)
Q Consensus 131 ~~ 132 (681)
..
T Consensus 88 ~~ 89 (270)
T cd01545 88 PG 89 (270)
T ss_pred cC
Confidence 43
No 79
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=22.53 E-value=5.4e+02 Score=26.41 Aligned_cols=73 Identities=16% Similarity=0.319 Sum_probs=44.5
Q ss_pred HHHHhHHHHHHHHHhCCCceEEEeCC-ChH---HHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTKRST-DSV---SSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~~~g-~~~---~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
|..+-+..+.+.++++|..+.+...+ ++. +.+..+. +.+++.|++... ++.. -...++ .+.+.|++|..++
T Consensus 13 ~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~i~~~~-~~~vdgiii~~~-~~~~--~~~~l~-~l~~~~ipvV~~~ 87 (288)
T cd01538 13 RWIRDRPNFEAALKELGAEVIVQNANGDPAKQISQIENMI-AKGVDVLVIAPV-DGEA--LASAVE-KAADAGIPVIAYD 87 (288)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHH-HcCCCEEEEecC-Chhh--HHHHHH-HHHHCCCCEEEEC
Confidence 55677778888899999998886543 222 2343433 458888887521 1111 112333 3567899999886
Q ss_pred CC
Q 005710 131 AD 132 (681)
Q Consensus 131 ~~ 132 (681)
..
T Consensus 88 ~~ 89 (288)
T cd01538 88 RL 89 (288)
T ss_pred CC
Confidence 43
No 80
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=22.50 E-value=5.5e+02 Score=25.54 Aligned_cols=73 Identities=16% Similarity=0.207 Sum_probs=44.4
Q ss_pred HHHHhHHHHHHHHHhCCCceEEEeCC-ChH---HHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTKRST-DSV---SSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~~~g-~~~---~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
|..+-+..+.+.+++.|..+++...+ ++. +.+.+ +.+.+++.|++... ....-...++ .+.+.||++..++
T Consensus 13 ~~~~~~~~i~~~~~~~g~~v~~~~~~~~~~~~~~~~~~-~~~~~~dgii~~~~---~~~~~~~~l~-~l~~~~ipvv~~~ 87 (268)
T cd06323 13 FFVTLKDGAQKEAKELGYELTVLDAQNDAAKQLNDIED-LITRGVDAIIINPT---DSDAVVPAVK-AANEAGIPVFTID 87 (268)
T ss_pred HHHHHHHHHHHHHHHcCceEEecCCCCCHHHHHHHHHH-HHHcCCCEEEEcCC---ChHHHHHHHH-HHHHCCCcEEEEc
Confidence 66788888999999999998776432 222 23334 33457898777421 1111112233 3567799998886
Q ss_pred CC
Q 005710 131 AD 132 (681)
Q Consensus 131 ~~ 132 (681)
..
T Consensus 88 ~~ 89 (268)
T cd06323 88 RE 89 (268)
T ss_pred cC
Confidence 53
No 81
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=22.40 E-value=5.1e+02 Score=26.34 Aligned_cols=73 Identities=15% Similarity=0.207 Sum_probs=44.4
Q ss_pred HHHHhHHHHHHHHHhCCCceEEEeCCChH---HHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecC
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTKRSTDSV---SSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNA 131 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~~~g~~~---~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~ 131 (681)
|..+-++.+.+.+++.|..+.+....+.. ..+.. +...+++.|++.- .....-+..+ +.+.+.||++..++.
T Consensus 13 ~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~i~~-~~~~~~dgiii~~---~~~~~~~~~~-~~~~~~~iPvV~~~~ 87 (289)
T cd01540 13 WFQTEWKFAKKAAKEKGFTVVKIDVPDGEKVLSAIDN-LGAQGAKGFVICV---PDVKLGPAIV-AKAKAYNMKVVAVDD 87 (289)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEccCCCHHHHHHHHHH-HHHcCCCEEEEcc---CchhhhHHHH-HHHHhCCCeEEEecC
Confidence 55567778888899999998776433322 22333 3346788888762 1111112223 346678999998864
Q ss_pred C
Q 005710 132 D 132 (681)
Q Consensus 132 ~ 132 (681)
.
T Consensus 88 ~ 88 (289)
T cd01540 88 R 88 (289)
T ss_pred C
Confidence 3
No 82
>PF05368 NmrA: NmrA-like family; InterPro: IPR008030 NmrA is a negative transcriptional regulator involved in the post-translational modification of the transcription factor AreA. NmrA is part of a system controlling nitrogen metabolite repression in fungi []. This family only contains a few sequences as iteration results in significant matches to other Rossmann fold families.; PDB: 2ZCV_A 2ZCU_A 2R6J_B 3C3X_A 2QZZ_B 2QYS_A 2QX7_A 2QW8_A 2R2G_B 3E5M_B ....
Probab=22.09 E-value=2.5e+02 Score=28.10 Aligned_cols=64 Identities=23% Similarity=0.284 Sum_probs=42.2
Q ss_pred HHHHHHhCCCceEEEeCCChHHHHHHHHHHcCCCEEEEecccC-hhhHHHHHHHHHHHHhCCeEEEEe
Q 005710 63 LDSSLRSLGTSLVTKRSTDSVSSLLEVVKATGATQLFFNHLYD-PLSLVRDHRAKEALTAQGIAVRSF 129 (681)
Q Consensus 63 L~~~L~~~G~~L~v~~~g~~~~~L~~L~~~~~~~~V~~n~~y~-p~~~~rD~~v~~~l~~~gI~v~~~ 129 (681)
..++|++.|..++.. .-+..+.|.+.++ |++.|++.-... +.+......+.+++++.||+...+
T Consensus 36 ~~~~l~~~g~~vv~~-d~~~~~~l~~al~--g~d~v~~~~~~~~~~~~~~~~~li~Aa~~agVk~~v~ 100 (233)
T PF05368_consen 36 RAQQLQALGAEVVEA-DYDDPESLVAALK--GVDAVFSVTPPSHPSELEQQKNLIDAAKAAGVKHFVP 100 (233)
T ss_dssp HHHHHHHTTTEEEES--TT-HHHHHHHHT--TCSEEEEESSCSCCCHHHHHHHHHHHHHHHT-SEEEE
T ss_pred hhhhhhcccceEeec-ccCCHHHHHHHHc--CCceEEeecCcchhhhhhhhhhHHHhhhccccceEEE
Confidence 345577788876532 2234566666665 899999885543 566777778888899999877654
No 83
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=21.99 E-value=3.9e+02 Score=26.79 Aligned_cols=71 Identities=6% Similarity=0.113 Sum_probs=44.9
Q ss_pred HHHHhHHHHHHHHHhCCCceEEEeCCCh---HHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecC
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTKRSTDS---VSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNA 131 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~~~g~~---~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~ 131 (681)
|..+-+..+.+.+++.|..+.+....+. .+.+.+++.+.+++.|+....... + .+.+.+.+.||++..++.
T Consensus 18 ~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~dgiii~~~~~~-----~-~~~~~~~~~~ipvV~~~~ 91 (270)
T cd06294 18 FFIEVLRGISAVANENGYDISLATGKNEEELLEEVKKMIQQKRVDGFILLYSRED-----D-PIIDYLKEEKFPFVVIGK 91 (270)
T ss_pred CHHHHHHHHHHHHHHCCCEEEEecCCCcHHHHHHHHHHHHHcCcCEEEEecCcCC-----c-HHHHHHHhcCCCEEEECC
Confidence 5556677788888889999877543222 234555566667898887522111 1 223345778999998864
No 84
>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]
Probab=21.81 E-value=6.6e+02 Score=25.46 Aligned_cols=103 Identities=17% Similarity=0.162 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHcCCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeCCChHHHHHHHHHHcCCCE
Q 005710 18 EDNPALAAGVRAGAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKATGATQ 97 (681)
Q Consensus 18 ~DN~AL~aA~~~~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~~~~~~ 97 (681)
.|-.+|..|.+.+ +|.++++++ .+++|... =.+|.+.|++.+.+|++. .|-..-.=+.+++.+.-.-
T Consensus 38 ~~A~~lerA~~~g--Ipt~~~~~k----~~~~r~~~------d~~l~~~l~~~~~dlvvL-AGyMrIL~~~fl~~~~grI 104 (200)
T COG0299 38 ADAYALERAAKAG--IPTVVLDRK----EFPSREAF------DRALVEALDEYGPDLVVL-AGYMRILGPEFLSRFEGRI 104 (200)
T ss_pred CCCHHHHHHHHcC--CCEEEeccc----cCCCHHHH------HHHHHHHHHhcCCCEEEE-cchHHHcCHHHHHHhhcce
Q ss_pred EEEecccChh---hHHHHHHHHHHHHhCCeEEEEecCCe
Q 005710 98 LFFNHLYDPL---SLVRDHRAKEALTAQGIAVRSFNADL 133 (681)
Q Consensus 98 V~~n~~y~p~---~~~rD~~v~~~l~~~gI~v~~~~~~~ 133 (681)
|-.+-..-|. -..-++.++.-.+..||.|+.++..+
T Consensus 105 lNIHPSLLP~f~G~h~~~~A~~aG~k~sG~TVH~V~e~v 143 (200)
T COG0299 105 LNIHPSLLPAFPGLHAHEQALEAGVKVSGCTVHFVTEGV 143 (200)
T ss_pred EecCcccccCCCCchHHHHHHHcCCCccCcEEEEEccCC
No 85
>TIGR00083 ribF riboflavin kinase/FMN adenylyltransferase. multifunctional enzyme: riboflavin kinase (EC 2.7.1.26) (flavokinase) / FMN adenylyltransferase (EC 2.7.7.2) (FAD pyrophosphorylase) (FAD synthetase).
Probab=21.64 E-value=4.1e+02 Score=28.37 Aligned_cols=97 Identities=10% Similarity=-0.042 Sum_probs=57.5
Q ss_pred CCeEEEEEEcCCCCCCCCCchhhHHHHHHhHHHHHHHHHhCCCceEEEeC-------CChHHHHHHHH-HHcCCCEEEEe
Q 005710 30 GAVIAVFIWAPEEEGPYYPGRVSRWWLKHSLSHLDSSLRSLGTSLVTKRS-------TDSVSSLLEVV-KATGATQLFFN 101 (681)
Q Consensus 30 ~~vlpVfI~dP~~~~~~~~~r~~r~FL~esL~dL~~~L~~~G~~L~v~~~-------g~~~~~L~~L~-~~~~~~~V~~n 101 (681)
+....|+.|+|.-..-..+.... . +-++++=.+-|+++|++.++.-. -++.+-+.+++ +..++.+|++-
T Consensus 29 ~~~~~V~tF~phP~~~~~~~~~~--~-l~~~~~k~~~l~~~Gvd~~~~~~F~~~~a~ls~e~Fi~~~l~~~l~~~~ivvG 105 (288)
T TIGR00083 29 GLPPAVLLFEPHPSEQFNWLTAP--A-LTPLEDKARQLQIKGVEQLLVVVFDEEFANLSALQFIDQLIVKHLHVKFLVVG 105 (288)
T ss_pred CCCEEEEEeCCChHHHhCccCCC--C-CCCHHHHHHHHHHcCCCEEEEeCCCHHHHcCCHHHHHHHHHHhccCCcEEEEC
Confidence 44456788887521111111111 2 56677777888999999655421 23444555665 45899999998
Q ss_pred cccChh--hHHHHHHHHHHHHhCCeEEEEe
Q 005710 102 HLYDPL--SLVRDHRAKEALTAQGIAVRSF 129 (681)
Q Consensus 102 ~~y~p~--~~~rD~~v~~~l~~~gI~v~~~ 129 (681)
.++... ..---..+++.+++.|+.|...
T Consensus 106 ~Df~FG~~~~G~~~~L~~~~~~~g~~v~~~ 135 (288)
T TIGR00083 106 DDFRFGHDRQGDFLLLQLFGNTTIFCVIVK 135 (288)
T ss_pred CCccCCCCCCCCHHHHHHhccccCcEEEEe
Confidence 776422 1111245777788888877654
No 86
>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=20.90 E-value=4.9e+02 Score=26.58 Aligned_cols=71 Identities=15% Similarity=0.129 Sum_probs=46.3
Q ss_pred HHHHhHHHHHHHHHhCCCceEEEeCCChHHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEecCC
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTKRSTDSVSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFNAD 132 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~~~g~~~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~~~ 132 (681)
|..+-+..+.+.+++.|..+.+..... .....+.+...+++.|++.-.. . . +..+ +.+++.|+++..++..
T Consensus 18 ~~~~~~~gi~~~a~~~g~~~~~~~~~~-~~~~~~~~~~~~~dgiii~~~~-~-~---~~~~-~~~~~~~ipvV~~~~~ 88 (283)
T cd06279 18 VASQFLAGVAEVLDAAGVNLLLLPASS-EDSDSALVVSALVDGFIVYGVP-R-D---DPLV-AALLRRGLPVVVVDQP 88 (283)
T ss_pred cHHHHHHHHHHHHHHCCCEEEEecCcc-HHHHHHHHHhcCCCEEEEeCCC-C-C---hHHH-HHHHHcCCCEEEEecC
Confidence 566777888899999999988765333 2333344556789988886321 1 1 1223 3456789999888653
No 87
>PF01171 ATP_bind_3: PP-loop family; InterPro: IPR011063 This entry represents the PP-loop motif superfamily [,]. The PP-loop motif appears to be a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding []. Named PP-motif, since it appears to be a part of a previously uncharacterised ATP pyrophophatase domain. ATP sulfurylases, Escherichia coli NtrL, and Bacillus subtilis OutB consist of this domain alone. In other proteins, the pyrophosphatase domain is associated with amidotransferase domains (type I or type II), a putative citrulline-aspartate ligase domain or a nitrilase/amidase domain.; PDB: 3A2K_A 2E89_B 2E21_D 1WY5_B 1NI5_A.
Probab=20.46 E-value=2.2e+02 Score=27.67 Aligned_cols=36 Identities=14% Similarity=0.038 Sum_probs=20.4
Q ss_pred CCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 95 ATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 95 ~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
+..|++|+...+....-.+.|++.|++.||++....
T Consensus 30 ~~~~~vdh~~~~~s~~~~~~v~~~~~~~~i~~~~~~ 65 (182)
T PF01171_consen 30 LIAVHVDHGLREESDEEAEFVEEICEQLGIPLYIVR 65 (182)
T ss_dssp EEEEEEE-STSCCHHHHHHHHHHHHHHTT-EEEEEE
T ss_pred eEEEEEecCCCcccchhHHHHHHHHHhcCCceEEEE
Confidence 455666665554444444566777777777776654
No 88
>PRK10660 tilS tRNA(Ile)-lysidine synthetase; Provisional
Probab=20.40 E-value=2.2e+02 Score=32.23 Aligned_cols=68 Identities=9% Similarity=0.069 Sum_probs=41.6
Q ss_pred HHHHHHHhCCCceEE-EeCCChHHHHHHHHHH-------cCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEec
Q 005710 62 HLDSSLRSLGTSLVT-KRSTDSVSSLLEVVKA-------TGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSFN 130 (681)
Q Consensus 62 dL~~~L~~~G~~L~v-~~~g~~~~~L~~L~~~-------~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~~ 130 (681)
.|++.|+. |.+++| ..+|...-+|..++.+ +.+..|++|+...+.+..-.+.+++.|++.||+++...
T Consensus 7 ~l~~~l~~-~~~ilvavSGG~DS~~Ll~~l~~~~~~~~~~~l~a~hvnhglr~~s~~~~~~~~~~~~~l~i~~~~~~ 82 (436)
T PRK10660 7 TLNRQLLT-SRQILVAFSGGLDSTVLLHLLVQWRTENPGVTLRAIHVHHGLSPNADSWVKHCEQVCQQWQVPLVVER 82 (436)
T ss_pred HHHHhcCC-CCeEEEEecCCHHHHHHHHHHHHHHHhcCCCeEEEEEEeCCCCcchHHHHHHHHHHHHHcCCcEEEEE
Confidence 34444554 555544 3445444455555542 24567888877666554444678889999999887654
No 89
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=20.39 E-value=6.3e+02 Score=27.23 Aligned_cols=73 Identities=15% Similarity=0.204 Sum_probs=45.7
Q ss_pred HHHHhHHHHHHHHHhCCCceEEEeCC--Ch---HHHHHHHHHHcCCCEEEEecccChhhHHHHHHHHHHHHhCCeEEEEe
Q 005710 55 WLKHSLSHLDSSLRSLGTSLVTKRST--DS---VSSLLEVVKATGATQLFFNHLYDPLSLVRDHRAKEALTAQGIAVRSF 129 (681)
Q Consensus 55 FL~esL~dL~~~L~~~G~~L~v~~~g--~~---~~~L~~L~~~~~~~~V~~n~~y~p~~~~rD~~v~~~l~~~gI~v~~~ 129 (681)
|+.+-..-+++..+++|..+.+.... +. .+.+..++ +.+++.|++.. .++. ..+..++ .+.+.||+|..+
T Consensus 37 f~~~~~~Gi~~aa~~~G~~v~~~~~~~~d~~~q~~~i~~li-~~~vdgIiv~~-~d~~--al~~~l~-~a~~~gIpVV~~ 111 (336)
T PRK15408 37 FFTSGGNGAKEAGKELGVDVTYDGPTEPSVSGQVQLINNFV-NQGYNAIIVSA-VSPD--GLCPALK-RAMQRGVKVLTW 111 (336)
T ss_pred HHHHHHHHHHHHHHHhCCEEEEECCCCCCHHHHHHHHHHHH-HcCCCEEEEec-CCHH--HHHHHHH-HHHHCCCeEEEe
Confidence 55566777888888999998763211 11 22344444 45899988862 2222 2233444 356789999999
Q ss_pred cCC
Q 005710 130 NAD 132 (681)
Q Consensus 130 ~~~ 132 (681)
+..
T Consensus 112 d~~ 114 (336)
T PRK15408 112 DSD 114 (336)
T ss_pred CCC
Confidence 865
No 90
>cd02953 DsbDgamma DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD alpha). DsbD beta, a transmembrane domain comprising of eight helices, acquires its reducing potential from the cytoplasmic thioredoxin. DsbD alpha transfers the acquired reducing potential from DsbD gamma to target proteins such as the periplasmic protein disulphide isomerases, DsbC and DsbG. This flow of reducing potential from the cytoplasm through DsbD allows DsbC and DsbG to act as isomerases in the oxidizing environment of the bacterial periplasm. DsbD also transfers reducing potential from the cytoplasm to specific reductases in the periplasm which are involved in the maturation of cytochromes.
Probab=20.24 E-value=5e+02 Score=22.22 Aligned_cols=20 Identities=30% Similarity=0.154 Sum_probs=12.6
Q ss_pred HHHHHHHcCCeEEEEEEcCC
Q 005710 22 ALAAGVRAGAVIAVFIWAPE 41 (681)
Q Consensus 22 AL~aA~~~~~vlpVfI~dP~ 41 (681)
+|..|.+.+..+-|+++-+.
T Consensus 3 ~~~~~~~~~k~vlv~f~a~w 22 (104)
T cd02953 3 ALAQALAQGKPVFVDFTADW 22 (104)
T ss_pred HHHHHHHcCCeEEEEEEcch
Confidence 46677777765566665553
Done!