Query 023087
Match_columns 287
No_of_seqs 108 out of 213
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 08:21:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023087.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023087hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04084 ORC2: Origin recognit 100.0 1.1E-90 2.4E-95 654.0 25.7 260 2-278 51-326 (326)
2 KOG2928 Origin recognition com 100.0 1E-82 2.2E-87 606.3 26.6 267 2-286 246-515 (518)
3 COG5575 ORC2 Origin recognitio 100.0 3.9E-67 8.5E-72 488.9 19.4 268 2-286 253-532 (535)
4 PRK00411 cdc6 cell division co 97.8 0.0051 1.1E-07 59.0 21.0 255 6-285 56-387 (394)
5 TIGR02928 orc1/cdc6 family rep 97.3 0.026 5.6E-07 53.5 18.4 232 6-261 41-351 (365)
6 COG1474 CDC6 Cdc6-related prot 84.2 42 0.00091 32.5 17.5 250 5-284 42-362 (366)
7 PF13730 HTH_36: Helix-turn-he 83.9 2.8 6.1E-05 28.7 4.8 52 198-257 2-55 (55)
8 PF13401 AAA_22: AAA domain; P 83.8 4.7 0.0001 31.7 6.8 110 7-138 6-123 (131)
9 PF05621 TniB: Bacterial TniB 80.0 18 0.00039 34.3 10.1 137 7-167 63-214 (302)
10 PF03444 HrcA_DNA-bdg: Winged 79.5 6.4 0.00014 30.0 5.6 59 199-264 2-60 (78)
11 PRK11331 5-methylcytosine-spec 75.0 11 0.00023 37.9 7.4 140 2-163 191-357 (459)
12 PF00931 NB-ARC: NB-ARC domain 74.3 23 0.0005 31.9 9.0 113 6-140 20-138 (287)
13 PRK14086 dnaA chromosomal repl 74.2 47 0.001 34.7 11.9 167 5-212 313-491 (617)
14 PTZ00112 origin recognition co 73.9 76 0.0016 35.0 13.6 144 7-174 782-941 (1164)
15 PF01726 LexA_DNA_bind: LexA D 71.9 8.9 0.00019 27.9 4.5 60 196-261 1-60 (65)
16 PF13412 HTH_24: Winged helix- 71.5 8.2 0.00018 25.6 4.0 48 199-258 1-48 (48)
17 PF02082 Rrf2: Transcriptional 69.7 15 0.00033 27.4 5.6 56 223-283 26-81 (83)
18 smart00347 HTH_MARR helix_turn 69.6 31 0.00068 25.5 7.4 67 198-276 7-73 (101)
19 PF12775 AAA_7: P-loop contain 68.2 4.9 0.00011 37.3 3.1 199 1-233 29-249 (272)
20 cd08768 Cdc6_C Winged-helix do 61.5 50 0.0011 24.4 7.1 62 203-265 4-70 (87)
21 PF01978 TrmB: Sugar-specific 58.5 17 0.00038 25.8 3.9 63 198-275 5-67 (68)
22 PRK09462 fur ferric uptake reg 57.6 53 0.0012 27.2 7.3 64 199-267 15-78 (148)
23 PF10483 Elong_Iki1: Elongator 56.9 19 0.00041 33.5 4.9 98 17-138 26-127 (280)
24 COG0505 CarA Carbamoylphosphat 56.2 24 0.00052 34.3 5.4 40 4-49 178-217 (368)
25 PF08784 RPA_C: Replication pr 55.4 20 0.00043 27.8 4.1 57 198-262 44-100 (102)
26 PF05729 NACHT: NACHT domain 52.9 1E+02 0.0022 24.7 8.2 42 98-139 79-128 (166)
27 COG0735 Fur Fe2+/Zn2+ uptake r 50.7 80 0.0017 26.4 7.2 65 199-269 19-83 (145)
28 PF07693 KAP_NTPase: KAP famil 50.6 44 0.00095 30.8 6.2 41 98-140 170-213 (325)
29 PRK10141 DNA-binding transcrip 50.3 75 0.0016 25.8 6.8 68 191-272 5-74 (117)
30 PRK04841 transcriptional regul 49.2 2E+02 0.0043 30.5 11.6 114 12-137 42-158 (903)
31 PF14453 ThiS-like: ThiS-like 47.6 20 0.00043 25.6 2.6 21 20-40 18-38 (57)
32 cd07153 Fur_like Ferric uptake 46.9 78 0.0017 24.6 6.3 47 221-267 15-61 (116)
33 TIGR02698 CopY_TcrY copper tra 46.7 1.6E+02 0.0035 24.0 8.4 71 198-278 1-72 (130)
34 PF01475 FUR: Ferric uptake re 46.6 78 0.0017 25.0 6.4 65 199-269 6-70 (120)
35 PF12840 HTH_20: Helix-turn-he 46.6 63 0.0014 22.4 5.2 49 201-261 10-58 (61)
36 PF09079 Cdc6_C: CDC6, C termi 45.8 1.2E+02 0.0026 22.4 7.5 62 221-282 14-85 (85)
37 cd00383 trans_reg_C Effector d 45.3 25 0.00054 26.1 3.1 47 198-249 23-69 (95)
38 TIGR02010 IscR iron-sulfur clu 44.6 81 0.0018 25.7 6.3 74 207-285 9-83 (135)
39 PF12157 DUF3591: Protein of u 43.6 68 0.0015 32.2 6.6 74 200-281 236-313 (457)
40 COG1959 Predicted transcriptio 43.1 92 0.002 26.2 6.5 50 236-285 34-83 (150)
41 PRK14088 dnaA chromosomal repl 43.0 2.9E+02 0.0063 27.3 11.0 104 103-213 197-309 (440)
42 PF13601 HTH_34: Winged helix 42.7 1.2E+02 0.0025 22.7 6.4 60 221-285 13-76 (80)
43 COG1307 DegV Uncharacterized p 42.1 1.7E+02 0.0036 27.4 8.6 112 2-140 77-194 (282)
44 PF00486 Trans_reg_C: Transcri 41.4 26 0.00055 25.1 2.5 46 198-248 5-50 (77)
45 PRK11014 transcriptional repre 40.1 33 0.00071 28.3 3.3 48 237-284 35-82 (141)
46 PF09673 TrbC_Ftype: Type-F co 39.8 82 0.0018 25.2 5.4 39 19-58 12-50 (113)
47 TIGR02944 suf_reg_Xantho FeS a 39.2 70 0.0015 25.7 5.1 61 221-286 24-84 (130)
48 cd06406 PB1_P67 A PB1 domain i 37.3 1E+02 0.0022 23.6 5.2 50 221-285 19-68 (80)
49 PRK11920 rirA iron-responsive 36.4 37 0.0008 28.6 3.1 49 237-285 34-82 (153)
50 PRK05541 adenylylsulfate kinas 36.3 74 0.0016 26.6 4.9 38 1-38 3-43 (176)
51 PRK06526 transposase; Provisio 35.9 2.6E+02 0.0056 25.5 8.8 45 3-53 96-142 (254)
52 PF05990 DUF900: Alpha/beta hy 35.9 2.1E+02 0.0045 25.7 8.0 89 32-129 20-117 (233)
53 PF07317 YcgR: Flagellar regul 35.7 44 0.00095 26.5 3.2 36 235-270 1-36 (108)
54 PF15335 CAAP1: Caspase activi 35.6 54 0.0012 24.0 3.4 45 204-248 17-64 (64)
55 PF04337 DUF480: Protein of un 34.4 63 0.0014 27.5 4.0 61 199-259 1-66 (148)
56 PRK11639 zinc uptake transcrip 32.6 2.6E+02 0.0057 23.8 7.8 69 191-265 12-84 (169)
57 PRK08116 hypothetical protein; 32.5 3.9E+02 0.0085 24.4 11.0 100 7-141 116-221 (268)
58 PF05991 NYN_YacP: YacP-like N 32.3 35 0.00077 29.2 2.3 41 1-41 1-55 (166)
59 PF08157 NUC129: NUC129 domain 32.0 18 0.00038 26.2 0.3 17 9-25 26-42 (63)
60 PF12138 Spherulin4: Spherulat 30.6 1.9E+02 0.004 26.6 6.9 179 83-285 18-219 (253)
61 smart00862 Trans_reg_C Transcr 30.3 78 0.0017 22.4 3.6 32 198-234 5-36 (78)
62 PF14532 Sigma54_activ_2: Sigm 29.4 87 0.0019 25.2 4.1 42 101-145 70-114 (138)
63 PRK10161 transcriptional regul 28.9 48 0.001 28.3 2.6 46 198-248 154-199 (229)
64 TIGR00738 rrf2_super rrf2 fami 28.7 1.6E+02 0.0035 23.3 5.6 61 220-285 23-83 (132)
65 COG2909 MalT ATP-dependent tra 28.5 6.2E+02 0.014 27.7 11.0 117 12-138 47-167 (894)
66 PF13177 DNA_pol3_delta2: DNA 27.8 3.6E+02 0.0078 22.5 11.0 26 5-30 19-46 (162)
67 PF03965 Penicillinase_R: Peni 27.8 2.7E+02 0.0059 21.8 6.7 69 199-277 1-70 (115)
68 PF12048 DUF3530: Protein of u 27.7 1.4E+02 0.0031 28.1 5.8 50 4-53 191-243 (310)
69 PRK08939 primosomal protein Dn 27.3 5.3E+02 0.011 24.2 9.7 25 102-126 219-243 (306)
70 TIGR01738 bioH putative pimelo 26.8 70 0.0015 26.7 3.2 29 8-36 8-36 (245)
71 TIGR03695 menH_SHCHC 2-succiny 26.5 2.5E+02 0.0054 23.1 6.6 30 8-37 5-34 (251)
72 PF00248 Aldo_ket_red: Aldo/ke 26.5 4.2E+02 0.0092 23.6 8.5 42 99-141 99-140 (283)
73 COG1166 SpeA Arginine decarbox 26.0 58 0.0013 33.6 2.9 28 13-41 145-172 (652)
74 KOG2543 Origin recognition com 25.7 4.9E+02 0.011 26.0 9.0 115 7-137 32-155 (438)
75 PF00004 AAA: ATPase family as 24.8 3.2E+02 0.0068 20.8 9.4 102 8-147 1-121 (132)
76 PLN03219 uncharacterized prote 24.7 1.3E+02 0.0028 24.3 4.1 16 269-284 89-104 (108)
77 PRK12423 LexA repressor; Provi 24.4 2.5E+02 0.0055 24.5 6.4 60 197-262 2-61 (202)
78 TIGR02154 PhoB phosphate regul 24.1 64 0.0014 27.0 2.5 49 198-251 154-202 (226)
79 PF13463 HTH_27: Winged helix 23.0 1.8E+02 0.0038 20.0 4.3 58 199-267 1-59 (68)
80 COG0623 FabI Enoyl-[acyl-carri 22.7 2.5E+02 0.0055 26.0 6.1 93 1-111 2-94 (259)
81 PRK00082 hrcA heat-inducible t 22.6 1.7E+02 0.0038 27.9 5.4 64 197-265 2-65 (339)
82 PF12802 MarR_2: MarR family; 22.3 2.3E+02 0.0049 19.1 4.7 55 199-263 3-57 (62)
83 PLN02771 carbamoyl-phosphate s 21.9 1.6E+02 0.0035 29.2 5.1 21 6-26 241-261 (415)
84 COG0616 SppA Periplasmic serin 21.9 1.7E+02 0.0036 27.8 5.0 61 82-144 81-141 (317)
85 TIGR00762 DegV EDD domain prot 21.8 3E+02 0.0065 25.1 6.6 111 2-139 75-190 (275)
86 cd04881 ACT_HSDH-Hom ACT_HSDH_ 21.6 2.6E+02 0.0055 19.1 5.0 44 243-286 13-64 (79)
87 COG1223 Predicted ATPase (AAA+ 21.4 2.8E+02 0.0061 26.4 6.2 69 81-157 197-276 (368)
88 cd01091 CDC68-like Related to 21.2 1.2E+02 0.0025 27.5 3.7 69 147-234 83-154 (243)
89 PF07540 NOC3p: Nucleolar comp 21.0 82 0.0018 24.7 2.3 52 202-253 3-55 (95)
90 COG2924 Uncharacterized protei 21.0 78 0.0017 24.4 2.1 28 15-42 61-88 (90)
91 TIGR03611 RutD pyrimidine util 20.9 2.8E+02 0.0061 23.3 6.0 14 99-112 79-92 (257)
92 COG3682 Predicted transcriptio 20.6 1.1E+02 0.0024 25.3 3.0 47 224-273 22-68 (123)
93 KOG2501 Thioredoxin, nucleored 20.4 93 0.002 26.8 2.7 50 225-284 55-110 (157)
94 PHA02530 pseT polynucleotide k 20.2 6.5E+02 0.014 22.7 11.0 36 19-54 63-98 (300)
95 PF02645 DegV: Uncharacterised 20.2 2.2E+02 0.0049 26.0 5.4 111 2-140 76-193 (280)
96 PF13289 SIR2_2: SIR2-like dom 20.0 4.3E+02 0.0094 20.6 7.1 23 17-40 73-95 (143)
No 1
>PF04084 ORC2: Origin recognition complex subunit 2 ; InterPro: IPR007220 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. This entry represents subunit 2, which binds the origin of replication. It plays a role in chromosome replication and mating type transcriptional silencing.; GO: 0006260 DNA replication, 0000808 origin recognition complex, 0005634 nucleus
Probab=100.00 E-value=1.1e-90 Score=654.00 Aligned_cols=260 Identities=42% Similarity=0.700 Sum_probs=231.0
Q ss_pred ccCCccEEEEeccchHHHHHHHHHhhcCC---CcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCC
Q 023087 2 LRCGFGLLMYGFGSKKALLEDFASTALTE---YSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQPF 78 (287)
Q Consensus 2 L~~GFnlL~YG~GSKr~lL~~Fa~~~l~~---~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~~ 78 (287)
|.+||||||||+||||+||++|+++++.+ +++||||||+|++++|+||++|++++.... . .
T Consensus 51 L~~GFnlL~YG~GSKr~lL~~Fa~~~l~~~~~~~~vvvnGy~p~~~~k~il~~I~~~l~~~~---------~-------~ 114 (326)
T PF04084_consen 51 LSQGFNLLFYGYGSKRKLLNDFAEKYLSDWGDGPVVVVNGYFPSLSIKDILNTIEEALLPEP---------S-------K 114 (326)
T ss_pred HhCCCeEEEEecChHHHHHHHHHHHHhhccCCCcEEEEEccCCCCcHHHHHHHHHHHHhhhc---------c-------c
Confidence 68999999999999999999999999999 999999999999999999999999998741 0 0
Q ss_pred CCCcHHHHHHHHhcccccC-CCceEEEEEEcCCCcCCCChhHHHHHHHHhcCCCeEEEEeecCCCCccccCccccccccc
Q 023087 79 NSRSMDDLFAFLDGSELKE-NDYFVCVVIHNIDGPGLRDSETQQHLGRIAFCSHIRMIASIDHVNAPLLWDKKMVHTQFN 157 (287)
Q Consensus 79 ~~~~~~~l~~~i~~~~~~~-~~~~l~lvIHnIDg~~LR~~~~q~~La~La~~~~I~lIaSiDhinaplLWd~~~~~~~fn 157 (287)
...++.+.++.+.+..... .++++||||||||||+||++++|++||+||++|+||+||||||||||||||..+. .+||
T Consensus 115 ~~~~~~~~~~~i~~~l~~~~~~~~l~lvIHnIDg~~LR~~~~Q~~La~LA~~p~I~lIASiDhinapLLWd~~~~-~~fn 193 (326)
T PF04084_consen 115 KPKSPSEQLDFIISYLESRPSPPPLYLVIHNIDGPSLRNEKAQSLLAQLASIPNIHLIASIDHINAPLLWDSSKL-SRFN 193 (326)
T ss_pred ccCCHHHHHHHHHHHHhccCCCCceEEEEECCCChhhcChHHHHHHHHHHcCCCeEEEEeccCCCcccccChhhH-hhCC
Confidence 1123333444443322222 3889999999999999999999999999999999999999999999999999998 9999
Q ss_pred EEEEeCCCCCCcccccccchhh--hhcCC-cc-chhhHHHHHHhhcCHhHHHHHHHHHHHHhc--------CCCCCCCCH
Q 023087 158 WHWYHVPTFAPYKVEGMFFPLI--LAHGS-SA-QTAKTAAIVLQSLTPNAQSVFKILAEYQLS--------HPDEEGMPI 225 (287)
Q Consensus 158 f~~~d~tT~~pY~~E~~~~~~l--~~~~~-~~-~~~~g~~~VL~SLt~nar~lf~lLa~~QL~--------~~~~~gv~~ 225 (287)
|+|||||||+||++|+++.+++ +.+++ +. .+.+|+.+||+|||+|||+||++||++||+ .....||+|
T Consensus 194 f~~hd~tT~~pY~~E~~~~~~l~~~~g~s~~~~~~~~~~~~VL~SLt~nar~lf~lL~~~QL~~~~~~~~~~~~~~gv~~ 273 (326)
T PF04084_consen 194 FLWHDVTTFAPYTEETSFEDSLHSLLGKSGSRVGGLSGAKHVLKSLTPNARNLFKLLAEHQLEEAAGADKDGSEYQGVEF 273 (326)
T ss_pred EEEEeCCCCCCHHHHhccccchhhhhcccccccccHHHHHHHHHHCCHHHHHHHHHHHHHHHhhccccccCCCCCCCccH
Confidence 9999999999999999998865 44443 32 789999999999999999999999999999 223479999
Q ss_pred HHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEeCCHHHH
Q 023087 226 DTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIPLASEAL 278 (287)
Q Consensus 226 ~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip~~~~~l 278 (287)
++||++|+++||||||++||++|+||+||+||+++|+++|+|+|+||+++++|
T Consensus 274 ~~Ly~~~~e~Fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~L~IP~~~~~m 326 (326)
T PF04084_consen 274 RDLYNKCREEFIVSSEMALRALLTEFIDHKLIKSKKDADGTEYLWIPFDKEEM 326 (326)
T ss_pred HHHHHHHHHHHhhCCHHHHHHHHHHHHcccceeeEeCCCCCEEEEEecCcCcC
Confidence 99999999999999999999999999999999999999999999999999875
No 2
>KOG2928 consensus Origin recognition complex, subunit 2 [Replication, recombination and repair]
Probab=100.00 E-value=1e-82 Score=606.25 Aligned_cols=267 Identities=45% Similarity=0.729 Sum_probs=245.6
Q ss_pred ccCCccEEEEeccchHHHHHHHHHhhcCCCcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCC
Q 023087 2 LRCGFGLLMYGFGSKKALLEDFASTALTEYSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQPFNSR 81 (287)
Q Consensus 2 L~~GFnlL~YG~GSKr~lL~~Fa~~~l~~~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (287)
|.+|||||||||||||.||++|+..++.+++++|||||+|++++|++|.+|.+.+...+.+++..
T Consensus 246 L~~gFNiLfYG~GSKr~lLe~F~~~~L~~~~~~ving~~p~ln~K~vl~si~e~l~~~~~sk~~~--------------- 310 (518)
T KOG2928|consen 246 LARGFNILFYGVGSKRALLEEFAPEALYDYTVLVINGYFPSLNVKDVLVSITELLEDAEVSKRST--------------- 310 (518)
T ss_pred HhccccEEEEecCcHHHHHHHHHHHhcccceEEEEeccCccchHHHHHHHHHHHHHHhhccCCcc---------------
Confidence 67999999999999999999999999999999999999999999999999999998866443221
Q ss_pred cHHHHHHHHhcccccCCCceEEEEEEcCCCcCCCChhHHHHHHHHhcCCCeEEEEeecCCCCccccCcccccccccEEEE
Q 023087 82 SMDDLFAFLDGSELKENDYFVCVVIHNIDGPGLRDSETQQHLGRIAFCSHIRMIASIDHVNAPLLWDKKMVHTQFNWHWY 161 (287)
Q Consensus 82 ~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~LR~~~~q~~La~La~~~~I~lIaSiDhinaplLWd~~~~~~~fnf~~~ 161 (287)
.+.+-..+. .+..+...+++|||||||||+||++++|++|+.|+++++|+|||||||||+|||||..++ .+|||+||
T Consensus 311 -~~~~~~~i~-~~k~~~~~kl~LvVhNiDg~~Lr~~~~Q~~L~~Lss~~nI~liASvDHInapllWD~~~~-ssfNFv~~ 387 (518)
T KOG2928|consen 311 -SRILDEIII-SFKEDSSQKLILVVHNIDGPMLRDEKFQAILARLSSIDNIALIASVDHINAPLLWDDVKL-SSFNFVWH 387 (518)
T ss_pred -hhhhhhhhh-ccccCCCceEEEEEeccCchhhcchHHHHHHHHhhcCCceEEEEeecccCcceecchhhh-cccceEEe
Confidence 121222222 223456779999999999999999999999999999999999999999999999999998 99999999
Q ss_pred eCCCCCCcccccccchhhhhcCCccchhhHHHHHHhhcCHhHHHHHHHHHHHHhcCCCC---CCCCHHHHHHHHHHHHhh
Q 023087 162 HVPTFAPYKVEGMFFPLILAHGSSAQTAKTAAIVLQSLTPNAQSVFKILAEYQLSHPDE---EGMPIDTLYATSRERFLV 238 (287)
Q Consensus 162 d~tT~~pY~~E~~~~~~l~~~~~~~~~~~g~~~VL~SLt~nar~lf~lLa~~QL~~~~~---~gv~~~~L~~~~~e~fi~ 238 (287)
|+|||+||++|++|.++++.+++.+.+.+++.+||+|||+|+|+||++|+++|+++++. .||+|++||++|+++|+|
T Consensus 388 d~tTFepy~~Et~~~~s~l~~~s~s~~~ss~~~Vl~SLt~NSr~ifkll~~~qld~~~n~~~~Gl~~~dlf~~cr~~Fl~ 467 (518)
T KOG2928|consen 388 DITTFEPYTEETMFENSLLVGASTSLTASSLKHVLRSLTVNSRGIFKLLLEYQLDNKGNTQYTGLEFRDLFQKCREDFLV 467 (518)
T ss_pred ecccccccchhhhccchhhhcccccchhhHHHHHHHhcCcchhHHHHHHHHHHHhcCCCccccCccHHHHHHHHHHHHhh
Confidence 99999999999999999999998888899999999999999999999999999999863 599999999999999999
Q ss_pred ccHHHHHHHhhhhcccceEEEeeCCCCceEEEEeCCHHHHHHHHHHhh
Q 023087 239 SSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIPLASEALEKLLSEIN 286 (287)
Q Consensus 239 sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip~~~~~l~~iLe~l~ 286 (287)
|||.+||+||+||+||+|++++|+.+|.|+||||++.+.++++||+.+
T Consensus 468 Ssd~alrSqLtEF~DHkllk~krg~dg~e~L~ip~~~~ll~~lLe~~~ 515 (518)
T KOG2928|consen 468 SSDLALRSQLTEFIDHKLLKIKRGSDGVECLSIPVTNALLTELLEDDN 515 (518)
T ss_pred cchHHHHHHHHHHhhccceeeecCCCCceEEeecccHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999865
No 3
>COG5575 ORC2 Origin recognition complex, subunit 2 [DNA replication, recombination, and repair]
Probab=100.00 E-value=3.9e-67 Score=488.95 Aligned_cols=268 Identities=26% Similarity=0.441 Sum_probs=236.1
Q ss_pred ccCCccEEEEeccchHHHHHHHHHhhcCCCcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCC
Q 023087 2 LRCGFGLLMYGFGSKKALLEDFASTALTEYSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQPFNSR 81 (287)
Q Consensus 2 L~~GFnlL~YG~GSKr~lL~~Fa~~~l~~~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (287)
|.+||||||||||||+.+|++|+..+++..||+++|||+|.++.|+||.+|.+++....+......+.+. .
T Consensus 253 L~~~FnLLFYG~GSK~~fL~~f~~~~LP~~P~~~lnGY~p~~~~r~Vl~ei~e~l~~~~~~~~~~~~~~~---------~ 323 (535)
T COG5575 253 LARSFNLLFYGYGSKTAFLRKFFPSALPCFPIFYLNGYCPIMSRREVLAEIMEALRHRSKLEAQDEVSKA---------P 323 (535)
T ss_pred HhhhceEEEEecCchHHHHHHHhHHhcCCcceeeecccCccccHHHHHHHHHHHhccchhhhhhhHhhcC---------c
Confidence 5789999999999999999999999999999999999999999999999999998654322111111111 1
Q ss_pred cHHHHHHHHhcccccCCCceEEEEEEcCCCcCCCChhHHHHHHHHhcCCCeEEEEeecCCCCccccCcccccccccEEEE
Q 023087 82 SMDDLFAFLDGSELKENDYFVCVVIHNIDGPGLRDSETQQHLGRIAFCSHIRMIASIDHVNAPLLWDKKMVHTQFNWHWY 161 (287)
Q Consensus 82 ~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~LR~~~~q~~La~La~~~~I~lIaSiDhinaplLWd~~~~~~~fnf~~~ 161 (287)
++. .........++.+++||+||+++|..++|..|+.++++.||.+|||+|||++|||||..+. ++|||++|
T Consensus 324 ~I~-------~i~~~~~~~ki~~~vHN~dg~sv~~n~Fq~~l~~~ss~rn~ai~aSvdhI~~~llwd~~~~-~sfNFVfh 395 (535)
T COG5575 324 TIR-------EIDSFSLGEKIGSRVHNEDGKSVMANRFQFGLLEFSSLRNFAILASVDHIGIRLLWDDVER-SSFNFVFH 395 (535)
T ss_pred eEE-------eccchhhhhheeEEeecccchHHHHHHHHHHHHHHHhhcceEEEEeecccceeeehhhhhh-cccceEee
Confidence 111 0001112368999999999999999999999999999999999999999999999999997 99999999
Q ss_pred eCCCCCCcccccccchhhhhcCC-ccchhhHHHHHHhhcCHhHHHHHHHHHHHHhcCCC-----------CCCCCHHHHH
Q 023087 162 HVPTFAPYKVEGMFFPLILAHGS-SAQTAKTAAIVLQSLTPNAQSVFKILAEYQLSHPD-----------EEGMPIDTLY 229 (287)
Q Consensus 162 d~tT~~pY~~E~~~~~~l~~~~~-~~~~~~g~~~VL~SLt~nar~lf~lLa~~QL~~~~-----------~~gv~~~~L~ 229 (287)
|+|||+||.+|..|.+++-+|.. .+.+++|+++||+|||.|+|.+||.|+.+||++|. ..||+++.+|
T Consensus 396 D~ttFepy~~E~T~en~l~mG~~~~S~~aea~k~Vl~slp~NSr~v~K~Ll~~Qle~M~~~~d~~~R~~ek~gVel~~ff 475 (535)
T COG5575 396 DLTTFEPYEEEATYENSLGMGIHLRSTRAEASKRVLRSLPRNSRLVLKELLSHQLERMMCNADFDARQGEKVGVELGEFF 475 (535)
T ss_pred cccccccccchhhhhhhhhhcccccccHHHHHHHHHHhcCchhHHHHHHHHHHHHHHhccchhhhhhccceeceeHHHHH
Confidence 99999999999999999877665 45678999999999999999999999999999973 2489999999
Q ss_pred HHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEeCCHHHHHHHHHHhh
Q 023087 230 ATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIPLASEALEKLLSEIN 286 (287)
Q Consensus 230 ~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip~~~~~l~~iLe~l~ 286 (287)
++|..+|+||||.++|++|+||+||+|+.++|+..|.|++|+|+++.+||.+|++++
T Consensus 476 ~kc~a~f~~Sne~~~rSmL~EFidH~l~~i~rn~S~~eI~wvpy~~nele~lL~~m~ 532 (535)
T COG5575 476 EKCKAKFFLSNETSVRSMLNEFIDHGLLKIKRNGSEIEICWVPYERNELEGLLDQMD 532 (535)
T ss_pred HHHHHHHhhcCcHHHHHHHHHHHhcchhheeccCCccEEEEeeccHHHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999999999875
No 4
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=97.79 E-value=0.0051 Score=59.00 Aligned_cols=255 Identities=16% Similarity=0.188 Sum_probs=153.3
Q ss_pred ccEEEEecc--chHHHHHHHHHhhcC---CCcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCC
Q 023087 6 FGLLMYGFG--SKKALLEDFASTALT---EYSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQPFNS 80 (287)
Q Consensus 6 FnlL~YG~G--SKr~lL~~Fa~~~l~---~~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 80 (287)
-|+++||-- -|..+++.++++.-. +..++.||+..- .+.++++..|...+.... . +...
T Consensus 56 ~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~-~~~~~~~~~i~~~l~~~~----------~-----~~~~ 119 (394)
T PRK00411 56 LNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQID-RTRYAIFSEIARQLFGHP----------P-----PSSG 119 (394)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcC-CCHHHHHHHHHHHhcCCC----------C-----CCCC
Confidence 579999874 299999998876533 356888999754 367788888877664310 0 1112
Q ss_pred CcHHHHHHHHhcccccCCCceEEEEEEcCCCcCCCChhHHHHHHHH----hcCC--CeEEEEeecCCCCccccCcccccc
Q 023087 81 RSMDDLFAFLDGSELKENDYFVCVVIHNIDGPGLRDSETQQHLGRI----AFCS--HIRMIASIDHVNAPLLWDKKMVHT 154 (287)
Q Consensus 81 ~~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~LR~~~~q~~La~L----a~~~--~I~lIaSiDhinaplLWd~~~~~~ 154 (287)
.+.+++++.+..... ....+++|||-.+|-.. ++ +.+..|..| ...+ ++.+|+..-..+.+-..+.... .
T Consensus 120 ~~~~~~~~~~~~~l~-~~~~~~viviDE~d~l~-~~-~~~~~l~~l~~~~~~~~~~~v~vI~i~~~~~~~~~l~~~~~-s 195 (394)
T PRK00411 120 LSFDELFDKIAEYLD-ERDRVLIVALDDINYLF-EK-EGNDVLYSLLRAHEEYPGARIGVIGISSDLTFLYILDPRVK-S 195 (394)
T ss_pred CCHHHHHHHHHHHHH-hcCCEEEEEECCHhHhh-cc-CCchHHHHHHHhhhccCCCeEEEEEEECCcchhhhcCHHHH-h
Confidence 234555555543221 24567999999999754 22 122333333 2233 5667777655554444455444 4
Q ss_pred cccEEEEeCCCCCCcccccc----------------cchhh-------hhc----------------------CCccc--
Q 023087 155 QFNWHWYHVPTFAPYKVEGM----------------FFPLI-------LAH----------------------GSSAQ-- 187 (287)
Q Consensus 155 ~fnf~~~d~tT~~pY~~E~~----------------~~~~l-------~~~----------------------~~~~~-- 187 (287)
+|.+... .|.||+.|-. +.+.. ..+ +....
T Consensus 196 ~~~~~~i---~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~ 272 (394)
T PRK00411 196 VFRPEEI---YFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTE 272 (394)
T ss_pred cCCccee---ecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCH
Confidence 5554333 5788876621 00000 000 00000
Q ss_pred ----------hhhHHHHHHhhcCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHH---HHhhc--cHHHHHHHhhhhc
Q 023087 188 ----------TAKTAAIVLQSLTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRE---RFLVS--SQVTLNSHLTEFK 252 (287)
Q Consensus 188 ----------~~~g~~~VL~SLt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e---~fi~s--se~~lr~~L~EF~ 252 (287)
.......++++||.++|.+...++...-. +...+++.++|+.-.+ .+=++ +...+...|.++.
T Consensus 273 ~~v~~a~~~~~~~~~~~~~~~L~~~~k~~L~ai~~~~~~--~~~~~~~~~i~~~y~~l~~~~~~~~~~~~~~~~~l~~L~ 350 (394)
T PRK00411 273 EDVRKAYEKSEIVHLSEVLRTLPLHEKLLLRAIVRLLKK--GGDEVTTGEVYEEYKELCEELGYEPRTHTRFYEYINKLD 350 (394)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhc--CCCcccHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHHH
Confidence 01223457899999999999999876522 2245788888765333 22221 5688999999999
Q ss_pred ccceEEEeeC---C-CCceEEEEeCCHHHHHHHHHHh
Q 023087 253 DHELVKTRRH---S-DGQDCFYIPLASEALEKLLSEI 285 (287)
Q Consensus 253 DH~li~~~k~---~-~G~e~l~Ip~~~~~l~~iLe~l 285 (287)
+.++|..++. . +.+..+..+++.+++.+.+.+.
T Consensus 351 ~~glI~~~~~~~g~~g~~~~~~~~~~~~~~~~~~~~~ 387 (394)
T PRK00411 351 MLGIINTRYSGKGGRGRTRLISLSYDPEDVLERLLED 387 (394)
T ss_pred hcCCeEEEEecCCCCCCeEEEEecCCHHHHHHHHHhh
Confidence 9999997653 2 2257788999999888777653
No 5
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=97.31 E-value=0.026 Score=53.50 Aligned_cols=232 Identities=19% Similarity=0.248 Sum_probs=134.2
Q ss_pred ccEEEEec-cc-hHHHHHHHHHhhc---CC----CcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCC
Q 023087 6 FGLLMYGF-GS-KKALLEDFASTAL---TE----YSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQ 76 (287)
Q Consensus 6 FnlL~YG~-GS-Kr~lL~~Fa~~~l---~~----~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~ 76 (287)
-|+++||- |+ |..+++.|++..- .+ ..++.||+.. ..+..+++..|.+.+.. .. .+.+
T Consensus 41 ~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~-~~~~~~~~~~i~~~l~~-~~-------~~~~---- 107 (365)
T TIGR02928 41 SNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQI-LDTLYQVLVELANQLRG-SG-------EEVP---- 107 (365)
T ss_pred CcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCC-CCCHHHHHHHHHHHHhh-cC-------CCCC----
Confidence 47999997 44 8888888876532 11 3577899875 34677888888888753 00 0001
Q ss_pred CCCCCcHHHHHHHHhcccccCCCceEEEEEEcCCCcCCCChhHHHHHHHHhcC--------CCeEEEEeecCCCCccccC
Q 023087 77 PFNSRSMDDLFAFLDGSELKENDYFVCVVIHNIDGPGLRDSETQQHLGRIAFC--------SHIRMIASIDHVNAPLLWD 148 (287)
Q Consensus 77 ~~~~~~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~LR~~~~q~~La~La~~--------~~I~lIaSiDhinaplLWd 148 (287)
....+.+++++.+.... .....+++|||-.+|--. + ..+..|..|... +++.+|+..-.+..+--.+
T Consensus 108 -~~~~~~~~~~~~l~~~l-~~~~~~~vlvIDE~d~L~-~--~~~~~L~~l~~~~~~~~~~~~~v~lI~i~n~~~~~~~l~ 182 (365)
T TIGR02928 108 -TTGLSTSEVFRRLYKEL-NERGDSLIIVLDEIDYLV-G--DDDDLLYQLSRARSNGDLDNAKVGVIGISNDLKFRENLD 182 (365)
T ss_pred -CCCCCHHHHHHHHHHHH-HhcCCeEEEEECchhhhc-c--CCcHHHHhHhccccccCCCCCeEEEEEEECCcchHhhcC
Confidence 11112333333332211 114567899999999864 2 224455555443 5688888886655432234
Q ss_pred cccccccccEEEEeCCCCCCcccccc----------------cchh---hh----h--cC--------------------
Q 023087 149 KKMVHTQFNWHWYHVPTFAPYKVEGM----------------FFPL---IL----A--HG-------------------- 183 (287)
Q Consensus 149 ~~~~~~~fnf~~~d~tT~~pY~~E~~----------------~~~~---l~----~--~~-------------------- 183 (287)
.... ++|.. ..+ .|.||+.|-. +.+. +. . .+
T Consensus 183 ~~~~-s~~~~--~~i-~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~ 258 (365)
T TIGR02928 183 PRVK-SSLCE--EEI-IFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREG 258 (365)
T ss_pred HHHh-ccCCc--cee-eeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcC
Confidence 4433 45532 222 4788876511 0011 00 0 00
Q ss_pred Cccch------------hhHHHHHHhhcCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHH---HHHh--hccHHHHHH
Q 023087 184 SSAQT------------AKTAAIVLQSLTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSR---ERFL--VSSQVTLNS 246 (287)
Q Consensus 184 ~~~~~------------~~g~~~VL~SLt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~---e~fi--~sse~~lr~ 246 (287)
....+ .+.....+++|+..++.++..++... +. +...+...++|+.-. +.+= --+...++.
T Consensus 259 ~~~it~~~v~~a~~~~~~~~~~~~i~~l~~~~~~~l~ai~~~~-~~-~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~ 336 (365)
T TIGR02928 259 AERVTEDHVEKAQEKIEKDRLLELIRGLPTHSKLVLLAIANLA-AN-DEDPFRTGEVYEVYKEVCEDIGVDPLTQRRISD 336 (365)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-hc-CCCCccHHHHHHHHHHHHHhcCCCCCcHHHHHH
Confidence 00000 12223567999999999999887653 22 345578888877333 2222 257899999
Q ss_pred HhhhhcccceEEEee
Q 023087 247 HLTEFKDHELVKTRR 261 (287)
Q Consensus 247 ~L~EF~DH~li~~~k 261 (287)
.|.++.+.++|..+.
T Consensus 337 ~l~~l~~~gli~~~~ 351 (365)
T TIGR02928 337 LLNELDMLGLVEAEE 351 (365)
T ss_pred HHHHHHhcCCeEEEE
Confidence 999999999999864
No 6
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=84.24 E-value=42 Score=32.55 Aligned_cols=250 Identities=20% Similarity=0.207 Sum_probs=151.7
Q ss_pred CccEEEEec-cchHHHHHHHHHhhcCC----CcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCC
Q 023087 5 GFGLLMYGF-GSKKALLEDFASTALTE----YSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQPFN 79 (287)
Q Consensus 5 GFnlL~YG~-GSKr~lL~~Fa~~~l~~----~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~ 79 (287)
..|+++||- |+=+...-+|+-+.+.+ ..++-||+..- -|..+|+..|.+.+.+. |..
T Consensus 42 p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~-~t~~~i~~~i~~~~~~~-----------------p~~ 103 (366)
T COG1474 42 PSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLEL-RTPYQVLSKILNKLGKV-----------------PLT 103 (366)
T ss_pred CccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeC-CCHHHHHHHHHHHcCCC-----------------CCC
Confidence 458999985 66566666666655532 23788999884 46788888888766421 111
Q ss_pred CCcHHHHHHHHhcccccCCCceEEEEEEcCCCcCCCChhHHHHHHHHhcCC-----CeEEEEeecCCCCccccCcccccc
Q 023087 80 SRSMDDLFAFLDGSELKENDYFVCVVIHNIDGPGLRDSETQQHLGRIAFCS-----HIRMIASIDHVNAPLLWDKKMVHT 154 (287)
Q Consensus 80 ~~~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~LR~~~~q~~La~La~~~-----~I~lIaSiDhinaplLWd~~~~~~ 154 (287)
..+..+.++.+.+.... ....+++|+.-+|.-.=++ +..|-.|...+ +|-+|+-.-..+..-..|.... +
T Consensus 104 g~~~~~~~~~l~~~~~~-~~~~~IvvLDEid~L~~~~---~~~LY~L~r~~~~~~~~v~vi~i~n~~~~~~~ld~rv~-s 178 (366)
T COG1474 104 GDSSLEILKRLYDNLSK-KGKTVIVILDEVDALVDKD---GEVLYSLLRAPGENKVKVSIIAVSNDDKFLDYLDPRVK-S 178 (366)
T ss_pred CCchHHHHHHHHHHHHh-cCCeEEEEEcchhhhcccc---chHHHHHHhhccccceeEEEEEEeccHHHHHHhhhhhh-h
Confidence 12234445444432222 5678999999999743333 26666665443 2346665555555545566654 5
Q ss_pred cccEEEEeCCCCCCccccccc-----------c-----hh---hh----h--cC--------------------Cccch-
Q 023087 155 QFNWHWYHVPTFAPYKVEGMF-----------F-----PL---IL----A--HG--------------------SSAQT- 188 (287)
Q Consensus 155 ~fnf~~~d~tT~~pY~~E~~~-----------~-----~~---l~----~--~~--------------------~~~~~- 188 (287)
+|.-.- =-|.||+.|=.+ . +. +. . ++ ++..+
T Consensus 179 ~l~~~~---I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~ 255 (366)
T COG1474 179 SLGPSE---IVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSE 255 (366)
T ss_pred ccCcce---eeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCH
Confidence 555433 358899887321 0 00 00 0 00 00000
Q ss_pred -----------hhHHHHHHhhcCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceE
Q 023087 189 -----------AKTAAIVLQSLTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELV 257 (287)
Q Consensus 189 -----------~~g~~~VL~SLt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li 257 (287)
..=...++++||.++|-+.+.+++.. .....|--|..+-..|.+-.. ++..+...++|+..=++|
T Consensus 256 ~~v~~a~~~~~~~~~~~~~~~L~~~~ki~L~~i~~~~--~~~~~~~~y~~y~~~~~~~~~--~~~~~~~ii~~L~~lgiv 331 (366)
T COG1474 256 DHVREAQEEIERDVLEEVLKTLPLHQKIVLLAIVELT--VEISTGELYDVYESLCERLRT--SQRRFSDIISELEGLGIV 331 (366)
T ss_pred HHHHHHHHHhhHHHHHHHHHcCCHhHHHHHHHHHHhc--CCCChHHHHHHHHHHHhhhCc--hHHHHHHHHHHHHhcCeE
Confidence 11123689999999999999998887 222344446666666666555 888999999999999999
Q ss_pred EEeeCCCC----ceEEEEeCCHHHHHHHHHH
Q 023087 258 KTRRHSDG----QDCFYIPLASEALEKLLSE 284 (287)
Q Consensus 258 ~~~k~~~G----~e~l~Ip~~~~~l~~iLe~ 284 (287)
..+....| +..+.+-.+.+.+.+.+++
T Consensus 332 ~~~~~~~g~~g~~~~i~~~~~~~~~~~~~~~ 362 (366)
T COG1474 332 SASLISRGERGRTREISLDLDPEVIREILKL 362 (366)
T ss_pred EeeeccCCCcCceeEeeecCCHHHHHHHHHh
Confidence 88755433 3556666666666666554
No 7
>PF13730 HTH_36: Helix-turn-helix domain
Probab=83.91 E-value=2.8 Score=28.65 Aligned_cols=52 Identities=27% Similarity=0.424 Sum_probs=37.8
Q ss_pred hcCHhHHHHHHHHHHHHhcCCCCCC--CCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceE
Q 023087 198 SLTPNAQSVFKILAEYQLSHPDEEG--MPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELV 257 (287)
Q Consensus 198 SLt~nar~lf~lLa~~QL~~~~~~g--v~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li 257 (287)
.|+++++.||-.|+.+- + +..+ .+.+.|-+.| =-|+.+++..++|+.|+++|
T Consensus 2 ~Ls~~~~~v~~~l~~~~--~-~~~~~~pS~~~la~~~-----g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYA--N-KNGGCFPSQETLAKDL-----GVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CCCHHHHHHHHHHHHhc--C-CCCCCCcCHHHHHHHH-----CcCHHHHHHHHHHHHHCcCC
Confidence 58999999999999885 1 1223 1345554444 23699999999999999875
No 8
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=83.79 E-value=4.7 Score=31.74 Aligned_cols=110 Identities=21% Similarity=0.175 Sum_probs=71.8
Q ss_pred cEEEEec-cc-hHHHHHHHHHhhcC------CCcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCC
Q 023087 7 GLLMYGF-GS-KKALLEDFASTALT------EYSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQPF 78 (287)
Q Consensus 7 nlL~YG~-GS-Kr~lL~~Fa~~~l~------~~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~~ 78 (287)
.++++|- || |..+++.+++.+.. +.+++.++.-.+. +.+++...|.+.+.....
T Consensus 6 ~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~i~~~l~~~~~----------------- 67 (131)
T PF13401_consen 6 ILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSR-TPRDFAQEILEALGLPLK----------------- 67 (131)
T ss_dssp -EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHS-SHHHHHHHHHHHHT-SSS-----------------
T ss_pred ccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCC-CHHHHHHHHHHHhCcccc-----------------
Confidence 4555653 33 99999999988765 5667777777665 899999999988754210
Q ss_pred CCCcHHHHHHHHhcccccCCCceEEEEEEcCCCcCCCChhHHHHHHHHhcCCCeEEEEee
Q 023087 79 NSRSMDDLFAFLDGSELKENDYFVCVVIHNIDGPGLRDSETQQHLGRIAFCSHIRMIASI 138 (287)
Q Consensus 79 ~~~~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~LR~~~~q~~La~La~~~~I~lIaSi 138 (287)
...+.+++.+.+...... ....+|||-++|--. +......|..|+..+++.+|-+-
T Consensus 68 ~~~~~~~l~~~~~~~l~~--~~~~~lviDe~~~l~--~~~~l~~l~~l~~~~~~~vvl~G 123 (131)
T PF13401_consen 68 SRQTSDELRSLLIDALDR--RRVVLLVIDEADHLF--SDEFLEFLRSLLNESNIKVVLVG 123 (131)
T ss_dssp STS-HHHHHHHHHHHHHH--CTEEEEEEETTHHHH--THHHHHHHHHHTCSCBEEEEEEE
T ss_pred ccCCHHHHHHHHHHHHHh--cCCeEEEEeChHhcC--CHHHHHHHHHHHhCCCCeEEEEE
Confidence 012334444444332111 223899999999843 47788888888888899887654
No 9
>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins. TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].
Probab=80.03 E-value=18 Score=34.31 Aligned_cols=137 Identities=18% Similarity=0.265 Sum_probs=87.1
Q ss_pred cEEEEecc--chHHHHHHHHHhhcCC-------CcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCC
Q 023087 7 GLLMYGFG--SKKALLEDFASTALTE-------YSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQP 77 (287)
Q Consensus 7 nlL~YG~G--SKr~lL~~Fa~~~l~~-------~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~ 77 (287)
|+|++|=. -|..++++|.+.+-.. .|||+|.. -|+-+.+.+...|.+.+.-.. .+.
T Consensus 63 ~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~-P~~p~~~~~Y~~IL~~lgaP~----------~~~---- 127 (302)
T PF05621_consen 63 NLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQM-PPEPDERRFYSAILEALGAPY----------RPR---- 127 (302)
T ss_pred ceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEec-CCCCChHHHHHHHHHHhCccc----------CCC----
Confidence 67888743 4999999999877532 26888883 577888999999998875421 000
Q ss_pred CCCCcHHH-HHHHHhcccccCCCceEEEE--EEcC-CCcCCCChhHHHHHHHHhcCCCeEEE--EeecCCCCccccCccc
Q 023087 78 FNSRSMDD-LFAFLDGSELKENDYFVCVV--IHNI-DGPGLRDSETQQHLGRIAFCSHIRMI--ASIDHVNAPLLWDKKM 151 (287)
Q Consensus 78 ~~~~~~~~-l~~~i~~~~~~~~~~~l~lv--IHnI-Dg~~LR~~~~q~~La~La~~~~I~lI--aSiDhinaplLWd~~~ 151 (287)
......+. .+..++. -..++.+| |||+ .|..-+...+-.+|..|++-=+|-+| ++-|-.++ +-=|...
T Consensus 128 ~~~~~~~~~~~~llr~-----~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~~A~~a-l~~D~QL 201 (302)
T PF05621_consen 128 DRVAKLEQQVLRLLRR-----LGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTREAYRA-LRTDPQL 201 (302)
T ss_pred CCHHHHHHHHHHHHHH-----cCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccHHHHHH-hccCHHH
Confidence 01111222 2344443 46678888 9995 88888778888889999875555555 45555553 4445555
Q ss_pred ccccccEEEEeCCCCC
Q 023087 152 VHTQFNWHWYHVPTFA 167 (287)
Q Consensus 152 ~~~~fnf~~~d~tT~~ 167 (287)
. .+|. -+.++.|.
T Consensus 202 a-~RF~--~~~Lp~W~ 214 (302)
T PF05621_consen 202 A-SRFE--PFELPRWE 214 (302)
T ss_pred H-hccC--CccCCCCC
Confidence 4 5543 34445554
No 10
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=79.45 E-value=6.4 Score=29.96 Aligned_cols=59 Identities=22% Similarity=0.354 Sum_probs=47.4
Q ss_pred cCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCC
Q 023087 199 LTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSD 264 (287)
Q Consensus 199 Lt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~ 264 (287)
||+.+|.|++.|.+.-.+.. ..|.-+++-++ +--|..+.|+.+..+.+-++|.+..+..
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~--~PVgSk~ia~~-----l~~s~aTIRN~M~~Le~lGlve~~p~~s 60 (78)
T PF03444_consen 2 LTERQREILKALVELYIETG--EPVGSKTIAEE-----LGRSPATIRNEMADLEELGLVESQPHPS 60 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcC--CCcCHHHHHHH-----HCCChHHHHHHHHHHHHCCCccCCCCCC
Confidence 89999999999999887764 44666776543 4457899999999999999998766543
No 11
>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional
Probab=75.01 E-value=11 Score=37.87 Aligned_cols=140 Identities=12% Similarity=0.115 Sum_probs=77.9
Q ss_pred ccCCccEEEEecc--chHHHHHHHHHhhcCCC--cEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCC
Q 023087 2 LRCGFGLLMYGFG--SKKALLEDFASTALTEY--SVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQP 77 (287)
Q Consensus 2 L~~GFnlL~YG~G--SKr~lL~~Fa~~~l~~~--~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~ 77 (287)
|..|=|++|||.. -|..+.+.++.....+. ..+..=.|.|+.+..+.+..+.-. +.+. .
T Consensus 191 L~~~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~rP~------------~vgy-----~ 253 (459)
T PRK11331 191 LTIKKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPN------------GVGF-----R 253 (459)
T ss_pred HhcCCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccCCC------------CCCe-----E
Confidence 3467799999975 48888899887765432 123333466777766655332100 0000 0
Q ss_pred CCCCcHHHHHHHHhcccccCCCceEEEEEEcCCCcCCCCh--hHHHHH--------------------HHHhcCCCeEEE
Q 023087 78 FNSRSMDDLFAFLDGSELKENDYFVCVVIHNIDGPGLRDS--ETQQHL--------------------GRIAFCSHIRMI 135 (287)
Q Consensus 78 ~~~~~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~LR~~--~~q~~L--------------------a~La~~~~I~lI 135 (287)
....-+-++++... ..+..+.+|||-.||-..+-.- ....+| ..+.--+|++||
T Consensus 254 ~~~G~f~~~~~~A~----~~p~~~~vliIDEINRani~kiFGel~~lLE~~~rg~~~~v~l~y~e~d~e~f~iP~Nl~II 329 (459)
T PRK11331 254 RKDGIFYNFCQQAK----EQPEKKYVFIIDEINRANLSKVFGEVMMLMEHDKRGENWSVPLTYSENDEERFYVPENVYII 329 (459)
T ss_pred ecCchHHHHHHHHH----hcccCCcEEEEehhhccCHHHhhhhhhhhccccccccccceeeeccccccccccCCCCeEEE
Confidence 00011112222221 2234567777877775543220 000111 123445799999
Q ss_pred EeecCCCCcc-ccCcccccccccEEEEeC
Q 023087 136 ASIDHVNAPL-LWDKKMVHTQFNWHWYHV 163 (287)
Q Consensus 136 aSiDhinapl-LWd~~~~~~~fnf~~~d~ 163 (287)
||+...+..+ +-|.+.. ++|.|+-...
T Consensus 330 gTMNt~Drs~~~lD~Alr-RRF~fi~i~p 357 (459)
T PRK11331 330 GLMNTADRSLAVVDYALR-RRFSFIDIEP 357 (459)
T ss_pred EecCccccchhhccHHHH-hhhheEEecC
Confidence 9999888764 5688886 9999987765
No 12
>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []. This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.
Probab=74.34 E-value=23 Score=31.89 Aligned_cols=113 Identities=12% Similarity=0.180 Sum_probs=62.8
Q ss_pred ccEEEEeccc--hHHHHHHHHHh--hcCCCc-EEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCC
Q 023087 6 FGLLMYGFGS--KKALLEDFAST--ALTEYS-VVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQPFNS 80 (287)
Q Consensus 6 FnlL~YG~GS--Kr~lL~~Fa~~--~l~~~~-~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 80 (287)
--+.++|.|- |..|..+++++ .-..+. ++-|+.-. ..+..+++..|...+..... .. ...
T Consensus 20 ~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~-~~~~~~~~~~i~~~l~~~~~--------~~------~~~ 84 (287)
T PF00931_consen 20 RVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSK-NPSLEQLLEQILRQLGEPDS--------SI------SDP 84 (287)
T ss_dssp EEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES--SCCHHHHHHHHHHHTCC-S--------TS------SCC
T ss_pred EEEEEEcCCcCCcceeeeeccccccccccccccccccccc-cccccccccccccccccccc--------cc------ccc
Confidence 3467888884 99999999866 333443 33355443 34558888888877754210 00 012
Q ss_pred CcHHHHHHHHhcccccCCCceEEEEEEcCCCcCCCChhHHHHHHHHh-cCCCeEEEEeecC
Q 023087 81 RSMDDLFAFLDGSELKENDYFVCVVIHNIDGPGLRDSETQQHLGRIA-FCSHIRMIASIDH 140 (287)
Q Consensus 81 ~~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~LR~~~~q~~La~La-~~~~I~lIaSiDh 140 (287)
...+++.+.+..... ..+..||+.|++.+. ..+.+...+- ..++.++|.|.-.
T Consensus 85 ~~~~~~~~~l~~~L~---~~~~LlVlDdv~~~~----~~~~l~~~~~~~~~~~kilvTTR~ 138 (287)
T PF00931_consen 85 KDIEELQDQLRELLK---DKRCLLVLDDVWDEE----DLEELREPLPSFSSGSKILVTTRD 138 (287)
T ss_dssp SSHHHHHHHHHHHHC---CTSEEEEEEEE-SHH----HH-------HCHHSS-EEEEEESC
T ss_pred cccccccccchhhhc---cccceeeeeeecccc----cccccccccccccccccccccccc
Confidence 345556666654322 238999999999876 2333333333 2347888888744
No 13
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=74.15 E-value=47 Score=34.68 Aligned_cols=167 Identities=13% Similarity=0.184 Sum_probs=90.3
Q ss_pred Ccc-EEEEe-ccc-hHHHHHHHHHhhcC---CCcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCC
Q 023087 5 GFG-LLMYG-FGS-KKALLEDFASTALT---EYSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQPF 78 (287)
Q Consensus 5 GFn-lL~YG-~GS-Kr~lL~~Fa~~~l~---~~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~~ 78 (287)
+|| |+||| .|+ |..|++..+...+. ...++. ++..++++.+...+..
T Consensus 313 ~~NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Y-------itaeef~~el~~al~~-------------------- 365 (617)
T PRK14086 313 AYNPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRY-------VSSEEFTNEFINSIRD-------------------- 365 (617)
T ss_pred cCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEE-------eeHHHHHHHHHHHHHh--------------------
Confidence 567 77887 465 88888888877653 223443 3455666555544322
Q ss_pred CCCcHHHHHHHHhcccccCCCceEEEEEEcCCCcCCCChhHHHHHHHHhc---CCCeEEEEeecCCCCcc-ccCcccccc
Q 023087 79 NSRSMDDLFAFLDGSELKENDYFVCVVIHNIDGPGLRDSETQQHLGRIAF---CSHIRMIASIDHVNAPL-LWDKKMVHT 154 (287)
Q Consensus 79 ~~~~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~LR~~~~q~~La~La~---~~~I~lIaSiDhinapl-LWd~~~~~~ 154 (287)
...++..+.+.. .=+|||.+||...-. +.+|..|-.+-. -.+-.+|-|-|..-..+ .++.... +
T Consensus 366 --~~~~~f~~~y~~--------~DLLlIDDIq~l~gk-e~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~-S 433 (617)
T PRK14086 366 --GKGDSFRRRYRE--------MDILLVDDIQFLEDK-ESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLR-N 433 (617)
T ss_pred --ccHHHHHHHhhc--------CCEEEEehhccccCC-HHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHH-h
Confidence 112333333332 235888999876543 334444433321 12456777777664444 2344444 7
Q ss_pred cccEEEEeCCCCCCcccccccc--hhhhhcCCccchhhHHHHHHhhcCHhHHHHHHHHHH
Q 023087 155 QFNWHWYHVPTFAPYKVEGMFF--PLILAHGSSAQTAKTAAIVLQSLTPNAQSVFKILAE 212 (287)
Q Consensus 155 ~fnf~~~d~tT~~pY~~E~~~~--~~l~~~~~~~~~~~g~~~VL~SLt~nar~lf~lLa~ 212 (287)
+|+|-. +..-.+.+.|+... .......+-....+-+.++++.++.|-|.|...|.+
T Consensus 434 Rf~~GL--vv~I~~PD~EtR~aIL~kka~~r~l~l~~eVi~yLa~r~~rnvR~LegaL~r 491 (617)
T PRK14086 434 RFEWGL--ITDVQPPELETRIAILRKKAVQEQLNAPPEVLEFIASRISRNIRELEGALIR 491 (617)
T ss_pred hhhcCc--eEEcCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhccCCHHHHHHHHHH
Confidence 888743 33445566665421 111111122345567777778877777777776654
No 14
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=73.93 E-value=76 Score=35.05 Aligned_cols=144 Identities=21% Similarity=0.248 Sum_probs=78.7
Q ss_pred cE-EEEec-cc-hHHHHHHHHHhh--------cCCCcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCC
Q 023087 7 GL-LMYGF-GS-KKALLEDFASTA--------LTEYSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQ 75 (287)
Q Consensus 7 nl-L~YG~-GS-Kr~lL~~Fa~~~--------l~~~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~ 75 (287)
|+ .+||. |. |...++.+.++. +....++-|||..- .+...++..|...+.+.. +
T Consensus 782 nvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~L-stp~sIYqvI~qqL~g~~-----------P--- 846 (1164)
T PTZ00112 782 QILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNV-VHPNAAYQVLYKQLFNKK-----------P--- 846 (1164)
T ss_pred ceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCcc-CCHHHHHHHHHHHHcCCC-----------C---
Confidence 44 47875 33 444444443321 12245678999762 456677777776664311 1
Q ss_pred CCCCCCcHHHHHHHHhcccccCCCceEEEEEEcCCCcCCCChhHHHHHHHHhcCC-----CeEEEEeecCCCCccccCcc
Q 023087 76 QPFNSRSMDDLFAFLDGSELKENDYFVCVVIHNIDGPGLRDSETQQHLGRIAFCS-----HIRMIASIDHVNAPLLWDKK 150 (287)
Q Consensus 76 ~~~~~~~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~LR~~~~q~~La~La~~~-----~I~lIaSiDhinaplLWd~~ 150 (287)
....+..++++.+-...........+|||-.||--.= +.|.+|-.|...+ .|-+||..-.+..|-..+..
T Consensus 847 --~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~k---K~QDVLYnLFR~~~~s~SKLiLIGISNdlDLperLdPR 921 (1164)
T PTZ00112 847 --PNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLIT---KTQKVLFTLFDWPTKINSKLVLIAISNTMDLPERLIPR 921 (1164)
T ss_pred --CccccHHHHHHHHHhhhhcccccceEEEeehHhhhCc---cHHHHHHHHHHHhhccCCeEEEEEecCchhcchhhhhh
Confidence 1111222333333221112233456889999996432 2577777665543 47788877666666543444
Q ss_pred cccccccEEEEeCCCCCCcccccc
Q 023087 151 MVHTQFNWHWYHVPTFAPYKVEGM 174 (287)
Q Consensus 151 ~~~~~fnf~~~d~tT~~pY~~E~~ 174 (287)
.. .++.| ..-+|.||+.|-.
T Consensus 922 LR-SRLg~---eeIvF~PYTaEQL 941 (1164)
T PTZ00112 922 CR-SRLAF---GRLVFSPYKGDEI 941 (1164)
T ss_pred hh-hcccc---ccccCCCCCHHHH
Confidence 43 67765 2347899998854
No 15
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=71.87 E-value=8.9 Score=27.87 Aligned_cols=60 Identities=17% Similarity=0.299 Sum_probs=43.2
Q ss_pred HhhcCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEee
Q 023087 196 LQSLTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRR 261 (287)
Q Consensus 196 L~SLt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k 261 (287)
++.||+++++++..|.++.-++.-. -+++++ .+.|=++|..+...+|.-+.+-++|+...
T Consensus 1 M~~LT~rQ~~vL~~I~~~~~~~G~~--Pt~rEI----a~~~g~~S~~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 1 MKELTERQKEVLEFIREYIEENGYP--PTVREI----AEALGLKSTSTVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp -----HHHHHHHHHHHHHHHHHSS-----HHHH----HHHHTSSSHHHHHHHHHHHHHTTSEEEGC
T ss_pred CCCCCHHHHHHHHHHHHHHHHcCCC--CCHHHH----HHHhCCCChHHHHHHHHHHHHCcCccCCC
Confidence 3679999999999999998765322 245555 45577899999999999999999997654
No 16
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=71.52 E-value=8.2 Score=25.60 Aligned_cols=48 Identities=19% Similarity=0.283 Sum_probs=35.4
Q ss_pred cCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEE
Q 023087 199 LTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVK 258 (287)
Q Consensus 199 Lt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~ 258 (287)
|+++.++|+..|.+. ++++.+++=+++- -|..+.+..|+++.+.++|+
T Consensus 1 l~~~~~~Il~~l~~~-------~~~t~~ela~~~~-----is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 1 LDETQRKILNYLREN-------PRITQKELAEKLG-----ISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp --HHHHHHHHHHHHC-------TTS-HHHHHHHHT-----S-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHHc-------CCCCHHHHHHHhC-----CCHHHHHHHHHHHHHCcCcC
Confidence 578889999888663 5688888855554 38999999999999999884
No 17
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=69.74 E-value=15 Score=27.38 Aligned_cols=56 Identities=18% Similarity=0.185 Sum_probs=43.0
Q ss_pred CCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEeCCHHHHHHHHH
Q 023087 223 MPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIPLASEALEKLLS 283 (287)
Q Consensus 223 v~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip~~~~~l~~iLe 283 (287)
++.+++=+. +--|+..++..|..+..+++|.++++.+|.=.|.-|.+.=.+-+|++
T Consensus 26 ~s~~eiA~~-----~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~~~Itl~dI~~ 81 (83)
T PF02082_consen 26 VSSKEIAER-----LGISPSYLRKILQKLKKAGLIESSRGRGGGYRLARPPEEITLLDIVR 81 (83)
T ss_dssp BEHHHHHHH-----HTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-CCGSBHHHHHH
T ss_pred CCHHHHHHH-----HCcCHHHHHHHHHHHhhCCeeEecCCCCCceeecCCHHHCCHHHHHH
Confidence 777777443 44599999999999999999999999988877877776655666554
No 18
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=69.58 E-value=31 Score=25.47 Aligned_cols=67 Identities=22% Similarity=0.322 Sum_probs=47.8
Q ss_pred hcCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEeCCHH
Q 023087 198 SLTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIPLASE 276 (287)
Q Consensus 198 SLt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip~~~~ 276 (287)
.++.++..++..|... +++..+++-+. +--+..++...|+++.++++|...++..|.....++++..
T Consensus 7 ~l~~~~~~il~~l~~~-------~~~~~~~la~~-----~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~ 73 (101)
T smart00347 7 GLTPTQFLVLRILYEE-------GPLSVSELAKR-----LGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEE 73 (101)
T ss_pred CCCHHHHHHHHHHHHc-------CCcCHHHHHHH-----HCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHh
Confidence 4778888888888764 35667766222 3447889999999999999999887755555555665443
No 19
>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=68.21 E-value=4.9 Score=37.26 Aligned_cols=199 Identities=15% Similarity=0.205 Sum_probs=91.5
Q ss_pred CccCCccEEEEec-cc-hHHHHHHHHHhhcCCCcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCC
Q 023087 1 MLRCGFGLLMYGF-GS-KKALLEDFASTALTEYSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQPF 78 (287)
Q Consensus 1 ~L~~GFnlL~YG~-GS-Kr~lL~~Fa~~~l~~~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~~ 78 (287)
|+.+|.++|+.|- || |..+++.+..+.-.+...+..--|.+..+.+.+ ..+.+ .... +++ +
T Consensus 29 l~~~~~pvLl~G~~GtGKT~li~~~l~~l~~~~~~~~~~~~s~~Tts~~~-q~~ie---~~l~---k~~------~---- 91 (272)
T PF12775_consen 29 LLSNGRPVLLVGPSGTGKTSLIQNFLSSLDSDKYLVITINFSAQTTSNQL-QKIIE---SKLE---KRR------G---- 91 (272)
T ss_dssp HHHCTEEEEEESSTTSSHHHHHHHHHHCSTTCCEEEEEEES-TTHHHHHH-HHCCC---TTEC---ECT------T----
T ss_pred HHHcCCcEEEECCCCCchhHHHHhhhccCCccccceeEeeccCCCCHHHH-HHHHh---hcEE---cCC------C----
Confidence 3578999999997 55 888888888664333322222233443333332 22211 1110 000 0
Q ss_pred CCCcHHHHHHHHhcccccCCCceEEEEEEcCCCcCCCChhHHHHHHHH---hc--------------CCCeEEEEeecCC
Q 023087 79 NSRSMDDLFAFLDGSELKENDYFVCVVIHNIDGPGLRDSETQQHLGRI---AF--------------CSHIRMIASIDHV 141 (287)
Q Consensus 79 ~~~~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~LR~~~~q~~La~L---a~--------------~~~I~lIaSiDhi 141 (287)
..+.-+...++++.|.++.-|..-...+|..+.-| .. +.+|.+||++.--
T Consensus 92 -------------~~~gP~~~k~lv~fiDDlN~p~~d~ygtq~~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~~p~ 158 (272)
T PF12775_consen 92 -------------RVYGPPGGKKLVLFIDDLNMPQPDKYGTQPPIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAMNPT 158 (272)
T ss_dssp -------------EEEEEESSSEEEEEEETTT-S---TTS--HHHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEESST
T ss_pred -------------CCCCCCCCcEEEEEecccCCCCCCCCCCcCHHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEecCCC
Confidence 00111245688999999999998887878655444 32 4588899998642
Q ss_pred CCccccCcccccccccEEEEeCCCCCCcccccccchhhhhcC-CccchhhHHHHHHhhcCHhHHHHHHHHHHHHhcCCCC
Q 023087 142 NAPLLWDKKMVHTQFNWHWYHVPTFAPYKVEGMFFPLILAHG-SSAQTAKTAAIVLQSLTPNAQSVFKILAEYQLSHPDE 220 (287)
Q Consensus 142 naplLWd~~~~~~~fnf~~~d~tT~~pY~~E~~~~~~l~~~~-~~~~~~~g~~~VL~SLt~nar~lf~lLa~~QL~~~~~ 220 (287)
...---+.... +.|+-++.+-.+-+ .....|. ..+..- ......+.+......+..-.-.+|+.+.+..+..+..
T Consensus 159 ~Gr~~is~R~~-r~f~i~~~~~p~~~--sl~~If~-~il~~~l~~~~f~~~v~~~~~~lv~ati~ly~~i~~~~~ptp~k 234 (272)
T PF12775_consen 159 GGRNPISPRFL-RHFNILNIPYPSDE--SLNTIFS-SILQSHLKNGGFPEDVQKLADKLVQATIELYQKIRQQFLPTPSK 234 (272)
T ss_dssp TT--SHHHHHH-TTEEEEE----TCC--HHHHHHH-HHHHHHTCHTTSSGGGCCCHHHHHHHHHHHHHHHHHHS-TTTTC
T ss_pred CCCCCCChHHh-hheEEEEecCCChH--HHHHHHH-HHHhhhcccCCCChHHHHHHHHHHHHHHHHHHhhhcccCCCCcc
Confidence 21111144555 77887776632211 1111122 111110 0000011122223344455678888888776655433
Q ss_pred CC--CCHHHHHHHHH
Q 023087 221 EG--MPIDTLYATSR 233 (287)
Q Consensus 221 ~g--v~~~~L~~~~~ 233 (287)
.- ...++|-+-..
T Consensus 235 ~HY~FnlRDlsrv~q 249 (272)
T PF12775_consen 235 PHYTFNLRDLSRVFQ 249 (272)
T ss_dssp TTTTSHHHHHHHHHH
T ss_pred ceeeccHHHHHHHHH
Confidence 21 33466644433
No 20
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=61.54 E-value=50 Score=24.38 Aligned_cols=62 Identities=21% Similarity=0.160 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHH-----hhccHHHHHHHhhhhcccceEEEeeCCCC
Q 023087 203 AQSVFKILAEYQLSHPDEEGMPIDTLYATSRERF-----LVSSQVTLNSHLTEFKDHELVKTRRHSDG 265 (287)
Q Consensus 203 ar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~f-----i~sse~~lr~~L~EF~DH~li~~~k~~~G 265 (287)
+|-+...++...-.. ....+.+.++|+.-++-. -.-+...+...|.|+-..++|..++...|
T Consensus 4 ~Kl~L~Al~~~~~~~-~~~~~~~~~vy~~Y~~~c~~~~~~~l~~~~~~~~l~~L~~~gli~~~~~~~g 70 (87)
T cd08768 4 QKLVLLALLLLFKRG-GEEEATTGEVYEVYEELCEEIGVDPLTQRRISDLLSELEMLGLLETEVSSKG 70 (87)
T ss_pred HHHHHHHHHHHHhcC-CCCCccHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHHHcCCeEEEEecCC
Confidence 344444444443222 123467777776666511 13578899999999999999998876444
No 21
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=58.47 E-value=17 Score=25.84 Aligned_cols=63 Identities=16% Similarity=0.211 Sum_probs=45.7
Q ss_pred hcCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEeCCH
Q 023087 198 SLTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIPLAS 275 (287)
Q Consensus 198 SLt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip~~~ 275 (287)
-|+++..++|..|+.. +++...++-+.+.- +..+....|..+.+.++|...++ ....+-|.+.
T Consensus 5 gLs~~E~~vy~~Ll~~-------~~~t~~eIa~~l~i-----~~~~v~~~L~~L~~~GlV~~~~~---~~~~Y~a~~p 67 (68)
T PF01978_consen 5 GLSENEAKVYLALLKN-------GPATAEEIAEELGI-----SRSTVYRALKSLEEKGLVEREEG---RPKVYRAVPP 67 (68)
T ss_dssp CHHHHHHHHHHHHHHH-------CHEEHHHHHHHHTS-----SHHHHHHHHHHHHHTTSEEEEEE---CCEEEEEE-H
T ss_pred CcCHHHHHHHHHHHHc-------CCCCHHHHHHHHCc-----CHHHHHHHHHHHHHCCCEEEEcC---ceEEEEEeCC
Confidence 3688999999999855 45667777555443 88999999999999999988763 3445544443
No 22
>PRK09462 fur ferric uptake regulator; Provisional
Probab=57.64 E-value=53 Score=27.21 Aligned_cols=64 Identities=19% Similarity=0.259 Sum_probs=50.9
Q ss_pred cCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCce
Q 023087 199 LTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQD 267 (287)
Q Consensus 199 Lt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e 267 (287)
+|+.-+.|+..|.+. ....++-.++|+..+++.---|-.++=--|.-|.+.++|......+|.-
T Consensus 15 ~T~qR~~Il~~l~~~-----~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~ 78 (148)
T PRK09462 15 VTLPRLKILEVLQEP-----DNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKS 78 (148)
T ss_pred CCHHHHHHHHHHHhC-----CCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCcE
Confidence 799999999998754 1245789999999999886557888888899999999998765545544
No 23
>PF10483 Elong_Iki1: Elongator subunit Iki1; InterPro: IPR019519 Histone acetylation protein (Hap) 2 (also known as Elongator complex protein 5) is one of three histone acetyltransferases proteins that, in yeasts, are found associated with elongating forms of RNA polymerase II (Elongator). The Haps can be isolated in two forms, as a six-subunit complex with Elongator, and as a complex of the three proteins on their own. The role of the Hap complex in transcription is still speculative, being possibly to keep the histone acetylation activity of free Elongator in check, allowing histone acetylation only in the presence of a transcribing polymerase, or the interaction with Haps might render Elongator susceptible to modifications thereby altering its activity []. This protein family also contains Dermal papilla-derived protein 6, which also belong to the ELP5 family. ; PDB: 4A8J_B 4EJS_B.
Probab=56.90 E-value=19 Score=33.48 Aligned_cols=98 Identities=13% Similarity=0.085 Sum_probs=47.9
Q ss_pred HHHHHHHHHhhcCCCcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCcHHHHHHHHhccc--
Q 023087 17 KALLEDFASTALTEYSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQPFNSRSMDDLFAFLDGSE-- 94 (287)
Q Consensus 17 r~lL~~Fa~~~l~~~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~-- 94 (287)
+.||++|+.+....+..|++=+|.-.-. -+.+.. .......+..++.+.+....
T Consensus 26 ~~Ll~e~i~~a~~~~~~V~~lsfEt~~~--------~~~~d~----------------~~~~~~~~~~~i~~~i~s~~~~ 81 (280)
T PF10483_consen 26 RPLLKEFIRRAKSRNEKVHFLSFETLNK--------PEYADS----------------FINARGKSLQDIVKEIKSHLPS 81 (280)
T ss_dssp HHHHHHHHHHHTS----EEEEESS--S----------TT-SE----------------EEETTSS-HHHHHHHHHHTS--
T ss_pred HHHHHHHHHHHHcCCCeEEEEEeEeCCC--------cccCCe----------------eccccCCCHHHHHHHHHhhccc
Confidence 7899999988766555555555652110 000000 00112345666777666541
Q ss_pred -ccCCCceEEEEEEcCCCcCCCC-hhHHHHHHHHhcCCCeEEEEee
Q 023087 95 -LKENDYFVCVVIHNIDGPGLRD-SETQQHLGRIAFCSHIRMIASI 138 (287)
Q Consensus 95 -~~~~~~~l~lvIHnIDg~~LR~-~~~q~~La~La~~~~I~lIaSi 138 (287)
......+..+||-++.--..+. ...-..|+.|.+.|++.+||..
T Consensus 82 ~~~~~~~~~lVvIDSLn~ll~~~~~~l~~fLssl~~~p~~svv~~~ 127 (280)
T PF10483_consen 82 SSSSPTKKFLVVIDSLNYLLNHHPCQLSQFLSSLLSSPQSSVVGLY 127 (280)
T ss_dssp SS-SS---EEEEES-GGGS-GG---GHHHHHHHH---TTEEEEEEE
T ss_pred ccccCCCCeEEEEEcchHHHHHHHHHHHHHHHhcccCCCcEEEEEE
Confidence 1245668999999998432221 1567788889989998888765
No 24
>COG0505 CarA Carbamoylphosphate synthase small subunit [Amino acid transport and metabolism / Nucleotide transport and metabolism]
Probab=56.19 E-value=24 Score=34.28 Aligned_cols=40 Identities=18% Similarity=0.349 Sum_probs=28.7
Q ss_pred CCccEEEEeccchHHHHHHHHHhhcCCCcEEEEeccCCCCCHHHHH
Q 023087 4 CGFGLLMYGFGSKKALLEDFASTALTEYSVVVINGYLQSINIKQVV 49 (287)
Q Consensus 4 ~GFnlL~YG~GSKr~lL~~Fa~~~l~~~~~vvvnGy~p~~~~k~il 49 (287)
.++++.+|=+|.||++|+.|+++-|. +.|| =|. .+..+|+
T Consensus 178 ~~~~Vv~iD~GvK~nIlr~L~~rg~~---vtVV-P~~--t~~eeIl 217 (368)
T COG0505 178 PGKHVVVIDFGVKRNILRELVKRGCR---VTVV-PAD--TSAEEIL 217 (368)
T ss_pred CCcEEEEEEcCccHHHHHHHHHCCCe---EEEE-cCC--CCHHHHH
Confidence 48999999999999999999955332 3333 333 5566654
No 25
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=55.38 E-value=20 Score=27.79 Aligned_cols=57 Identities=16% Similarity=0.249 Sum_probs=43.4
Q ss_pred hcCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeC
Q 023087 198 SLTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRH 262 (287)
Q Consensus 198 SLt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~ 262 (287)
++++-+++||..|-+ ....+.||+.+++-+++ --++..+|.-|.++.+-+.|=++-|
T Consensus 44 ~~~~~~~~Vl~~i~~---~~~~~~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsTiD 100 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQ---QPNSEEGVHVDEIAQQL-----GMSENEVRKALDFLSNEGHIYSTID 100 (102)
T ss_dssp -S-HHHHHHHHHHHC-------TTTEEHHHHHHHS-----TS-HHHHHHHHHHHHHTTSEEESSS
T ss_pred CCCHHHHHHHHHHHh---cCCCCCcccHHHHHHHh-----CcCHHHHHHHHHHHHhCCeEecccC
Confidence 899999999999977 22245799999998776 3379999999999999999977654
No 26
>PF05729 NACHT: NACHT domain
Probab=52.86 E-value=1e+02 Score=24.65 Aligned_cols=42 Identities=12% Similarity=0.180 Sum_probs=28.7
Q ss_pred CCceEEEEEEcCCCcCCCChh-----HHHHHHHHhc---CCCeEEEEeec
Q 023087 98 NDYFVCVVIHNIDGPGLRDSE-----TQQHLGRIAF---CSHIRMIASID 139 (287)
Q Consensus 98 ~~~~l~lvIHnIDg~~LR~~~-----~q~~La~La~---~~~I~lIaSiD 139 (287)
...+++|||.++|--.-.... ....|+.|.. .|++++|-|.=
T Consensus 79 ~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r 128 (166)
T PF05729_consen 79 KNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSR 128 (166)
T ss_pred cCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEc
Confidence 466899999999976654332 4455655543 57888888763
No 27
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=50.67 E-value=80 Score=26.37 Aligned_cols=65 Identities=25% Similarity=0.322 Sum_probs=53.4
Q ss_pred cCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCceEE
Q 023087 199 LTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCF 269 (287)
Q Consensus 199 Lt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l 269 (287)
+|++-..|+++|.+.. ...+-+++|+..++++-=-|-.++-.-|.=|.+-++|..-...+|...+
T Consensus 19 ~T~qR~~vl~~L~~~~------~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y 83 (145)
T COG0735 19 LTPQRLAVLELLLEAD------GHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRY 83 (145)
T ss_pred cCHHHHHHHHHHHhcC------CCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEE
Confidence 6999999999997762 3388999999999988777899999999999999999887655554444
No 28
>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].
Probab=50.59 E-value=44 Score=30.76 Aligned_cols=41 Identities=17% Similarity=0.229 Sum_probs=32.7
Q ss_pred CCceEEEEEEcCCCcCCCChhHHHHH---HHHhcCCCeEEEEeecC
Q 023087 98 NDYFVCVVIHNIDGPGLRDSETQQHL---GRIAFCSHIRMIASIDH 140 (287)
Q Consensus 98 ~~~~l~lvIHnIDg~~LR~~~~q~~L---a~La~~~~I~lIaSiDh 140 (287)
...+++++|-++|- ++.+.+.++| ..+...|+|..|-.+|.
T Consensus 170 ~~~~iViiIDdLDR--~~~~~i~~~l~~ik~~~~~~~i~~Il~~D~ 213 (325)
T PF07693_consen 170 SKKRIVIIIDDLDR--CSPEEIVELLEAIKLLLDFPNIIFILAFDP 213 (325)
T ss_pred CCceEEEEEcchhc--CCcHHHHHHHHHHHHhcCCCCeEEEEEecH
Confidence 67899999999997 5666555555 45678999999999983
No 29
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=50.31 E-value=75 Score=25.80 Aligned_cols=68 Identities=18% Similarity=0.303 Sum_probs=47.4
Q ss_pred HHHHHHhhcCHhHH-HHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCce-E
Q 023087 191 TAAIVLQSLTPNAQ-SVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQD-C 268 (287)
Q Consensus 191 g~~~VL~SLt~nar-~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e-~ 268 (287)
-+..|++.|....| +|+..|... +++...+|-+. +==+..++-.+|+.+.+-++|..++ .|.+ +
T Consensus 5 ~~~~~fkaLadptRl~IL~~L~~~-------~~~~v~ela~~-----l~lsqstvS~HL~~L~~AGLV~~~r--~Gr~~~ 70 (117)
T PRK10141 5 LPLQLFKILSDETRLGIVLLLRES-------GELCVCDLCTA-----LDQSQPKISRHLALLRESGLLLDRK--QGKWVH 70 (117)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHc-------CCcCHHHHHHH-----HCcCHHHHHHHHHHHHHCCceEEEE--EcCEEE
Confidence 34578888887777 888887642 23555555322 2237888999999999999999987 4554 4
Q ss_pred EEEe
Q 023087 269 FYIP 272 (287)
Q Consensus 269 l~Ip 272 (287)
+.+.
T Consensus 71 Y~l~ 74 (117)
T PRK10141 71 YRLS 74 (117)
T ss_pred EEEC
Confidence 5553
No 30
>PRK04841 transcriptional regulator MalT; Provisional
Probab=49.15 E-value=2e+02 Score=30.53 Aligned_cols=114 Identities=15% Similarity=0.128 Sum_probs=55.9
Q ss_pred eccchHHHHHHHHHhhcCCCcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCC-CCCCCCCcHHHHHHHH
Q 023087 12 GFGSKKALLEDFASTALTEYSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRA-QQPFNSRSMDDLFAFL 90 (287)
Q Consensus 12 G~GSKr~lL~~Fa~~~l~~~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~i 90 (287)
||| |..++.+|++.. . ++.-+.=-..+-+....+..++..+....... +..... ...........++..+
T Consensus 42 G~G-KTtl~~~~~~~~-~--~~~w~~l~~~d~~~~~f~~~l~~~l~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~ 112 (903)
T PRK04841 42 GYG-KTTLISQWAAGK-N--NLGWYSLDESDNQPERFASYLIAALQQATNGH-----CSKSEALAQKRQYASLSSLFAQL 112 (903)
T ss_pred CCC-HHHHHHHHHHhC-C--CeEEEecCcccCCHHHHHHHHHHHHHHhcCcc-----cchhhhhhccCCcCCHHHHHHHH
Confidence 555 999999998643 2 44333222233444555666666553211000 000000 0000111222233222
Q ss_pred hcccccCCCceEEEEEEcCCCcCCCChhHHHHHHHHhc--CCCeEEEEe
Q 023087 91 DGSELKENDYFVCVVIHNIDGPGLRDSETQQHLGRIAF--CSHIRMIAS 137 (287)
Q Consensus 91 ~~~~~~~~~~~l~lvIHnIDg~~LR~~~~q~~La~La~--~~~I~lIaS 137 (287)
-... ...+.|++|||-++.- +.++.....|..|.. .+++|+|.+
T Consensus 113 ~~~l-~~~~~~~~lvlDD~h~--~~~~~~~~~l~~l~~~~~~~~~lv~~ 158 (903)
T PRK04841 113 FIEL-ADWHQPLYLVIDDYHL--ITNPEIHEAMRFFLRHQPENLTLVVL 158 (903)
T ss_pred HHHH-hcCCCCEEEEEeCcCc--CCChHHHHHHHHHHHhCCCCeEEEEE
Confidence 1111 1136789999877765 345566778888874 478999543
No 31
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=47.64 E-value=20 Score=25.63 Aligned_cols=21 Identities=19% Similarity=0.475 Sum_probs=16.5
Q ss_pred HHHHHHhhcCCCcEEEEeccC
Q 023087 20 LEDFASTALTEYSVVVINGYL 40 (287)
Q Consensus 20 L~~Fa~~~l~~~~~vvvnGy~ 40 (287)
|.++..+.-++..++|+|||.
T Consensus 18 l~~lr~~~k~~~DI~I~NGF~ 38 (57)
T PF14453_consen 18 LFELRKESKPDADIVILNGFP 38 (57)
T ss_pred HHHHHHhhCCCCCEEEEcCcc
Confidence 455666666788899999998
No 32
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=46.88 E-value=78 Score=24.63 Aligned_cols=47 Identities=19% Similarity=0.261 Sum_probs=39.0
Q ss_pred CCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCce
Q 023087 221 EGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQD 267 (287)
Q Consensus 221 ~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e 267 (287)
..++-.++++..+++.---|..++=..|..|.+.++|......+|..
T Consensus 15 ~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~ 61 (116)
T cd07153 15 GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKA 61 (116)
T ss_pred CCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCce
Confidence 45789999999999876668888989999999999998876555533
No 33
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=46.74 E-value=1.6e+02 Score=24.05 Aligned_cols=71 Identities=14% Similarity=0.215 Sum_probs=51.8
Q ss_pred hcCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEe-CCHH
Q 023087 198 SLTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIP-LASE 276 (287)
Q Consensus 198 SLt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip-~~~~ 276 (287)
+||+....+.++|=+ .++...+++.+...++. --+..+..+.|.-+.+.++|..++ +|.-+++-| .+++
T Consensus 1 ~Lt~~E~~VM~vlW~-------~~~~t~~eI~~~l~~~~-~~~~tTv~T~L~rL~~KG~v~~~k--~gr~~~Y~p~vs~e 70 (130)
T TIGR02698 1 SISDAEWEVMRVVWT-------LGETTSRDIIRILAEKK-DWSDSTIKTLLGRLVDKGCLTTEK--EGRKFIYTALVSED 70 (130)
T ss_pred CCCHHHHHHHHHHHc-------CCCCCHHHHHHHHhhcc-CCcHHHHHHHHHHHHHCCceeeec--CCCcEEEEecCCHH
Confidence 367777777777642 23467888888776653 346889999999999999997664 577777878 5666
Q ss_pred HH
Q 023087 277 AL 278 (287)
Q Consensus 277 ~l 278 (287)
+.
T Consensus 71 e~ 72 (130)
T TIGR02698 71 EA 72 (130)
T ss_pred HH
Confidence 66
No 34
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=46.63 E-value=78 Score=24.99 Aligned_cols=65 Identities=22% Similarity=0.379 Sum_probs=51.3
Q ss_pred cCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCceEE
Q 023087 199 LTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCF 269 (287)
Q Consensus 199 Lt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l 269 (287)
+|+.-+.|+..|.+.. ..++-+++|+..+++.---|-+++=.-|..|.+-++|......+|...+
T Consensus 6 ~T~~R~~Il~~l~~~~------~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y 70 (120)
T PF01475_consen 6 LTPQRLAILELLKESP------EHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRY 70 (120)
T ss_dssp HHHHHHHHHHHHHHHS------SSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEE
T ss_pred CCHHHHHHHHHHHcCC------CCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceE
Confidence 4788888888887772 3678999999999988778889999999999999999887765554433
No 35
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=46.57 E-value=63 Score=22.44 Aligned_cols=49 Identities=24% Similarity=0.427 Sum_probs=38.5
Q ss_pred HhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEee
Q 023087 201 PNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRR 261 (287)
Q Consensus 201 ~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k 261 (287)
|.-++|++.|. ...+++..+|-+.+- -+..++.-+|+++.+.++|...+
T Consensus 10 p~R~~Il~~L~-------~~~~~t~~ela~~l~-----~~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 10 PTRLRILRLLA-------SNGPMTVSELAEELG-----ISQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHHHHHHH-------HCSTBEHHHHHHHHT-----S-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHh-------cCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHCCCeEEec
Confidence 66677888872 236788998877764 48888999999999999999876
No 36
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=45.84 E-value=1.2e+02 Score=22.42 Aligned_cols=62 Identities=18% Similarity=0.226 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHHH---H--HhhccHHHHHHHhhhhcccceEEEeeCC----CC-ceEEEEeCCHHHHHHHH
Q 023087 221 EGMPIDTLYATSRE---R--FLVSSQVTLNSHLTEFKDHELVKTRRHS----DG-QDCFYIPLASEALEKLL 282 (287)
Q Consensus 221 ~gv~~~~L~~~~~e---~--fi~sse~~lr~~L~EF~DH~li~~~k~~----~G-~e~l~Ip~~~~~l~~iL 282 (287)
..+...++|+.=++ . .=.-+...++.+|+|+-+.++|..++.. .| .-.+.+..+++++.+.|
T Consensus 14 ~~~~~~~vy~~Y~~lc~~~~~~pls~~r~~~~l~eL~~~gli~~~~~~~G~~~G~~~~~~l~~d~~~v~~aL 85 (85)
T PF09079_consen 14 EEVTTGEVYEVYEELCESLGVDPLSYRRFSDYLSELEMLGLIESERKGRGRGRGRTREISLNVDPEDVLEAL 85 (85)
T ss_dssp SSEEHHHHHHHHHHHHHHTTS----HHHHHHHHHHHHHTTSEEEEEEE-TT-CTEEEEEEECSSSHHHHHHH
T ss_pred CceeHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEEeecCCCCCCeEEEEEecCCHHHHHhhC
Confidence 34555555443332 1 1124788999999999999999998732 33 35578888888776643
No 37
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=45.26 E-value=25 Score=26.13 Aligned_cols=47 Identities=17% Similarity=0.234 Sum_probs=32.0
Q ss_pred hcCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhh
Q 023087 198 SLTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLT 249 (287)
Q Consensus 198 SLt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~ 249 (287)
+||++...|+.+|++. ....++.++|++.+-.+--..++.++++.+.
T Consensus 23 ~Lt~~e~~lL~~L~~~-----~~~~vs~~~l~~~lw~~~~~~~~~~l~~~I~ 69 (95)
T cd00383 23 ELTPKEFELLELLARN-----PGRVLSREQLLEAVWGDDYDVDDRTVDVHIS 69 (95)
T ss_pred EeCHHHHHHHHHHHhC-----CCCcCCHHHHHHHhcCCCCCCCcccHHHHHH
Confidence 4799999999999887 2456888999888754322234445554443
No 38
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=44.64 E-value=81 Score=25.71 Aligned_cols=74 Identities=15% Similarity=0.221 Sum_probs=49.9
Q ss_pred HHHHHHHHhcCC-CCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEeCCHHHHHHHHHHh
Q 023087 207 FKILAEYQLSHP-DEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIPLASEALEKLLSEI 285 (287)
Q Consensus 207 f~lLa~~QL~~~-~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip~~~~~l~~iLe~l 285 (287)
|-+.+-..|+.. +...++-+++ |.. +--+..-++..|..+..+++|.++++..|.=.+.-|.+.=.+-+|++-+
T Consensus 9 YAl~~l~~La~~~~~~~~s~~~i---a~~--~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~~~~~Itl~dv~~a~ 83 (135)
T TIGR02010 9 YAVTAMLDLALNAETGPVTLADI---SER--QGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGRPAEDISVADIIDAV 83 (135)
T ss_pred HHHHHHHHHHhCCCCCcCcHHHH---HHH--HCcCHHHHHHHHHHHHHCCceEEEeCCCCCEeccCCHHHCcHHHHHHHh
Confidence 334333444432 2234666666 333 4458999999999999999999999988876666666666666666654
No 39
>PF12157 DUF3591: Protein of unknown function (DUF3591); InterPro: IPR022591 This functionally uncharacterised domain is found centrally in the eukaryotic transcription initiation factor TFIID subunit 1.
Probab=43.63 E-value=68 Score=32.24 Aligned_cols=74 Identities=20% Similarity=0.327 Sum_probs=46.3
Q ss_pred CHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEe----CCH
Q 023087 200 TPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIP----LAS 275 (287)
Q Consensus 200 t~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip----~~~ 275 (287)
|.-.++-.+.++-.++.......+..+++ .+.|=-.||++.|.-|+||.|.+ |++.+...|..-| -+.
T Consensus 236 t~~~knrL~~~iyRlf~~~~~~ri~~~di----~~~Fp~~se~~iRkrLKe~~~~~----R~g~~~~~W~lk~~~~lp~e 307 (457)
T PF12157_consen 236 TNFSKNRLKMIIYRLFNKSQPRRIKVDDI----KKHFPDQSESQIRKRLKEFADFQ----RTGDDSGWWVLKPGFRLPDE 307 (457)
T ss_pred HHHHHHHHHHHHHHHHhhccCCccCHHHH----HHhCCCCcHHHHHHHHHHHHhcc----CCCCCCCeEEECCCCCCCCH
Confidence 33344445555555554444567888777 34467789999999999999984 4544555555545 244
Q ss_pred HHHHHH
Q 023087 276 EALEKL 281 (287)
Q Consensus 276 ~~l~~i 281 (287)
++|.++
T Consensus 308 eelr~m 313 (457)
T PF12157_consen 308 EELRKM 313 (457)
T ss_pred HHHHhh
Confidence 555544
No 40
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=43.14 E-value=92 Score=26.18 Aligned_cols=50 Identities=20% Similarity=0.183 Sum_probs=40.3
Q ss_pred HhhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEeCCHHHHHHHHHHh
Q 023087 236 FLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIPLASEALEKLLSEI 285 (287)
Q Consensus 236 fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip~~~~~l~~iLe~l 285 (287)
..-.|..-|+..|.++..+++|+++||+.|.=.|.-|.+.=.+-+|++-+
T Consensus 34 ~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~~~~Isl~dVv~av 83 (150)
T COG1959 34 RQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLARPPEEITLGDVVRAL 83 (150)
T ss_pred HhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccCCCChHHCcHHHHHHHh
Confidence 35569999999999999999999999998887777776665566665544
No 41
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=42.98 E-value=2.9e+02 Score=27.32 Aligned_cols=104 Identities=12% Similarity=0.125 Sum_probs=57.1
Q ss_pred EEEEEcCCCcCCCChhHHHHH----HHHhcCCCeEEEEeecCCCCccccCc---ccccccccEEEEeCCCCCCccccccc
Q 023087 103 CVVIHNIDGPGLRDSETQQHL----GRIAFCSHIRMIASIDHVNAPLLWDK---KMVHTQFNWHWYHVPTFAPYKVEGMF 175 (287)
Q Consensus 103 ~lvIHnIDg~~LR~~~~q~~L----a~La~~~~I~lIaSiDhinaplLWd~---~~~~~~fnf~~~d~tT~~pY~~E~~~ 175 (287)
+|+|-++|... -.+.+|..| -.+... +..+|-+.||.-. -|+. ... ++|.|- -+..+.|++.|+..
T Consensus 197 vLlIDDi~~l~-~~~~~q~elf~~~n~l~~~-~k~iIitsd~~p~--~l~~l~~rL~-SR~~~g--l~v~i~~pd~e~r~ 269 (440)
T PRK14088 197 VLLIDDVQFLI-GKTGVQTELFHTFNELHDS-GKQIVICSDREPQ--KLSEFQDRLV-SRFQMG--LVAKLEPPDEETRK 269 (440)
T ss_pred EEEEechhhhc-CcHHHHHHHHHHHHHHHHc-CCeEEEECCCCHH--HHHHHHHHHh-hHHhcC--ceEeeCCCCHHHHH
Confidence 67788887532 123344333 333333 3467777775433 3332 222 566653 34467888888653
Q ss_pred c--hhhhhcCCccchhhHHHHHHhhcCHhHHHHHHHHHHH
Q 023087 176 F--PLILAHGSSAQTAKTAAIVLQSLTPNAQSVFKILAEY 213 (287)
Q Consensus 176 ~--~~l~~~~~~~~~~~g~~~VL~SLt~nar~lf~lLa~~ 213 (287)
. .......+-....+-+.++.+..+.|.|.|-..|...
T Consensus 270 ~IL~~~~~~~~~~l~~ev~~~Ia~~~~~~~R~L~g~l~~l 309 (440)
T PRK14088 270 KIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAIIKL 309 (440)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHhccccCHHHHHHHHHHH
Confidence 2 1111111223455677788888888888877777544
No 42
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=42.71 E-value=1.2e+02 Score=22.71 Aligned_cols=60 Identities=18% Similarity=0.332 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCc-eEEEEeC---CHHHHHHHHHHh
Q 023087 221 EGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQ-DCFYIPL---ASEALEKLLSEI 285 (287)
Q Consensus 221 ~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~-e~l~Ip~---~~~~l~~iLe~l 285 (287)
.+++|.+|-+... -++.++..+|+.+.|.+.|..+|...|. ..-++-+ +++.+++.++.|
T Consensus 13 ~~~~f~~L~~~l~-----lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~~L 76 (80)
T PF13601_consen 13 EEATFSELKEELG-----LTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVAAL 76 (80)
T ss_dssp SEEEHHHHHHHTT-------HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHhC-----cCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHHHH
Confidence 4578888855443 3999999999999999999999876543 3445544 556666665554
No 43
>COG1307 DegV Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.06 E-value=1.7e+02 Score=27.39 Aligned_cols=112 Identities=18% Similarity=0.200 Sum_probs=73.4
Q ss_pred ccCCc-cEEEEeccchHHHH---HHHHHhhcCCCcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCC
Q 023087 2 LRCGF-GLLMYGFGSKKALL---EDFASTALTEYSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQP 77 (287)
Q Consensus 2 L~~GF-nlL~YG~GSKr~lL---~~Fa~~~l~~~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~ 77 (287)
+.+|| .++.--+.|+..=- ...+.++...-.+.|||.-.-+..+.-.+..+.+.+-.
T Consensus 77 ~~~g~~~vi~i~iSs~LSgty~~a~~a~~~~~~~~v~viDS~~~s~~~g~~v~~a~~l~~~------------------- 137 (282)
T COG1307 77 LQKGYDEVISIHISSGLSGTYQSAQLAAELVEGAKVHVIDSKSVSMGLGFLVLEAAELAKA------------------- 137 (282)
T ss_pred HhCCCcEEEEEEcCCCccHHHHHHHHHHHhccCceEEEEcCcchhhHHHHHHHHHHHHHHc-------------------
Confidence 35677 68888888874311 23343444445799999998888887777777665432
Q ss_pred CCCCcHHHHHHHHhcccccCCCceEEEEEEcCCCcC--CCChhHHHHHHHHhcCCCeEEEEeecC
Q 023087 78 FNSRSMDDLFAFLDGSELKENDYFVCVVIHNIDGPG--LRDSETQQHLGRIAFCSHIRMIASIDH 140 (287)
Q Consensus 78 ~~~~~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~--LR~~~~q~~La~La~~~~I~lIaSiDh 140 (287)
..+++++++.+.... ....+|+++.++|.-. =|-.+++. .+.++=+|+.|-++|.
T Consensus 138 --G~s~~ei~~~l~~~~---~~t~~~~~v~~L~~L~kgGRIs~~~a---~lg~lL~ikPIl~~~~ 194 (282)
T COG1307 138 --GKSFEEILKKLEEIR---EKTKAYFVVDDLDNLVKGGRISKAAA---FLGNLLKIKPILSFED 194 (282)
T ss_pred --CCCHHHHHHHHHHHH---hhcEEEEEECchhHHHhCCCcchhHH---HHHhhhcceEEEEEeC
Confidence 134677777776532 4678999999999521 14444444 4555557899999987
No 44
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=41.35 E-value=26 Score=25.05 Aligned_cols=46 Identities=17% Similarity=0.183 Sum_probs=32.3
Q ss_pred hcCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHh
Q 023087 198 SLTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHL 248 (287)
Q Consensus 198 SLt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L 248 (287)
.||++...|+..|+.+. ..-++.++|++.+-.+-...++.++++++
T Consensus 5 ~Lt~~e~~lL~~L~~~~-----~~~vs~~~l~~~~w~~~~~~~~~~l~~~I 50 (77)
T PF00486_consen 5 KLTPKEFRLLELLLRNP-----GRVVSREELIEALWGDEEDVSDNSLDVHI 50 (77)
T ss_dssp ESSHHHHHHHHHHHHTT-----TSEEEHHHHHHHHTSSSSTTCTHHHHHHH
T ss_pred ecCHHHHHHHHHHHhCC-----CCCCCHHHhCChhhhcccccchhhHHHHH
Confidence 48999999999998772 34578888888776655544555544443
No 45
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=40.14 E-value=33 Score=28.27 Aligned_cols=48 Identities=13% Similarity=0.134 Sum_probs=36.2
Q ss_pred hhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEeCCHHHHHHHHHH
Q 023087 237 LVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIPLASEALEKLLSE 284 (287)
Q Consensus 237 i~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip~~~~~l~~iLe~ 284 (287)
+--|..-+|..|..+..+++|.++++..|.=.+.-|-+.-.+-++.+-
T Consensus 35 ~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~~~~~itl~dI~~a 82 (141)
T PRK11014 35 YGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGKPASTIRIGDVVRE 82 (141)
T ss_pred HCcCHHHHHHHHHHHHhCCEEEEecCCCCCeeecCCHHHCCHHHHHHH
Confidence 556899999999999999999999998776556555444444455443
No 46
>PF09673 TrbC_Ftype: Type-F conjugative transfer system pilin assembly protein; InterPro: IPR019106 This entry represents TrbC, a protein that is an essential component of the F-type conjugative pilus assembly system (aka type 4 secretion system) for the transfer of plasmid DNA [, ]. The N-terminal portion of these proteins is heterogeneous.
Probab=39.76 E-value=82 Score=25.19 Aligned_cols=39 Identities=23% Similarity=0.315 Sum_probs=28.8
Q ss_pred HHHHHHHhhcCCCcEEEEeccCCCCCHHHHHHHHHHHHHh
Q 023087 19 LLEDFASTALTEYSVVVINGYLQSINIKQVVITLAEVLWN 58 (287)
Q Consensus 19 lL~~Fa~~~l~~~~~vvvnGy~p~~~~k~il~~i~~~l~~ 58 (287)
-|++.+.+.-.-+..+|++|+.++ ++++-...+.+.+..
T Consensus 12 ~L~~l~~~a~~~~~~~V~RG~~~g-~~~~t~~~~~~l~~~ 50 (113)
T PF09673_consen 12 SLRNLLKQAERAGVVVVFRGFPDG-SFKPTAKAIQELLRK 50 (113)
T ss_pred HHHHHHHHHHhCCcEEEEECCCCC-CHHHHHHHHHHHhhc
Confidence 344444444445889999999999 999988888776543
No 47
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=39.20 E-value=70 Score=25.70 Aligned_cols=61 Identities=8% Similarity=0.137 Sum_probs=44.2
Q ss_pred CCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEeCCHHHHHHHHHHhh
Q 023087 221 EGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIPLASEALEKLLSEIN 286 (287)
Q Consensus 221 ~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip~~~~~l~~iLe~l~ 286 (287)
..++.+++ |.. +--|...++..|..+...++|...++.+|.-.+.-|.+.-.+.++++.+.
T Consensus 24 ~~~s~~ei---a~~--l~is~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~~~it~~~v~~~l~ 84 (130)
T TIGR02944 24 QPYSAAEI---AEQ--TGLNAPTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDITVADIVKAVE 84 (130)
T ss_pred CCccHHHH---HHH--HCcCHHHHHHHHHHHHHCCcEEecCCCCCChhhcCCccccCHHHHHHHHc
Confidence 45777766 333 55699999999999999999998887777655555554555677776653
No 48
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=37.32 E-value=1e+02 Score=23.56 Aligned_cols=50 Identities=14% Similarity=0.280 Sum_probs=37.7
Q ss_pred CCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEeCCHHHHHHHHHHh
Q 023087 221 EGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIPLASEALEKLLSEI 285 (287)
Q Consensus 221 ~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip~~~~~l~~iLe~l 285 (287)
.|++|.+|+++.++++=... ||-.+..+. .++.|. +|++.+.|+..+...
T Consensus 19 ~~~~y~~L~~ki~~kLkl~~------------e~i~LsYkd-e~s~~~--v~l~d~dle~aws~~ 68 (80)
T cd06406 19 RGLSYATLLQKISSKLELPA------------EHITLSYKS-EASGED--VILSDTNMEDVWSQA 68 (80)
T ss_pred CCCCHHHHHHHHHHHhCCCc------------hhcEEEecc-CCCCCc--cCcChHHHHHHHHhh
Confidence 68999999999999886653 666665554 455563 777999999988764
No 49
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=36.43 E-value=37 Score=28.63 Aligned_cols=49 Identities=22% Similarity=0.156 Sum_probs=39.7
Q ss_pred hhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEeCCHHHHHHHHHHh
Q 023087 237 LVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIPLASEALEKLLSEI 285 (287)
Q Consensus 237 i~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip~~~~~l~~iLe~l 285 (287)
.--|+.-++..|..+...++|.+.||..|.=.|.-|-..-.|-+|++-+
T Consensus 34 ~~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p~eItl~dIi~av 82 (153)
T PRK11920 34 YGVSELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAADISLFDVVRVT 82 (153)
T ss_pred HCcCHHHHHHHHHHHHHCCCEEeecCCCCCeeecCCHHHCcHHHHHHHH
Confidence 4559999999999999999999999998887677766655566666544
No 50
>PRK05541 adenylylsulfate kinase; Provisional
Probab=36.27 E-value=74 Score=26.65 Aligned_cols=38 Identities=21% Similarity=0.412 Sum_probs=27.7
Q ss_pred CccCCccEEEEec-cc-hHHHHHHHHHhhcCC-CcEEEEec
Q 023087 1 MLRCGFGLLMYGF-GS-KKALLEDFASTALTE-YSVVVING 38 (287)
Q Consensus 1 ~L~~GFnlL~YG~-GS-Kr~lL~~Fa~~~l~~-~~~vvvnG 38 (287)
|...|+.|+|.|+ || |..+.+.++..+... ..+++++|
T Consensus 3 ~~~~~~~I~i~G~~GsGKst~a~~l~~~l~~~~~~~~~~~~ 43 (176)
T PRK05541 3 MKPNGYVIWITGLAGSGKTTIAKALYERLKLKYSNVIYLDG 43 (176)
T ss_pred CCCCCCEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEec
Confidence 5678999999998 66 878887777665433 34566765
No 51
>PRK06526 transposase; Provisional
Probab=35.93 E-value=2.6e+02 Score=25.53 Aligned_cols=45 Identities=22% Similarity=0.156 Sum_probs=25.9
Q ss_pred cCCccEEEEe-ccc-hHHHHHHHHHhhcCCCcEEEEeccCCCCCHHHHHHHHH
Q 023087 3 RCGFGLLMYG-FGS-KKALLEDFASTALTEYSVVVINGYLQSINIKQVVITLA 53 (287)
Q Consensus 3 ~~GFnlL~YG-~GS-Kr~lL~~Fa~~~l~~~~~vvvnGy~p~~~~k~il~~i~ 53 (287)
..+.||++|| -|+ |-.+....+...+..|..+.+ .+..+++..+.
T Consensus 96 ~~~~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f------~t~~~l~~~l~ 142 (254)
T PRK06526 96 TGKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLF------ATAAQWVARLA 142 (254)
T ss_pred hcCceEEEEeCCCCchHHHHHHHHHHHHHCCCchhh------hhHHHHHHHHH
Confidence 3566788887 343 777777777666655443322 34455555554
No 52
>PF05990 DUF900: Alpha/beta hydrolase of unknown function (DUF900); InterPro: IPR010297 This domain is associated with proteins of unknown function, which are hydrolase-like.
Probab=35.89 E-value=2.1e+02 Score=25.70 Aligned_cols=89 Identities=15% Similarity=0.122 Sum_probs=45.4
Q ss_pred cEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCC-CCCCCCC-CCC-CC------CCCcHHHHHHHHhcccccCCCceE
Q 023087 32 SVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKT-PSGNLPR-AQQ-PF------NSRSMDDLFAFLDGSELKENDYFV 102 (287)
Q Consensus 32 ~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~-~~~~~~~-~~~-~~------~~~~~~~l~~~i~~~~~~~~~~~l 102 (287)
.+|.|.||+ .++.+-+...++.... ...+... .+. =|+ +.. .+ ...+-+.+.++|......+...++
T Consensus 20 vlvfVHGyn--~~f~~a~~r~aql~~~-~~~~~~~i~Fs-WPS~g~~~~Y~~d~~~a~~s~~~l~~~L~~L~~~~~~~~I 95 (233)
T PF05990_consen 20 VLVFVHGYN--NSFEDALRRAAQLAHD-LGFPGVVILFS-WPSDGSLLGYFYDRESARFSGPALARFLRDLARAPGIKRI 95 (233)
T ss_pred EEEEEeCCC--CCHHHHHHHHHHHHHH-hCCCceEEEEE-cCCCCChhhhhhhhhhHHHHHHHHHHHHHHHHhccCCceE
Confidence 356699999 7788887777654433 1111000 000 000 000 00 001223344444433234467899
Q ss_pred EEEEEcCCCcCCCChhHHHHHHHHhcC
Q 023087 103 CVVIHNIDGPGLRDSETQQHLGRIAFC 129 (287)
Q Consensus 103 ~lvIHnIDg~~LR~~~~q~~La~La~~ 129 (287)
.||-|++=+.-+ ..+|..|+..
T Consensus 96 ~ilaHSMG~rv~-----~~aL~~l~~~ 117 (233)
T PF05990_consen 96 HILAHSMGNRVL-----LEALRQLASE 117 (233)
T ss_pred EEEEeCchHHHH-----HHHHHHHHhc
Confidence 999999876555 4566666544
No 53
>PF07317 YcgR: Flagellar regulator YcgR; InterPro: IPR009926 This entry represents the N-terminal domain of YcgR proteins. The function of this domain is not known, but it is known to interact with the C-terminal which has cyclic-di-GMP bound []. YcgR is involved in the flagellar motor function and is a member of the flagellar regulon [, ].; PDB: 2GJG_A 3KYF_A.
Probab=35.74 E-value=44 Score=26.46 Aligned_cols=36 Identities=19% Similarity=0.270 Sum_probs=24.4
Q ss_pred HHhhccHHHHHHHhhhhcccceEEEeeCCCCceEEE
Q 023087 235 RFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFY 270 (287)
Q Consensus 235 ~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~ 270 (287)
+|++++...+.+.|.++.+|+-...-....|+++++
T Consensus 1 ~f~~~~p~eI~~~Lr~L~~~~~~l~v~~~~g~~f~T 36 (108)
T PF07317_consen 1 QFRLRNPREILAVLRDLAKQRSPLTVRHPRGQSFIT 36 (108)
T ss_dssp ---E-SHHHHHHHHHHHHHTT--EEEETT-SSEEEE
T ss_pred CccccCHHHHHHHHHHHHhCCCeEEEEeCCCCEEEE
Confidence 588999999999999999999877777777775443
No 54
>PF15335 CAAP1: Caspase activity and apoptosis inhibitor 1
Probab=35.63 E-value=54 Score=23.99 Aligned_cols=45 Identities=24% Similarity=0.247 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHhcCCCC---CCCCHHHHHHHHHHHHhhccHHHHHHHh
Q 023087 204 QSVFKILAEYQLSHPDE---EGMPIDTLYATSRERFLVSSQVTLNSHL 248 (287)
Q Consensus 204 r~lf~lLa~~QL~~~~~---~gv~~~~L~~~~~e~fi~sse~~lr~~L 248 (287)
+.+|+.+.+..|.++-. .|++.+++-..|.+++..=|+..+.+.|
T Consensus 17 ~Q~F~~l~~kkl~~MlPd~LK~~~l~elk~lCl~eL~~~S~krl~~Il 64 (64)
T PF15335_consen 17 RQCFSVLKEKKLQKMLPDILKGCSLEELKELCLEELEGMSEKRLLSIL 64 (64)
T ss_pred HHHHHHcCHHHHHHHCHHHHhcCCHHHHHHHHHHHHHcccHHHHHhhC
Confidence 55666666665555422 5789999999999999998888877643
No 55
>PF04337 DUF480: Protein of unknown function, DUF480; InterPro: IPR007432 This family consists of several proteins of uncharacterised function.; PDB: 3BZ6_A.
Probab=34.41 E-value=63 Score=27.53 Aligned_cols=61 Identities=25% Similarity=0.428 Sum_probs=48.0
Q ss_pred cCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHH-----HHHHhhccHHHHHHHhhhhcccceEEE
Q 023087 199 LTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATS-----RERFLVSSQVTLNSHLTEFKDHELVKT 259 (287)
Q Consensus 199 Lt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~-----~e~fi~sse~~lr~~L~EF~DH~li~~ 259 (287)
||+...++...|.+.|..-+|.-.++...|-..| |+--+--+|....+-|.++++.++|..
T Consensus 1 Ls~~E~RVLG~LiEK~~TTPd~YPLtLNaL~~aCNQKsnR~PVm~l~e~eV~~ald~L~~~~Lv~~ 66 (148)
T PF04337_consen 1 LSPVEARVLGCLIEKEVTTPDQYPLTLNALTTACNQKSNREPVMNLSESEVQAALDELRAKGLVRE 66 (148)
T ss_dssp B-HHHHHHHHHHHHHHHH-GGG-SEEHHHHHHHHT-SSS-SS-----HHHHHHHHHHHHHTTSEEE
T ss_pred CchhHhhHHHhhheecccCCCcCcchHHHHHHHhccccccCccccCCHHHHHHHHHHHHHCcCeee
Confidence 6888999999999999999988888999999988 444666789999999999999999988
No 56
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=32.57 E-value=2.6e+02 Score=23.81 Aligned_cols=69 Identities=16% Similarity=0.171 Sum_probs=54.3
Q ss_pred HHHHHHhh----cCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCC
Q 023087 191 TAAIVLQS----LTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDG 265 (287)
Q Consensus 191 g~~~VL~S----Lt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G 265 (287)
.+...|++ +|+.=+.|+..|.+. ...++-.+||+..+++.---|-.++=.-|.-|.++++|......+|
T Consensus 12 ~~~~~L~~~GlR~T~qR~~IL~~l~~~------~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~~~~~ 84 (169)
T PRK11639 12 QAEKLCAQRNVRLTPQRLEVLRLMSLQ------PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVESTNS 84 (169)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHHHhc------CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEecCCc
Confidence 44455665 688888999988764 2457899999999999876788888889999999999987654444
No 57
>PRK08116 hypothetical protein; Validated
Probab=32.55 E-value=3.9e+02 Score=24.44 Aligned_cols=100 Identities=14% Similarity=0.220 Sum_probs=53.8
Q ss_pred cEEEEe-ccc-hHHHHHHHHHhhcCCC-cEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCcH
Q 023087 7 GLLMYG-FGS-KKALLEDFASTALTEY-SVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQPFNSRSM 83 (287)
Q Consensus 7 nlL~YG-~GS-Kr~lL~~Fa~~~l~~~-~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (287)
.++||| .|+ |..|+..++...+..+ +++.++ ..+++..|.....+. .....
T Consensus 116 gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~-------~~~ll~~i~~~~~~~-------------------~~~~~ 169 (268)
T PRK08116 116 GLLLWGSVGTGKTYLAACIANELIEKGVPVIFVN-------FPQLLNRIKSTYKSS-------------------GKEDE 169 (268)
T ss_pred eEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEE-------HHHHHHHHHHHHhcc-------------------ccccH
Confidence 488888 665 7778888887766543 444444 556666555432110 00123
Q ss_pred HHHHHHHhcccccCCCceEEEEEEcCCCcCCCChhHHHHHHHHhcC---CCeEEEEeecCC
Q 023087 84 DDLFAFLDGSELKENDYFVCVVIHNIDGPGLRDSETQQHLGRIAFC---SHIRMIASIDHV 141 (287)
Q Consensus 84 ~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~LR~~~~q~~La~La~~---~~I~lIaSiDhi 141 (287)
.++++.+.. .+ +|||-++..... ++..|..|-.+... ..-.+|.|.+..
T Consensus 170 ~~~~~~l~~-------~d-lLviDDlg~e~~-t~~~~~~l~~iin~r~~~~~~~IiTsN~~ 221 (268)
T PRK08116 170 NEIIRSLVN-------AD-LLILDDLGAERD-TEWAREKVYNIIDSRYRKGLPTIVTTNLS 221 (268)
T ss_pred HHHHHHhcC-------CC-EEEEecccCCCC-CHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence 345555432 23 688888865544 44556666555432 223455555543
No 58
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=32.30 E-value=35 Score=29.16 Aligned_cols=41 Identities=22% Similarity=0.350 Sum_probs=26.1
Q ss_pred CccCCccEEEE-----------eccchHHHHHHHHHhhcCC--C-cEEEEeccCC
Q 023087 1 MLRCGFGLLMY-----------GFGSKKALLEDFASTALTE--Y-SVVVINGYLQ 41 (287)
Q Consensus 1 ~L~~GFnlL~Y-----------G~GSKr~lL~~Fa~~~l~~--~-~~vvvnGy~p 41 (287)
||--||||++- .+..-|..|-+....|..- + .+||+|||..
T Consensus 1 LlIDGYNli~~~~~l~~~~~~~~l~~aR~~Li~~L~~y~~~~~~~v~VVFDa~~~ 55 (166)
T PF05991_consen 1 LLIDGYNLIHAWPELRSLAERGDLEAARERLIEMLSEYAQFSGYEVIVVFDAYKV 55 (166)
T ss_pred CeEcchhhhCCCHHHHhhcCcCCHHHHHHHHHHHHHHHhcccCCEEEEEEeCCcC
Confidence 46679999877 2233565555555555432 2 3789999874
No 59
>PF08157 NUC129: NUC129 domain; InterPro: IPR012579 This C-terminal domain is found in a novel family of hypothetical nucleolar proteins [].; GO: 0005634 nucleus
Probab=31.97 E-value=18 Score=26.24 Aligned_cols=17 Identities=35% Similarity=0.710 Sum_probs=15.5
Q ss_pred EEEeccchHHHHHHHHH
Q 023087 9 LMYGFGSKKALLEDFAS 25 (287)
Q Consensus 9 L~YG~GSKr~lL~~Fa~ 25 (287)
++||-||.|.-.|+|..
T Consensus 26 ~LYGpgsnRTT~N~flS 42 (63)
T PF08157_consen 26 RLYGPGSNRTTVNEFLS 42 (63)
T ss_pred hccCCCCCcccHHHHhh
Confidence 58999999999999984
No 60
>PF12138 Spherulin4: Spherulation-specific family 4; InterPro: IPR021986 This protein is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 250 and 398 amino acids in length. There is a conserved NPG sequence motif and there are two completely conserved G residues that may be functionally important. Starvation will often induce spherulation - the production of spores - and this process may involve DNA-methylation. Changes in the methylation of spherulin4 are associated with the formation of spherules, but these changes are probably transient. Methylation of the gene accompanies its transcriptional activation, and spherulin4 mRNA is only detectable in late spherulating cultures and mature spherules. It is a spherulation-specific protein.
Probab=30.57 E-value=1.9e+02 Score=26.63 Aligned_cols=179 Identities=16% Similarity=0.211 Sum_probs=102.2
Q ss_pred HHHHHHHHhcccccCCCceEEEEEEcCCCcCC-----CChhHHHHHHHHhcCCCeEEEEeecCCCCccccCccccccccc
Q 023087 83 MDDLFAFLDGSELKENDYFVCVVIHNIDGPGL-----RDSETQQHLGRIAFCSHIRMIASIDHVNAPLLWDKKMVHTQFN 157 (287)
Q Consensus 83 ~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~L-----R~~~~q~~La~La~~~~I~lIaSiDhinaplLWd~~~~~~~fn 157 (287)
.+.+.+.+.. .+..+.++||+==+||+- -++..+..+.+|.+.+++++|+.|+.=... +...
T Consensus 18 W~~l~~a~~~----~p~~~f~vIiNP~sGPG~~~~~~pd~~Y~~~i~~L~~~~nv~vlGYV~T~Yg~---------R~~~ 84 (253)
T PF12138_consen 18 WDPLYDAIAA----HPSVPFTVIINPNSGPGSAPDPWPDANYAAAIPRLNSYANVRVLGYVHTSYGS---------RPLS 84 (253)
T ss_pred hHHHHHHHhc----CCCCcEEEEEcCCCCCCCCCCCCCCHHHHHHHHHHHhcCCCcEEEEEEccccC---------CCHH
Confidence 4667666654 255668888888889983 467899999999999999999999886642 3333
Q ss_pred EEEEeCCCCCCcccc---------cccchhhhhcCCccchhhHHHHHHhhcCHhHHHHHHHHHHHHhcCCCCCCC--CHH
Q 023087 158 WHWYHVPTFAPYKVE---------GMFFPLILAHGSSAQTAKTAAIVLQSLTPNAQSVFKILAEYQLSHPDEEGM--PID 226 (287)
Q Consensus 158 f~~~d~tT~~pY~~E---------~~~~~~l~~~~~~~~~~~g~~~VL~SLt~nar~lf~lLa~~QL~~~~~~gv--~~~ 226 (287)
=+.-|++||..+..+ -.|.+.. .+.....--+++|+...|+.+..-...-.- -..|. +-.
T Consensus 85 ~V~~dI~~Y~~W~~~~~~~~~~vdGIFfDE~-------p~~~~~~~y~~~l~~~vk~~~~~~~~~~VV--~NPGt~~p~~ 155 (253)
T PF12138_consen 85 EVKADIDTYASWYGQSEDYGYRVDGIFFDEA-------PNDYANLPYYQNLYNYVKSAFGLGGDGLVV--LNPGTAVPDP 155 (253)
T ss_pred HHHHHHHHHhhccccccCCCcccceEEEecC-------CCcHHHHHHHHHHHHHHHhccccCCCCEEE--eCCCCCCCcc
Confidence 344556666555432 2233321 111122334555555555443300000000 02454 335
Q ss_pred HHHHHHHHHHhhccHHHHHHHhhhhcccceEEEe---eCCCCceEEEEeC----CHHHHHHHHHHh
Q 023087 227 TLYATSRERFLVSSQVTLNSHLTEFKDHELVKTR---RHSDGQDCFYIPL----ASEALEKLLSEI 285 (287)
Q Consensus 227 ~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~---k~~~G~e~l~Ip~----~~~~l~~iLe~l 285 (287)
.+++. -+.+|.-|....+....+..+.+=... +.....-+..+|= +.++++.+...+
T Consensus 156 ~y~~~--aD~~V~fE~~~~~y~~~~~~~~~~~~~~~~~~k~~~ivh~vP~~~g~~~~~~~~l~~~~ 219 (253)
T PF12138_consen 156 GYASI--ADVVVVFENSYADYRNSYVPENLAWTAPYPRSKFAHIVHSVPDSLGTSASELEALVKAV 219 (253)
T ss_pred hhhcc--cCEEEEEeccHHHhhhhhcccccccccCCChHHEEEEEecCCCcccccHHHHHHHHHHH
Confidence 55554 567788888888887777776432111 1112234445562 577888877654
No 61
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=30.31 E-value=78 Score=22.38 Aligned_cols=32 Identities=16% Similarity=0.219 Sum_probs=23.4
Q ss_pred hcCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHH
Q 023087 198 SLTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRE 234 (287)
Q Consensus 198 SLt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e 234 (287)
+||++...++..|+.+ ...-++.++|.+.+-.
T Consensus 5 ~Lt~~e~~lL~~L~~~-----~~~~vs~~~l~~~lw~ 36 (78)
T smart00862 5 KLTPKEFRLLELLLRN-----PGRVVSREELLEAVWG 36 (78)
T ss_pred ecCHHHHHHHHHHHhC-----CCCccCHHHHHHHHcC
Confidence 4789999999999877 2335778888776543
No 62
>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H.
Probab=29.45 E-value=87 Score=25.24 Aligned_cols=42 Identities=31% Similarity=0.287 Sum_probs=29.2
Q ss_pred eEEEEEEcCCCcCCCChhHHHHHHHHhc---CCCeEEEEeecCCCCcc
Q 023087 101 FVCVVIHNIDGPGLRDSETQQHLGRIAF---CSHIRMIASIDHVNAPL 145 (287)
Q Consensus 101 ~l~lvIHnIDg~~LR~~~~q~~La~La~---~~~I~lIaSiDhinapl 145 (287)
.-+|+|.|||. | ++..|..|..... ..++++|+|.++--..+
T Consensus 70 ~gtL~l~~i~~--L-~~~~Q~~L~~~l~~~~~~~~RlI~ss~~~l~~l 114 (138)
T PF14532_consen 70 GGTLYLKNIDR--L-SPEAQRRLLDLLKRQERSNVRLIASSSQDLEEL 114 (138)
T ss_dssp TSEEEEECGCC--S--HHHHHHHHHHHHHCTTTTSEEEEEECC-CCCH
T ss_pred CCEEEECChHH--C-CHHHHHHHHHHHHhcCCCCeEEEEEeCCCHHHH
Confidence 45688999998 4 4566777776643 36899999988765443
No 63
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=28.88 E-value=48 Score=28.27 Aligned_cols=46 Identities=11% Similarity=0.163 Sum_probs=33.7
Q ss_pred hcCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHh
Q 023087 198 SLTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHL 248 (287)
Q Consensus 198 SLt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L 248 (287)
.||++..+|+++|++. ...+++.++++++.-..-+..++.++++++
T Consensus 154 ~Lt~~E~~ll~~l~~~-----~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i 199 (229)
T PRK10161 154 EMGPTEFKLLHFFMTH-----PERVYSREQLLNHVWGTNVYVEDRTVDVHI 199 (229)
T ss_pred EcCHHHHHHHHHHHhC-----CCceEcHHHHHHHhcCCCCCCCCCCHHHHH
Confidence 5999999999999887 357889999988886544444555554444
No 64
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=28.67 E-value=1.6e+02 Score=23.34 Aligned_cols=61 Identities=15% Similarity=0.180 Sum_probs=41.3
Q ss_pred CCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEeCCHHHHHHHHHHh
Q 023087 220 EEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIPLASEALEKLLSEI 285 (287)
Q Consensus 220 ~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip~~~~~l~~iLe~l 285 (287)
..+++.++| |. -+--+...++..|..+.+.++|.+.++.+|.=.+.-|...-.+.+|++-+
T Consensus 23 ~~~~s~~ei---a~--~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy~l~~~~~~itl~~I~~~~ 83 (132)
T TIGR00738 23 EGPVSVKEI---AE--RQGISRSYLEKILRTLRRAGLVESVRGPGGGYRLARPPEEITVGDVVRAV 83 (132)
T ss_pred CCcCcHHHH---HH--HHCcCHHHHHHHHHHHHHCCcEEeccCCCCCccCCCCHHHCCHHHHHHHH
Confidence 346777776 22 35668999999999999999999877766643344444443455665544
No 65
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=28.46 E-value=6.2e+02 Score=27.73 Aligned_cols=117 Identities=15% Similarity=0.173 Sum_probs=62.5
Q ss_pred eccchHHHHHHHHHhhcCCCcEEE-EeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCC-CCCCCCCcHHHHHHH
Q 023087 12 GFGSKKALLEDFASTALTEYSVVV-INGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRA-QQPFNSRSMDDLFAF 89 (287)
Q Consensus 12 G~GSKr~lL~~Fa~~~l~~~~~vv-vnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~ 89 (287)
||| |..++-+|++ ...++.-|. .+-=..+-..--.+..+.+++-...... |..... .+.-...+++.+++.
T Consensus 47 GfG-Kttl~aq~~~-~~~~~~~v~Wlslde~dndp~rF~~yLi~al~~~~p~~-----~~~a~~l~q~~~~~~l~~l~~~ 119 (894)
T COG2909 47 GFG-KTTLLAQWRE-LAADGAAVAWLSLDESDNDPARFLSYLIAALQQATPTL-----GDEAQTLLQKHQYVSLESLLSS 119 (894)
T ss_pred CCc-HHHHHHHHHH-hcCcccceeEeecCCccCCHHHHHHHHHHHHHHhCccc-----cHHHHHHHHhcccccHHHHHHH
Confidence 677 9999999998 555554333 2222233444444555555543211100 000000 000011234445544
Q ss_pred HhcccccCCCceEEEEEEcCCCcCCCChhHHHHHHHHh--cCCCeEEEEee
Q 023087 90 LDGSELKENDYFVCVVIHNIDGPGLRDSETQQHLGRIA--FCSHIRMIASI 138 (287)
Q Consensus 90 i~~~~~~~~~~~l~lvIHnIDg~~LR~~~~q~~La~La--~~~~I~lIaSi 138 (287)
+-... .+...|+|||+- |-.-.+++..+++|-.|- +.||+++|.+.
T Consensus 120 L~~El-a~~~~pl~LVlD--DyHli~~~~l~~~l~fLl~~~P~~l~lvv~S 167 (894)
T COG2909 120 LLNEL-ASYEGPLYLVLD--DYHLISDPALHEALRFLLKHAPENLTLVVTS 167 (894)
T ss_pred HHHHH-HhhcCceEEEec--cccccCcccHHHHHHHHHHhCCCCeEEEEEe
Confidence 43211 124567999985 334567788899999995 68899999875
No 66
>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A ....
Probab=27.82 E-value=3.6e+02 Score=22.51 Aligned_cols=26 Identities=42% Similarity=0.473 Sum_probs=20.1
Q ss_pred CccEEEEec-cc-hHHHHHHHHHhhcCC
Q 023087 5 GFGLLMYGF-GS-KKALLEDFASTALTE 30 (287)
Q Consensus 5 GFnlL~YG~-GS-Kr~lL~~Fa~~~l~~ 30 (287)
...+||||- |+ |..+...|+...+.+
T Consensus 19 ~ha~L~~G~~g~gk~~~a~~~a~~ll~~ 46 (162)
T PF13177_consen 19 PHALLFHGPSGSGKKTLALAFARALLCS 46 (162)
T ss_dssp -SEEEEECSTTSSHHHHHHHHHHHHC-T
T ss_pred ceeEEEECCCCCCHHHHHHHHHHHHcCC
Confidence 356899995 66 999999999987754
No 67
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=27.80 E-value=2.7e+02 Score=21.82 Aligned_cols=69 Identities=16% Similarity=0.254 Sum_probs=47.8
Q ss_pred cCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEe-CCHHH
Q 023087 199 LTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIP-LASEA 277 (287)
Q Consensus 199 Lt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip-~~~~~ 277 (287)
||+....|-++|=+. ++++-+++.+.+.++ -=-+..+.++.|.-+.+=++|..++. |.-+++-| .++++
T Consensus 1 Ls~~E~~IM~~lW~~-------~~~t~~eI~~~l~~~-~~~~~sTv~t~L~rL~~Kg~l~~~~~--gr~~~Y~p~is~~e 70 (115)
T PF03965_consen 1 LSDLELEIMEILWES-------GEATVREIHEALPEE-RSWAYSTVQTLLNRLVEKGFLTREKI--GRAYVYSPLISREE 70 (115)
T ss_dssp --HHHHHHHHHHHHH-------SSEEHHHHHHHHCTT-SS--HHHHHHHHHHHHHTTSEEEEEE--TTCEEEEESSSHHH
T ss_pred CCHHHHHHHHHHHhC-------CCCCHHHHHHHHHhc-cccchhHHHHHHHHHHhCCceeEeec--CCceEEEeCCcHHH
Confidence 455666666666554 337899999988886 22278999999999999999988764 55555555 46555
No 68
>PF12048 DUF3530: Protein of unknown function (DUF3530); InterPro: IPR022529 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 272 to 336 amino acids in length. These proteins are distantly related to alpa/beta hydrolases so they may act as enzymes.
Probab=27.65 E-value=1.4e+02 Score=28.06 Aligned_cols=50 Identities=18% Similarity=0.297 Sum_probs=38.7
Q ss_pred CCccEEEEeccchHHHHHHHHHhhcCC--CcEEEEeccCCCCCH-HHHHHHHH
Q 023087 4 CGFGLLMYGFGSKKALLEDFASTALTE--YSVVVINGYLQSINI-KQVVITLA 53 (287)
Q Consensus 4 ~GFnlL~YG~GSKr~lL~~Fa~~~l~~--~~~vvvnGy~p~~~~-k~il~~i~ 53 (287)
.|+|+++.|.|+=-..+.++..+.-.. ...|+||.|.|.-.. +++-..+.
T Consensus 191 ~~~~ivlIg~G~gA~~~~~~la~~~~~~~daLV~I~a~~p~~~~n~~l~~~la 243 (310)
T PF12048_consen 191 GGKNIVLIGHGTGAGWAARYLAEKPPPMPDALVLINAYWPQPDRNPALAEQLA 243 (310)
T ss_pred CCceEEEEEeChhHHHHHHHHhcCCCcccCeEEEEeCCCCcchhhhhHHHHhh
Confidence 578899999999999998888665432 246889999999988 66555444
No 69
>PRK08939 primosomal protein DnaI; Reviewed
Probab=27.32 E-value=5.3e+02 Score=24.23 Aligned_cols=25 Identities=16% Similarity=0.282 Sum_probs=14.9
Q ss_pred EEEEEEcCCCcCCCChhHHHHHHHH
Q 023087 102 VCVVIHNIDGPGLRDSETQQHLGRI 126 (287)
Q Consensus 102 l~lvIHnIDg~~LR~~~~q~~La~L 126 (287)
=+|||-.|...++-.-....+|..+
T Consensus 219 dlLiIDDiG~e~~s~~~~~~ll~~I 243 (306)
T PRK08939 219 PVLMLDDIGAEQMSSWVRDEVLGVI 243 (306)
T ss_pred CEEEEecCCCccccHHHHHHHHHHH
Confidence 3678888888776333222455544
No 70
>TIGR01738 bioH putative pimeloyl-BioC--CoA transferase BioH. This CoA-binding enzyme is required for the production of pimeloyl-coenzyme A, the substrate of the BioF protein early in the biosynthesis of biotin. Its exact function is unknown, but is proposed in ref 2. This enzyme belongs to the alpha/beta hydrolase fold family (pfam model pfam00561). Members of this family are restricted to the Proteobacteria.
Probab=26.77 E-value=70 Score=26.65 Aligned_cols=29 Identities=10% Similarity=0.388 Sum_probs=18.5
Q ss_pred EEEEeccchHHHHHHHHHhhcCCCcEEEE
Q 023087 8 LLMYGFGSKKALLEDFASTALTEYSVVVI 36 (287)
Q Consensus 8 lL~YG~GSKr~lL~~Fa~~~l~~~~~vvv 36 (287)
|+++|+|+.......+++.....+.|+.+
T Consensus 8 v~~HG~~~~~~~~~~~~~~l~~~~~vi~~ 36 (245)
T TIGR01738 8 VLIHGWGMNAEVFRCLDEELSAHFTLHLV 36 (245)
T ss_pred EEEcCCCCchhhHHHHHHhhccCeEEEEe
Confidence 57788888777777776554444444444
No 71
>TIGR03695 menH_SHCHC 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase. This protein catalyzes the formation of SHCHC, or (1 R,6 R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate, by elmination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC). Note that SHCHC synthase activity previously was attributed to MenD, which in fact is SEPHCHC synthase.
Probab=26.53 E-value=2.5e+02 Score=23.07 Aligned_cols=30 Identities=13% Similarity=0.225 Sum_probs=20.4
Q ss_pred EEEEeccchHHHHHHHHHhhcCCCcEEEEe
Q 023087 8 LLMYGFGSKKALLEDFASTALTEYSVVVIN 37 (287)
Q Consensus 8 lL~YG~GSKr~lL~~Fa~~~l~~~~~vvvn 37 (287)
|+++|.|.-......++...-..+.|+.+|
T Consensus 5 v~~hG~~~~~~~~~~~~~~L~~~~~v~~~d 34 (251)
T TIGR03695 5 VFLHGFLGSGADWQALIELLGPHFRCLAID 34 (251)
T ss_pred EEEcCCCCchhhHHHHHHHhcccCeEEEEc
Confidence 577888877777777775544455666666
No 72
>PF00248 Aldo_ket_red: Aldo/keto reductase family; InterPro: IPR023210 The aldo-keto reductase family includes a number of related monomeric NADPH-dependent oxidoreductases, such as aldehyde reductase, aldose reductase, prostaglandin F synthase, xylose reductase, rho crystallin, and many others []. All possess a similar structure, with a beta-alpha-beta fold characteristic of nucleotide binding proteins []. The fold comprises a parallel beta-8/alpha-8-barrel, which contains a novel NADP-binding motif. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the beta sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones []. Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases []. Some proteins of this entry contain a K+ ion channel beta chain regulatory domain; these are reported to have oxidoreductase activity []. This entry represents the NADP-dependent oxidoreductase domain found in these proteins.; PDB: 1C9W_A 4F40_B 1VBJ_A 1XGD_A 1X97_A 2ACS_A 1EF3_A 2ACU_A 1PWM_A 2NVD_A ....
Probab=26.45 E-value=4.2e+02 Score=23.61 Aligned_cols=42 Identities=17% Similarity=0.032 Sum_probs=32.4
Q ss_pred CceEEEEEEcCCCcCCCChhHHHHHHHHhcCCCeEEEEeecCC
Q 023087 99 DYFVCVVIHNIDGPGLRDSETQQHLGRIAFCSHIRMIASIDHV 141 (287)
Q Consensus 99 ~~~l~lvIHnIDg~~LR~~~~q~~La~La~~~~I~lIaSiDhi 141 (287)
...++ .+|+.|...-+..+....|.+|-.--.|+-|+--.|-
T Consensus 99 ~iDl~-~lH~~~~~~~~~~~~~~~l~~l~~~G~ir~iGvs~~~ 140 (283)
T PF00248_consen 99 YIDLL-LLHWPDPSEDALEEVWEALEELKKEGKIRHIGVSNFS 140 (283)
T ss_dssp SEEEE-EESSSSTTSSHHHHHHHHHHHHHHTTSEEEEEEES--
T ss_pred chhcc-ccccccccccccchhhhhhhhcccccccccccccccc
Confidence 33444 4699998888788888999999999999999876554
No 73
>COG1166 SpeA Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism]
Probab=25.95 E-value=58 Score=33.63 Aligned_cols=28 Identities=36% Similarity=0.488 Sum_probs=22.6
Q ss_pred ccchHHHHHHHHHhhcCCCcEEEEeccCC
Q 023087 13 FGSKKALLEDFASTALTEYSVVVINGYLQ 41 (287)
Q Consensus 13 ~GSKr~lL~~Fa~~~l~~~~~vvvnGy~p 41 (287)
-|||-+|+--.|... ..++.+|+|||..
T Consensus 145 AGSK~ELm~vLA~~~-~~~~~IvCNGyKD 172 (652)
T COG1166 145 AGSKAELMAVLAHAG-NPGSLIVCNGYKD 172 (652)
T ss_pred CCCHHHHHHHHHhcC-CCCCeEEecCccc
Confidence 499999998888432 5678999999984
No 74
>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]
Probab=25.67 E-value=4.9e+02 Score=25.99 Aligned_cols=115 Identities=17% Similarity=0.171 Sum_probs=60.9
Q ss_pred cEEEEeccc--hHHHHHHHHHhh-cCCCcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCcH
Q 023087 7 GLLMYGFGS--KKALLEDFASTA-LTEYSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQPFNSRSM 83 (287)
Q Consensus 7 nlL~YG~GS--Kr~lL~~Fa~~~-l~~~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (287)
++.+||.-+ |..+++++.+.. +..-.+-.+..| |.+..+..|...+... ++.+. +.......+
T Consensus 32 ~~~iyG~sgTGKT~~~r~~l~~~n~~~vw~n~~ecf----t~~~lle~IL~~~~~~---------d~dg~-~~~~~~en~ 97 (438)
T KOG2543|consen 32 IVHIYGHSGTGKTYLVRQLLRKLNLENVWLNCVECF----TYAILLEKILNKSQLA---------DKDGD-KVEGDAENF 97 (438)
T ss_pred eEEEeccCCCchhHHHHHHHhhcCCcceeeehHHhc----cHHHHHHHHHHHhccC---------CCchh-hhhhHHHHH
Confidence 357888754 888888888654 111112334454 4677777776554210 01100 000011122
Q ss_pred HHHHHHHhccc-ccCCCceEEEEEEcCCCcCCCChhH--HHH---HHHHhcCCCeEEEEe
Q 023087 84 DDLFAFLDGSE-LKENDYFVCVVIHNIDGPGLRDSET--QQH---LGRIAFCSHIRMIAS 137 (287)
Q Consensus 84 ~~l~~~i~~~~-~~~~~~~l~lvIHnIDg~~LR~~~~--q~~---La~La~~~~I~lIaS 137 (287)
-+.+..+.+.. ....+..+|||+.|+|. +|+-.+ -.. |-+|+..|.|.+|-|
T Consensus 98 ~d~i~~l~q~~~~t~~d~~~~liLDnad~--lrD~~a~ll~~l~~L~el~~~~~i~iils 155 (438)
T KOG2543|consen 98 SDFIYLLVQWPAATNRDQKVFLILDNADA--LRDMDAILLQCLFRLYELLNEPTIVIILS 155 (438)
T ss_pred HHHHHHHHhhHHhhccCceEEEEEcCHHh--hhccchHHHHHHHHHHHHhCCCceEEEEe
Confidence 33444444311 12236799999999998 665322 222 345678888888866
No 75
>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....
Probab=24.79 E-value=3.2e+02 Score=20.80 Aligned_cols=102 Identities=19% Similarity=0.201 Sum_probs=59.2
Q ss_pred EEEEec--cchHHHHHHHHHhhcCCCcEEEEeccCCC-CCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCcHH
Q 023087 8 LLMYGF--GSKKALLEDFASTALTEYSVVVINGYLQS-INIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQPFNSRSMD 84 (287)
Q Consensus 8 lL~YG~--GSKr~lL~~Fa~~~l~~~~~vvvnGy~p~-~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (287)
||+||- =-|..+.+.+++.. +.+++.+++..-. ....+. ...+.
T Consensus 1 ill~G~~G~GKT~l~~~la~~l--~~~~~~i~~~~~~~~~~~~~-------------------------------~~~i~ 47 (132)
T PF00004_consen 1 ILLHGPPGTGKTTLARALAQYL--GFPFIEIDGSELISSYAGDS-------------------------------EQKIR 47 (132)
T ss_dssp EEEESSTTSSHHHHHHHHHHHT--TSEEEEEETTHHHTSSTTHH-------------------------------HHHHH
T ss_pred CEEECcCCCCeeHHHHHHHhhc--cccccccccccccccccccc-------------------------------ccccc
Confidence 578886 45889999988764 4567888887611 100110 11223
Q ss_pred HHHHHHhcccccCCCceEEEEEEcCCCcCCCC---------hhHHHHHHHHhcCC----CeEEEEeecC---CCCcccc
Q 023087 85 DLFAFLDGSELKENDYFVCVVIHNIDGPGLRD---------SETQQHLGRIAFCS----HIRMIASIDH---VNAPLLW 147 (287)
Q Consensus 85 ~l~~~i~~~~~~~~~~~l~lvIHnIDg~~LR~---------~~~q~~La~La~~~----~I~lIaSiDh---inaplLW 147 (287)
++++.... ...|.+|+|-++|.-.-.. .-.+.++..+.... ++-+|++... +..++++
T Consensus 48 ~~~~~~~~-----~~~~~vl~iDe~d~l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~~i~~~l~~ 121 (132)
T PF00004_consen 48 DFFKKAKK-----SAKPCVLFIDEIDKLFPKSQPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPDKIDPALLR 121 (132)
T ss_dssp HHHHHHHH-----TSTSEEEEEETGGGTSHHCSTSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGGGSCHHHHS
T ss_pred cccccccc-----cccceeeeeccchhcccccccccccccccccceeeecccccccccccceeEEeeCChhhCCHhHHh
Confidence 33333332 1147999999999765443 12455555555444 4899998766 3444443
No 76
>PLN03219 uncharacterized protein; Provisional
Probab=24.65 E-value=1.3e+02 Score=24.30 Aligned_cols=16 Identities=25% Similarity=0.476 Sum_probs=14.3
Q ss_pred EEEeCCHHHHHHHHHH
Q 023087 269 FYIPLASEALEKLLSE 284 (287)
Q Consensus 269 l~Ip~~~~~l~~iLe~ 284 (287)
|.||-+.+..+.+|..
T Consensus 89 L~IPCd~~~F~~ll~~ 104 (108)
T PLN03219 89 LTIPCREESFLHLITS 104 (108)
T ss_pred EEEeCCHHHHHHHHHh
Confidence 8999999999999875
No 77
>PRK12423 LexA repressor; Provisional
Probab=24.39 E-value=2.5e+02 Score=24.46 Aligned_cols=60 Identities=13% Similarity=0.248 Sum_probs=45.6
Q ss_pred hhcCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeC
Q 023087 197 QSLTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRH 262 (287)
Q Consensus 197 ~SLt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~ 262 (287)
+.||++.|.++..|.++..+..- .-+.++|-+ .|=+.|..+.+.+|..+..=++|....+
T Consensus 2 ~~lt~~q~~il~~l~~~i~~~g~--~Ps~~eia~----~~g~~s~~~v~~~l~~L~~~G~l~~~~~ 61 (202)
T PRK12423 2 DTLTPKRAAILAFIRERIAQAGQ--PPSLAEIAQ----AFGFASRSVARKHVQALAEAGLIEVVPN 61 (202)
T ss_pred CcCCHHHHHHHHHHHHHHHHcCC--CCCHHHHHH----HhCCCChHHHHHHHHHHHHCCCEEecCC
Confidence 34899999999999988766521 125666643 4555799999999999999999987654
No 78
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.
Probab=24.09 E-value=64 Score=26.98 Aligned_cols=49 Identities=16% Similarity=0.217 Sum_probs=34.8
Q ss_pred hcCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhh
Q 023087 198 SLTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEF 251 (287)
Q Consensus 198 SLt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF 251 (287)
.||++.++|+.+|++. ...|++.++++++.-.+=+-.|+.++++++...
T Consensus 154 ~Lt~~E~~il~~l~~~-----~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l 202 (226)
T TIGR02154 154 SLGPTEFRLLHFFMTH-----PERVYSREQLLDRVWGRDVYVEERTVDVHIRRL 202 (226)
T ss_pred EcCHHHHHHHHHHHhC-----CCceEcHHHHHHHhcCCCCCCCCccHHHHHHHH
Confidence 5999999999999984 356788889988775543444555555555443
No 79
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=23.05 E-value=1.8e+02 Score=20.03 Aligned_cols=58 Identities=24% Similarity=0.297 Sum_probs=35.2
Q ss_pred cCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCC-CCce
Q 023087 199 LTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHS-DGQD 267 (287)
Q Consensus 199 Lt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~-~G~e 267 (287)
||+++-.+...|. ....+++..+|-+ .+--+..++...++++.++++|...+++ |+.+
T Consensus 1 lt~~q~~vL~~l~------~~~~~~t~~~l~~-----~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~ 59 (68)
T PF13463_consen 1 LTRPQWQVLRALA------HSDGPMTQSDLAE-----RLGISKSTVSRIIKKLEEKGLVEKERDPHDKRS 59 (68)
T ss_dssp --HHHHHHHHHHT--------TS-BEHHHHHH-----HTT--HHHHHHHHHHHHHTTSEEEEEESSCTTS
T ss_pred CCHHHHHHHHHHH------ccCCCcCHHHHHH-----HHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCe
Confidence 4555555555554 1234566666532 3445788888999999999999887765 5543
No 80
>COG0623 FabI Enoyl-[acyl-carrier-protein]
Probab=22.68 E-value=2.5e+02 Score=26.02 Aligned_cols=93 Identities=19% Similarity=0.128 Sum_probs=59.3
Q ss_pred CccCCccEEEEeccchHHHHHHHHHhhcCCCcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCC
Q 023087 1 MLRCGFGLLMYGFGSKKALLEDFASTALTEYSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQPFNS 80 (287)
Q Consensus 1 ~L~~GFnlL~YG~GSKr~lL~~Fa~~~l~~~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 80 (287)
++.+|=..|+-|+.++|.+-=--|+.+...|.-+++-...+ .++.=+..+++.+-... .-.......
T Consensus 2 g~L~GK~~lI~Gvan~rSIAwGIAk~l~~~GAeL~fTy~~e--~l~krv~~la~~~~s~~-----------v~~cDV~~d 68 (259)
T COG0623 2 GLLEGKRILIMGVANNRSIAWGIAKALAEQGAELAFTYQGE--RLEKRVEELAEELGSDL-----------VLPCDVTND 68 (259)
T ss_pred CccCCceEEEEEecccccHHHHHHHHHHHcCCEEEEEeccH--HHHHHHHHHHhhccCCe-----------EEecCCCCH
Confidence 35689999999999999998888877777777777655544 45444445544331100 000111233
Q ss_pred CcHHHHHHHHhcccccCCCceEEEEEEcCCC
Q 023087 81 RSMDDLFAFLDGSELKENDYFVCVVIHNIDG 111 (287)
Q Consensus 81 ~~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg 111 (287)
.+++.+.+.+.+ .-.++=.++|+|-.
T Consensus 69 ~~i~~~f~~i~~-----~~g~lD~lVHsIaF 94 (259)
T COG0623 69 ESIDALFATIKK-----KWGKLDGLVHSIAF 94 (259)
T ss_pred HHHHHHHHHHHH-----hhCcccEEEEEecc
Confidence 467777888775 34578889998854
No 81
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=22.59 E-value=1.7e+02 Score=27.95 Aligned_cols=64 Identities=17% Similarity=0.266 Sum_probs=50.0
Q ss_pred hhcCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCC
Q 023087 197 QSLTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDG 265 (287)
Q Consensus 197 ~SLt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G 265 (287)
+.|+++++.|++.+.+..++.. ..|.-++|- ....+--|..+.|.-|.++-+-+++....+..|
T Consensus 2 ~~l~~R~~~Il~~IV~~yi~~~--~pv~s~~l~---~~~~l~~S~aTIR~dm~~Le~~G~l~~~h~sag 65 (339)
T PRK00082 2 SMLDERQREILRAIVEDYIATG--EPVGSKTLS---KRYGLGVSSATIRNDMADLEELGLLEKPHTSSG 65 (339)
T ss_pred CccCHHHHHHHHHHHHHHHhcC--CCcCHHHHH---HHhCCCCChHHHHHHHHHHHhCCCcCCCcCCCC
Confidence 3589999999999999988875 345666663 334456679999999999999999987666555
No 82
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=22.28 E-value=2.3e+02 Score=19.09 Aligned_cols=55 Identities=25% Similarity=0.296 Sum_probs=39.8
Q ss_pred cCHhHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCC
Q 023087 199 LTPNAQSVFKILAEYQLSHPDEEGMPIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHS 263 (287)
Q Consensus 199 Lt~nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~ 263 (287)
||+.+-.++..|... +..++...+|-+. +--+..++...++.+..-++|...++.
T Consensus 3 lt~~q~~vL~~l~~~-----~~~~~t~~~la~~-----l~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 3 LTPSQFRVLMALARH-----PGEELTQSELAER-----LGISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp STHHHHHHHHHHHHS-----TTSGEEHHHHHHH-----HTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred cCHHHHHHHHHHHHC-----CCCCcCHHHHHHH-----HCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 677777777777665 2234777777433 455889999999999999999988764
No 83
>PLN02771 carbamoyl-phosphate synthase (glutamine-hydrolyzing)
Probab=21.89 E-value=1.6e+02 Score=29.23 Aligned_cols=21 Identities=33% Similarity=0.673 Sum_probs=19.5
Q ss_pred ccEEEEeccchHHHHHHHHHh
Q 023087 6 FGLLMYGFGSKKALLEDFAST 26 (287)
Q Consensus 6 FnlL~YG~GSKr~lL~~Fa~~ 26 (287)
+.|+.|++|.|+++++.+.+.
T Consensus 241 ~~IvviD~G~K~nIlr~L~~~ 261 (415)
T PLN02771 241 YHVIAYDFGIKHNILRRLASY 261 (415)
T ss_pred CEEEEECCChHHHHHHHHHHc
Confidence 789999999999999999964
No 84
>COG0616 SppA Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=21.88 E-value=1.7e+02 Score=27.78 Aligned_cols=61 Identities=16% Similarity=0.155 Sum_probs=47.2
Q ss_pred cHHHHHHHHhcccccCCCceEEEEEEcCCCcCCCChhHHHHHHHHhcCCCeEEEEeecCCCCc
Q 023087 82 SMDDLFAFLDGSELKENDYFVCVVIHNIDGPGLRDSETQQHLGRIAFCSHIRMIASIDHVNAP 144 (287)
Q Consensus 82 ~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~LR~~~~q~~La~La~~~~I~lIaSiDhinap 144 (287)
..++..+.++....++....+.|.||+==|..+-.....+.|..|..-. -++++|+|+.+.
T Consensus 81 ~~~~~~~~l~~~~~~~~vk~vvL~inSPGG~v~as~~i~~~l~~l~~~~--PV~v~v~~~AAS 141 (317)
T COG0616 81 GGDDIEEILRAARADPSVKAVVLRINSPGGSVVASELIARALKRLRAKK--PVVVSVGGYAAS 141 (317)
T ss_pred cHHHHHHHHHHHhcCCCCceEEEEEECcCCchhHHHHHHHHHHHHhhcC--CEEEEECCeecc
Confidence 3566666666655567788999999998888887777777777777665 799999999873
No 85
>TIGR00762 DegV EDD domain protein, DegV family. This family of proteins is related to DegV of Bacillus subtilis and includes paralogous sets in several species (B. subtilis, Deinococcus radiodurans, Mycoplasma pneumoniae) that are closer in percent identity to each than to most homologs from other species. This suggests both recent paralogy and diversity of function. DegV itself is encoded immediately downstream of DegU, a transcriptional regulator of degradation, but is itself uncharacterized. Crystallography suggested a lipid-binding site, while comparison of the crystal structure to dihydroxyacetone kinase and to a mannose transporter EIIA domain suggests a conserved domain, EDD, with phosphotransferase activity.
Probab=21.79 E-value=3e+02 Score=25.15 Aligned_cols=111 Identities=20% Similarity=0.215 Sum_probs=71.0
Q ss_pred ccCCccEEEEeccchHHHHHHHHH---hhcCCCcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCC
Q 023087 2 LRCGFGLLMYGFGSKKALLEDFAS---TALTEYSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQPF 78 (287)
Q Consensus 2 L~~GFnlL~YG~GSKr~lL~~Fa~---~~l~~~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~~~ 78 (287)
+.+|..+++-.+.||-.=--+-+. +.+.+-++-|||...-+.....+...+.+.+-.
T Consensus 75 ~~~~~~vi~i~iSs~lSgty~~a~~aa~~~~~~~i~ViDS~~~s~~~g~~v~~a~~~~~~-------------------- 134 (275)
T TIGR00762 75 LEEGDEVLSIHLSSGLSGTYQSARQAAEMVDEAKVTVIDSKSASMGLGLLVLEAAKLAEE-------------------- 134 (275)
T ss_pred HhCCCeEEEEEcCCchhHHHHHHHHHHhhCCCCCEEEECChHHHHHHHHHHHHHHHHHHc--------------------
Confidence 456778888889888753222222 223334799999998777777777766655432
Q ss_pred CCCcHHHHHHHHhcccccCCCceEEEEEEcCCCcC--CCChhHHHHHHHHhcCCCeEEEEeec
Q 023087 79 NSRSMDDLFAFLDGSELKENDYFVCVVIHNIDGPG--LRDSETQQHLGRIAFCSHIRMIASID 139 (287)
Q Consensus 79 ~~~~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~--LR~~~~q~~La~La~~~~I~lIaSiD 139 (287)
..+++++++.+... ....++++++.++|.-. =|=.+++..++.| =+|+-|=++|
T Consensus 135 -G~s~~eI~~~l~~~---~~~~~~~f~v~~L~~L~~gGRis~~~~~~g~l---L~ikPIi~~~ 190 (275)
T TIGR00762 135 -GKSLEEILAKLEEL---RERTKLYFVVDTLEYLVKGGRISKAAALIGSL---LNIKPILTVD 190 (275)
T ss_pred -CCCHHHHHHHHHHH---HhhcEEEEEECcHHHHHhcCCccHHHHHHHHh---hcceeEEEEe
Confidence 13578888888753 24568999999999631 1334455555544 4566666665
No 86
>cd04881 ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains. The ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) encoded by the hom gene of Bacillus subtilis and other related sequences. HSDH reduces aspartate semi-aldehyde to the amino acid homoserine, one that is required for the biosynthesis of Met, Thr, and Ile from Asp. Neither the enzyme nor the aspartate pathway is found in the animal kingdom. This mostly bacterial HSDH group has a C-terminal ACT domain and is believed to be involved in enzyme regulation. A C-terminal deletion in the Corynebacterium glutamicum HSDH abolished allosteric inhibition by L-threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.60 E-value=2.6e+02 Score=19.12 Aligned_cols=44 Identities=20% Similarity=0.234 Sum_probs=27.9
Q ss_pred HHHHHhhhhcccce----EEEeeCCC-CceEEEE---eCCHHHHHHHHHHhh
Q 023087 243 TLNSHLTEFKDHEL----VKTRRHSD-GQDCFYI---PLASEALEKLLSEIN 286 (287)
Q Consensus 243 ~lr~~L~EF~DH~l----i~~~k~~~-G~e~l~I---p~~~~~l~~iLe~l~ 286 (287)
.+......|-+|++ +......+ |...+.+ +.+.+++++++++|.
T Consensus 13 ~l~~i~~~l~~~~i~I~~~~~~~~~~~~~~~~~i~~~~~~~~~l~~~i~~L~ 64 (79)
T cd04881 13 VLAKITGILAEHGISIESVIQKEADGGETAPVVIVTHETSEAALNAALAEIE 64 (79)
T ss_pred HHHHHHHHHHHcCCCeEEEEEcccCCCCceeEEEEEccCCHHHHHHHHHHHH
Confidence 45566666777765 22222223 4444444 789999999999885
No 87
>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=21.35 E-value=2.8e+02 Score=26.44 Aligned_cols=69 Identities=22% Similarity=0.283 Sum_probs=45.0
Q ss_pred CcHHHHHHHHhcccccCCCceEEEEEEcCCCcCCCChhHHH-----------HHHHHhcCCCeEEEEeecCCCCccccCc
Q 023087 81 RSMDDLFAFLDGSELKENDYFVCVVIHNIDGPGLRDSETQQ-----------HLGRIAFCSHIRMIASIDHVNAPLLWDK 149 (287)
Q Consensus 81 ~~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~~LR~~~~q~-----------~La~La~~~~I~lIaSiDhinaplLWd~ 149 (287)
.++.++.++.+. ..|.++.|.-+|+.+| +.+.|+ +|-+|-.+..=.=||+|---|-|=+.|.
T Consensus 197 r~Ihely~rA~~------~aPcivFiDE~DAiaL-dRryQelRGDVsEiVNALLTelDgi~eneGVvtIaaTN~p~~LD~ 269 (368)
T COG1223 197 RRIHELYERARK------AAPCIVFIDELDAIAL-DRRYQELRGDVSEIVNALLTELDGIKENEGVVTIAATNRPELLDP 269 (368)
T ss_pred HHHHHHHHHHHh------cCCeEEEehhhhhhhh-hhhHHHhcccHHHHHHHHHHhccCcccCCceEEEeecCChhhcCH
Confidence 345555555543 4578888999999887 334554 4555655555555666666677777898
Q ss_pred cccccccc
Q 023087 150 KMVHTQFN 157 (287)
Q Consensus 150 ~~~~~~fn 157 (287)
+.. ++|-
T Consensus 270 aiR-sRFE 276 (368)
T COG1223 270 AIR-SRFE 276 (368)
T ss_pred HHH-hhhh
Confidence 875 7775
No 88
>cd01091 CDC68-like Related to aminopeptidase P and aminopeptidase M, a member of this domain family is present in cell division control protein 68, a transcription factor.
Probab=21.21 E-value=1.2e+02 Score=27.51 Aligned_cols=69 Identities=13% Similarity=0.174 Sum_probs=46.0
Q ss_pred cCcccccccccEEEEeCC-CCCCcccccccchhhhhcCCccchhhHHHHHHhhcCHhHHHHHHHHHHHHhcCCC--CCCC
Q 023087 147 WDKKMVHTQFNWHWYHVP-TFAPYKVEGMFFPLILAHGSSAQTAKTAAIVLQSLTPNAQSVFKILAEYQLSHPD--EEGM 223 (287)
Q Consensus 147 Wd~~~~~~~fnf~~~d~t-T~~pY~~E~~~~~~l~~~~~~~~~~~g~~~VL~SLt~nar~lf~lLa~~QL~~~~--~~gv 223 (287)
|+.... ...-.+..|+. .|.-|-..+.-. . ++. =|+.+|++|..+.+.|-+..+ .+|+
T Consensus 83 ~s~~~~-~~~~~vl~d~G~~y~gY~sditRT----------~-------~v~-p~~~~~~~y~~~~~a~~~~i~~lkpG~ 143 (243)
T cd01091 83 SSDKLL-YHFGVIICSLGARYKSYCSNIART----------F-------LID-PTSEQQKNYNFLLALQEEILKELKPGA 143 (243)
T ss_pred CCcccc-CCCCEEEEEeCcccCCEeecceEE----------E-------EcC-CCHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 444444 56666677776 566666555421 0 011 267889999999988865432 4799
Q ss_pred CHHHHHHHHHH
Q 023087 224 PIDTLYATSRE 234 (287)
Q Consensus 224 ~~~~L~~~~~e 234 (287)
++.++|+.|++
T Consensus 144 ~~~dv~~~a~~ 154 (243)
T cd01091 144 KLSDVYQKTLD 154 (243)
T ss_pred cHHHHHHHHHH
Confidence 99999999987
No 89
>PF07540 NOC3p: Nucleolar complex-associated protein; InterPro: IPR011501 Nucleolar complex-associated protein (Noc3p, Q07896 from SWISSPROT) is conserved in eukaryotes and plays essential roles in replication and rRNA processing in Saccharomyces cerevisiae [].
Probab=21.04 E-value=82 Score=24.70 Aligned_cols=52 Identities=23% Similarity=0.277 Sum_probs=42.3
Q ss_pred hHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHH-HhhccHHHHHHHhhhhcc
Q 023087 202 NAQSVFKILAEYQLSHPDEEGMPIDTLYATSRER-FLVSSQVTLNSHLTEFKD 253 (287)
Q Consensus 202 nar~lf~lLa~~QL~~~~~~gv~~~~L~~~~~e~-fi~sse~~lr~~L~EF~D 253 (287)
.+|.-..-|+..-+++|++.--.+++|+..|.+. .+.-...++-+++.=|+|
T Consensus 3 ~~K~~IA~l~~~ile~PE~ni~~lk~l~~~~~~~~~~~v~kLa~lSl~~VFkD 55 (95)
T PF07540_consen 3 EAKEEIASLASSILEDPEENIGSLKRLLKLCESKVDVTVRKLAILSLLAVFKD 55 (95)
T ss_pred HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHhh
Confidence 3555666778888999876555699999999999 777788888899988888
No 90
>COG2924 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.03 E-value=78 Score=24.44 Aligned_cols=28 Identities=32% Similarity=0.388 Sum_probs=24.0
Q ss_pred chHHHHHHHHHhhcCCCcEEEEeccCCC
Q 023087 15 SKKALLEDFASTALTEYSVVVINGYLQS 42 (287)
Q Consensus 15 SKr~lL~~Fa~~~l~~~~~vvvnGy~p~ 42 (287)
+-|++|++=..++|-.+..+-+.||.|-
T Consensus 61 e~Rk~Leqem~~flf~~~~~~~~GYvpp 88 (90)
T COG2924 61 EHRKLLEQEMVNFLFEGKAVHIEGYVPP 88 (90)
T ss_pred HHHHHHHHHHHHHhhcCccccccccCCC
Confidence 3478888888899999999999999974
No 91
>TIGR03611 RutD pyrimidine utilization protein D. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the hydrolase, alpha/beta fold family defined by pfam00067.
Probab=20.94 E-value=2.8e+02 Score=23.26 Aligned_cols=14 Identities=21% Similarity=0.026 Sum_probs=10.1
Q ss_pred CceEEEEEEcCCCc
Q 023087 99 DYFVCVVIHNIDGP 112 (287)
Q Consensus 99 ~~~l~lvIHnIDg~ 112 (287)
..+++++=|++-|.
T Consensus 79 ~~~~~l~G~S~Gg~ 92 (257)
T TIGR03611 79 IERFHFVGHALGGL 92 (257)
T ss_pred CCcEEEEEechhHH
Confidence 45678888888774
No 92
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=20.56 E-value=1.1e+02 Score=25.29 Aligned_cols=47 Identities=19% Similarity=0.292 Sum_probs=34.6
Q ss_pred CHHHHHHHHHHHHhhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEeC
Q 023087 224 PIDTLYATSRERFLVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIPL 273 (287)
Q Consensus 224 ~~~~L~~~~~e~fi~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip~ 273 (287)
+.++++....++ -==++.+.+++|.-+.+-++|+..| +|.-+.+=|+
T Consensus 22 t~~eI~~~l~~~-~ews~sTV~TLl~RL~KKg~l~~~k--dgr~~~y~pL 68 (123)
T COG3682 22 TVREIIEELPAD-REWSYSTVKTLLNRLVKKGLLTRKK--DGRAFRYSPL 68 (123)
T ss_pred cHHHHHHHHhhc-ccccHHHHHHHHHHHHhccchhhhh--cCCeeeeecc
Confidence 445555444443 1137899999999999999998887 6888888887
No 93
>KOG2501 consensus Thioredoxin, nucleoredoxin and related proteins [General function prediction only]
Probab=20.42 E-value=93 Score=26.77 Aligned_cols=50 Identities=24% Similarity=0.415 Sum_probs=35.5
Q ss_pred HHHHHHHHHHH---H---hhccHHHHHHHhhhhcccceEEEeeCCCCceEEEEeCCHHHHHHHHHH
Q 023087 225 IDTLYATSRER---F---LVSSQVTLNSHLTEFKDHELVKTRRHSDGQDCFYIPLASEALEKLLSE 284 (287)
Q Consensus 225 ~~~L~~~~~e~---f---i~sse~~lr~~L~EF~DH~li~~~k~~~G~e~l~Ip~~~~~l~~iLe~ 284 (287)
.+++|+...++ | +||+|..=..+.--|.+|. ..|+.|||..+..+++.+.
T Consensus 55 Lk~fYe~l~~~~~~fEVvfVS~D~~~~~~~~y~~~~~----------~~W~~iPf~d~~~~~l~~k 110 (157)
T KOG2501|consen 55 LKDFYEELKDNAAPFEVVFVSSDRDEESLDEYMLEHH----------GDWLAIPFGDDLIQKLSEK 110 (157)
T ss_pred HHHHHHHHHhcCCceEEEEEecCCCHHHHHHHHHhcC----------CCeEEecCCCHHHHHHHHh
Confidence 57778887777 3 4577666555555555544 3689999999999988765
No 94
>PHA02530 pseT polynucleotide kinase; Provisional
Probab=20.22 E-value=6.5e+02 Score=22.74 Aligned_cols=36 Identities=22% Similarity=0.076 Sum_probs=23.8
Q ss_pred HHHHHHHhhcCCCcEEEEeccCCCCCHHHHHHHHHH
Q 023087 19 LLEDFASTALTEYSVVVINGYLQSINIKQVVITLAE 54 (287)
Q Consensus 19 lL~~Fa~~~l~~~~~vvvnGy~p~~~~k~il~~i~~ 54 (287)
+..+.+...+..+..+||+++..+..-++.+..++.
T Consensus 63 ~~~~~~~~~l~~g~~vIid~~~~~~~~~~~~~~la~ 98 (300)
T PHA02530 63 AQEAAALAALKSGKSVIISDTNLNPERRRKWKELAK 98 (300)
T ss_pred HHHHHHHHHHHcCCeEEEeCCCCCHHHHHHHHHHHH
Confidence 444555666677788999999866555655555543
No 95
>PF02645 DegV: Uncharacterised protein, DegV family COG1307; InterPro: IPR003797 This family of proteins is related to DegV of Bacillus subtilis and includes paralogous sets in several species (B. subtilis, Deinococcus radiodurans, Mycoplasma pneumoniae) that are closer in percent identity to each other than to most homologs from other species. This suggests both recent paralogy and diversity of function.; PDB: 2DT8_A 3LUP_A 3NYI_B 3PL5_A 1PZX_B 1MGP_A 1VPV_B 3FYS_A 3EGL_C 3JR7_A ....
Probab=20.15 E-value=2.2e+02 Score=26.05 Aligned_cols=111 Identities=18% Similarity=0.191 Sum_probs=69.7
Q ss_pred ccCCcc-EEEEeccchHH----HHHHHHHhhcCCCcEEEEeccCCCCCHHHHHHHHHHHHHhhccccCCCCCCCCCCCCC
Q 023087 2 LRCGFG-LLMYGFGSKKA----LLEDFASTALTEYSVVVINGYLQSINIKQVVITLAEVLWNQCKSKRKTPSGNLPRAQQ 76 (287)
Q Consensus 2 L~~GFn-lL~YG~GSKr~----lL~~Fa~~~l~~~~~vvvnGy~p~~~~k~il~~i~~~l~~~~~~~~~~~~~~~~~~~~ 76 (287)
+.+|+. +++..+.||-. -.+.-++.+ ++..+-|||...-+....-++...++.+-.
T Consensus 76 ~~~gyd~ii~i~iSs~LSgty~~a~~aa~~~-~~~~i~ViDS~~~s~g~g~lv~~a~~l~~~------------------ 136 (280)
T PF02645_consen 76 LEEGYDEIIVITISSGLSGTYNSARLAAKML-PDIKIHVIDSKSVSAGQGLLVLEAAKLIEQ------------------ 136 (280)
T ss_dssp HHTTTSEEEEEES-TTT-THHHHHHHHHHHH-TTTEEEEEE-SS-HHHHHHHHHHHHHHHHT------------------
T ss_pred HHCCCCeEEEEeCCcchhhHHHHHHHHHhhc-CcCEEEEEeCCCcchhhhHHHHHHHHHHHc------------------
Confidence 457887 88888888853 334434333 677899999998777667766666654422
Q ss_pred CCCCCcHHHHHHHHhcccccCCCceEEEEEEcCCCc--CCCChhHHHHHHHHhcCCCeEEEEeecC
Q 023087 77 PFNSRSMDDLFAFLDGSELKENDYFVCVVIHNIDGP--GLRDSETQQHLGRIAFCSHIRMIASIDH 140 (287)
Q Consensus 77 ~~~~~~~~~l~~~i~~~~~~~~~~~l~lvIHnIDg~--~LR~~~~q~~La~La~~~~I~lIaSiDh 140 (287)
..+++++++.+.... ....+|+++.++|-- +=|=.+++. .+++.=+|+-|-++|.
T Consensus 137 ---G~s~~ei~~~l~~~~---~~~~~~f~~~~L~~L~kgGRis~~~a---~ig~lL~IkPIl~~~~ 193 (280)
T PF02645_consen 137 ---GKSFEEIVEKLEELR---ERTRTYFVVDDLKYLRKGGRISKAAA---FIGNLLNIKPILSFDD 193 (280)
T ss_dssp ---T--HHHHHHHHHHHH---HTEEEEEEES-SHHHHHCTSSGHHHH---HHHHCTTEEEEEEEET
T ss_pred ---CCCHHHHHHHHHHHH---hhceEEEEechHHHHHHCCCcCchhh---hhhhhhcCcEEEEEEC
Confidence 235788888887532 466899999999842 114444444 4555668888888887
No 96
>PF13289 SIR2_2: SIR2-like domain
Probab=20.02 E-value=4.3e+02 Score=20.64 Aligned_cols=23 Identities=22% Similarity=0.485 Sum_probs=14.6
Q ss_pred HHHHHHHHHhhcCCCcEEEEeccC
Q 023087 17 KALLEDFASTALTEYSVVVINGYL 40 (287)
Q Consensus 17 r~lL~~Fa~~~l~~~~~vvvnGy~ 40 (287)
...+.++....+...++|+| ||-
T Consensus 73 ~~~~~~~l~~~l~~~~~lfi-Gys 95 (143)
T PF13289_consen 73 NPWFPNFLRSLLRSKTLLFI-GYS 95 (143)
T ss_pred HHHHHHHHHHHHcCCCEEEE-EEC
Confidence 44555666666666666666 887
Done!