Query 012449
Match_columns 463
No_of_seqs 221 out of 414
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 02:45:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012449.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012449hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03162 golden-2 like transcr 100.0 1.5E-70 3.3E-75 549.9 21.5 240 215-456 229-524 (526)
2 TIGR01557 myb_SHAQKYF myb-like 99.8 7.3E-21 1.6E-25 147.8 5.7 55 221-275 1-56 (57)
3 PF00249 Myb_DNA-binding: Myb- 97.3 0.00039 8.5E-09 51.2 4.3 48 223-273 1-48 (48)
4 PLN03029 type-a response regul 94.5 0.04 8.6E-07 51.6 3.9 35 6-40 116-150 (222)
5 COG4565 CitB Response regulato 94.1 0.05 1.1E-06 53.5 3.7 35 5-39 87-121 (224)
6 COG4566 TtrR Response regulato 93.4 0.088 1.9E-06 51.2 4.0 31 7-37 91-121 (202)
7 COG0745 OmpR Response regulato 93.0 0.063 1.4E-06 51.4 2.3 37 4-41 85-121 (229)
8 COG4753 Response regulator con 91.1 0.19 4E-06 54.1 3.4 36 6-41 90-125 (475)
9 smart00426 TEA TEA domain. 90.6 0.36 7.8E-06 40.1 3.9 46 225-271 5-67 (68)
10 COG4567 Response regulator con 89.9 0.38 8.2E-06 46.1 4.0 26 4-30 94-119 (182)
11 PRK10766 DNA-binding transcrip 88.6 0.41 8.8E-06 42.0 3.1 33 7-39 88-120 (221)
12 PRK10643 DNA-binding transcrip 88.5 0.44 9.5E-06 41.3 3.2 34 6-39 86-119 (222)
13 COG2204 AtoC Response regulato 88.2 0.42 9.2E-06 51.2 3.4 32 7-38 91-122 (464)
14 PRK09581 pleD response regulat 88.2 0.65 1.4E-05 45.1 4.4 29 6-34 242-270 (457)
15 PRK13856 two-component respons 87.7 0.47 1E-05 43.0 2.9 34 6-39 87-120 (241)
16 PRK11173 two-component respons 87.5 0.43 9.4E-06 42.8 2.6 34 7-40 89-122 (237)
17 PRK10529 DNA-binding transcrip 87.0 0.52 1.1E-05 41.5 2.7 34 5-38 85-118 (225)
18 TIGR03787 marine_sort_RR prote 86.4 0.64 1.4E-05 41.0 3.0 34 6-39 88-121 (227)
19 PRK10161 transcriptional regul 86.1 0.61 1.3E-05 41.3 2.7 33 6-38 90-122 (229)
20 PRK10336 DNA-binding transcrip 85.7 0.63 1.4E-05 40.4 2.6 33 6-38 86-118 (219)
21 PRK13435 response regulator; P 84.6 0.77 1.7E-05 38.4 2.5 34 9-42 92-125 (145)
22 PRK10816 DNA-binding transcrip 84.1 0.89 1.9E-05 40.1 2.8 32 7-38 87-118 (223)
23 PRK09836 DNA-binding transcrip 83.8 0.87 1.9E-05 40.3 2.6 33 6-38 86-118 (227)
24 PRK10693 response regulator of 83.7 0.84 1.8E-05 44.7 2.7 34 6-39 59-93 (303)
25 PRK09468 ompR osmolarity respo 83.7 0.77 1.7E-05 41.1 2.3 33 6-38 91-123 (239)
26 PRK14084 two-component respons 82.6 1.1 2.4E-05 40.8 2.9 33 6-38 86-118 (246)
27 TIGR02154 PhoB phosphate regul 82.1 1.1 2.3E-05 38.9 2.5 33 6-38 90-122 (226)
28 PRK10046 dpiA two-component re 82.0 1.4 3E-05 40.4 3.3 33 6-38 92-124 (225)
29 PLN03162 golden-2 like transcr 81.9 3.4 7.5E-05 44.2 6.4 101 334-443 357-484 (526)
30 TIGR02875 spore_0_A sporulatio 81.2 1.1 2.4E-05 41.6 2.4 33 5-37 91-123 (262)
31 PRK11517 transcriptional regul 80.5 1.3 2.8E-05 38.8 2.4 33 5-37 84-116 (223)
32 TIGR01387 cztR_silR_copR heavy 80.5 1.3 2.8E-05 38.3 2.4 33 5-37 83-115 (218)
33 PRK10955 DNA-binding transcrip 80.4 1.4 3.1E-05 38.7 2.7 33 6-38 85-117 (232)
34 CHL00148 orf27 Ycf27; Reviewed 80.4 1.5 3.2E-05 38.8 2.8 32 6-37 91-122 (240)
35 PRK10701 DNA-binding transcrip 79.9 1.4 3.1E-05 39.5 2.6 33 6-38 86-118 (240)
36 smart00717 SANT SANT SWI3, AD 79.7 4.9 0.00011 27.5 4.7 43 224-271 2-45 (49)
37 PRK10360 DNA-binding transcrip 79.5 1.3 2.9E-05 37.9 2.2 33 5-37 85-117 (196)
38 PRK11697 putative two-componen 79.4 1.7 3.7E-05 39.2 2.9 33 6-38 86-118 (238)
39 PRK10430 DNA-binding transcrip 79.3 2 4.3E-05 39.7 3.4 36 5-40 90-125 (239)
40 KOG1601 GATA-4/5/6 transcripti 78.7 0.22 4.7E-06 44.4 -3.0 34 7-40 108-141 (340)
41 PRK15479 transcriptional regul 78.0 2.2 4.7E-05 37.0 3.0 33 6-38 86-118 (221)
42 TIGR02915 PEP_resp_reg putativ 77.5 1.7 3.8E-05 43.9 2.6 33 5-37 86-118 (445)
43 PRK11083 DNA-binding response 77.0 1.7 3.6E-05 37.9 2.1 33 6-38 89-121 (228)
44 PRK10840 transcriptional regul 76.0 2.1 4.5E-05 38.7 2.4 30 5-34 93-122 (216)
45 KOG1924 RhoA GTPase effector D 75.3 18 0.0004 42.1 9.9 28 429-456 610-637 (1102)
46 cd00167 SANT 'SWI3, ADA2, N-Co 74.6 7.8 0.00017 26.2 4.5 43 225-272 1-44 (45)
47 COG3437 Response regulator con 74.6 4.2 9E-05 42.9 4.5 36 5-40 102-138 (360)
48 PRK09958 DNA-binding transcrip 74.3 2.3 4.9E-05 36.8 2.2 32 6-37 87-118 (204)
49 PRK10710 DNA-binding transcrip 73.4 3.1 6.6E-05 36.8 2.8 33 7-39 96-128 (240)
50 PRK09935 transcriptional regul 72.1 2.8 6.1E-05 36.0 2.2 30 6-35 91-120 (210)
51 PRK10365 transcriptional regul 70.7 5.8 0.00013 39.8 4.4 34 6-39 91-124 (441)
52 PF01285 TEA: TEA/ATTS domain 69.4 4.3 9.3E-05 43.3 3.3 52 220-272 46-112 (431)
53 PRK15115 response regulator Gl 67.8 6.1 0.00013 40.0 3.9 33 6-38 91-123 (444)
54 TIGR01818 ntrC nitrogen regula 65.2 6.6 0.00014 39.9 3.6 32 6-37 84-115 (463)
55 PRK09581 pleD response regulat 65.2 6.2 0.00013 38.5 3.2 33 6-38 90-122 (457)
56 TIGR03815 CpaE_hom_Actino heli 65.0 5.6 0.00012 39.2 2.9 31 5-35 55-85 (322)
57 PRK10923 glnG nitrogen regulat 64.3 6.1 0.00013 40.4 3.1 33 6-38 89-121 (469)
58 PRK10403 transcriptional regul 63.1 5.4 0.00012 34.0 2.2 32 6-37 94-125 (215)
59 PRK09483 response regulator; P 59.6 7.1 0.00015 34.1 2.3 28 6-33 89-116 (217)
60 PRK09390 fixJ response regulat 58.9 16 0.00035 30.6 4.2 32 6-37 89-120 (202)
61 KOG0485 Transcription factor N 57.9 68 0.0015 32.6 8.9 26 259-284 142-167 (268)
62 PRK11107 hybrid sensory histid 57.3 6.8 0.00015 42.6 2.2 27 5-31 754-780 (919)
63 PRK15347 two component system 56.4 8.5 0.00018 42.0 2.7 31 6-36 780-810 (921)
64 COG3706 PleD Response regulato 55.6 6.5 0.00014 42.2 1.7 24 6-29 220-243 (435)
65 PRK11361 acetoacetate metaboli 55.4 7 0.00015 39.6 1.8 30 6-35 90-119 (457)
66 PRK15369 two component system 55.3 8.8 0.00019 32.3 2.1 30 6-35 91-120 (211)
67 PRK11466 hybrid sensory histid 51.3 12 0.00026 41.2 2.8 33 5-37 767-799 (914)
68 PF07830 PP2C_C: Protein serin 50.9 23 0.00049 30.3 3.8 39 413-456 27-65 (81)
69 TIGR02956 TMAO_torS TMAO reduc 49.7 12 0.00025 41.3 2.5 32 5-36 790-821 (968)
70 PRK10651 transcriptional regul 48.8 14 0.00031 31.7 2.4 31 6-36 94-124 (216)
71 PF12776 Myb_DNA-bind_3: Myb/S 44.2 24 0.00053 28.5 3.0 50 225-274 1-63 (96)
72 PRK11091 aerobic respiration c 40.9 18 0.00039 39.3 2.3 30 7-36 614-643 (779)
73 PRK12555 chemotaxis-specific m 40.1 19 0.00041 35.6 2.1 18 6-23 89-106 (337)
74 PRK09959 hybrid sensory histid 39.9 21 0.00045 40.8 2.6 28 5-32 1043-1070(1197)
75 PRK12515 RNA polymerase sigma 38.4 30 0.00066 31.1 3.0 57 229-288 120-188 (189)
76 KOG3841 TEF-1 and related tran 38.0 23 0.00049 38.2 2.4 52 223-275 76-144 (455)
77 PF11888 DUF3408: Protein of u 36.2 46 0.001 29.9 3.7 50 224-282 83-132 (136)
78 KOG0850 Transcription factor D 34.4 39 0.00085 34.3 3.2 60 216-281 119-182 (245)
79 PRK00742 chemotaxis-specific m 33.1 38 0.00082 33.7 2.9 19 6-24 92-110 (354)
80 PRK11475 DNA-binding transcrip 32.5 33 0.00071 32.5 2.3 25 7-31 83-108 (207)
81 PRK09642 RNA polymerase sigma 31.5 54 0.0012 28.4 3.3 51 230-283 96-157 (160)
82 cd03412 CbiK_N Anaerobic cobal 25.5 53 0.0011 29.0 2.2 22 432-453 52-73 (127)
83 cd03409 Chelatase_Class_II Cla 25.4 72 0.0016 25.7 2.8 19 434-452 43-61 (101)
84 COG3360 Uncharacterized conser 24.1 35 0.00076 28.9 0.8 15 410-424 15-29 (71)
85 PF01325 Fe_dep_repress: Iron 23.1 27 0.00059 27.5 -0.0 20 431-450 32-51 (60)
86 cd06171 Sigma70_r4 Sigma70, re 22.6 1.2E+02 0.0025 20.6 3.1 29 245-276 26-54 (55)
87 PF13921 Myb_DNA-bind_6: Myb-l 21.8 1.8E+02 0.0039 21.8 4.2 41 226-271 1-41 (60)
88 KOG0842 Transcription factor t 21.6 1.4E+02 0.0031 31.2 4.7 57 216-278 150-210 (307)
89 PRK11923 algU RNA polymerase s 21.5 87 0.0019 28.1 2.8 49 229-280 127-186 (193)
90 TIGR02989 Sig-70_gvs1 RNA poly 21.2 1.5E+02 0.0033 25.4 4.1 47 228-277 99-156 (159)
91 KOG2236 Uncharacterized conser 20.9 2.9E+02 0.0063 30.7 6.9 108 265-390 367-477 (483)
92 PF01408 GFO_IDH_MocA: Oxidore 20.8 1E+02 0.0023 25.2 3.0 34 4-37 76-111 (120)
93 PLN02878 homogentisate phytylt 20.2 42 0.00091 34.4 0.6 16 420-435 51-66 (280)
No 1
>PLN03162 golden-2 like transcription factor; Provisional
Probab=100.00 E-value=1.5e-70 Score=549.95 Aligned_cols=240 Identities=44% Similarity=0.750 Sum_probs=186.6
Q ss_pred CccCCCCCcccCCHHHHHHHHHHHHHhCCCCCCchHHHhhcCCCCCcHHHHHhhhchhhhhhcccCCccc-cccCchhhh
Q 012449 215 NKANRKKMKVDWTPELHKKFVQAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHILPKED-DRKWPHARD 293 (463)
Q Consensus 215 ~~~~~kK~Rl~WT~ELH~rFV~AV~qLG~dkAtPK~ILelM~V~gLTr~~VkSHLQKYRl~~k~~l~~e~-~~~w~~~R~ 293 (463)
+..++||+||+||+|||++||+||++||+++||||+||++|+|+||||+||||||||||+++++++.+++ +.+|+++|.
T Consensus 229 ~~~g~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~~rEaEa~swt~kr~ 308 (526)
T PLN03162 229 AAPGKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLAAREAEAASWTHRRA 308 (526)
T ss_pred cCCCCCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccccchhhhhccchhhhh
Confidence 4567899999999999999999999999999999999999999999999999999999999999999998 589999887
Q ss_pred hhhc-----ccCCCCC---CcCCCC-------------CCCCCCCCCCCCCcccCCCCcccccccccCCCC---CCCCCC
Q 012449 294 QMLR-----NYYPHKP---IMAFPP-------------YHSNHLVPTGPVYPVWGAPSNHLAAVQMWAPPG---YPPWQQ 349 (463)
Q Consensus 294 ~~~~-----ny~~~~p---~~~f~p-------------~~s~h~~p~~~~~~vwG~p~~~~~~~~~W~~p~---~~~w~p 349 (463)
.... ++....| -|+||+ ..+.|+.|...++||||||+++++.||||++.. .++|++
T Consensus 309 ~~~~P~~rs~~~~g~p~~~pigfP~~~P~P~~~~~~~P~~~~~Hhpf~rPLhVWGhPtvd~s~v~mWp~h~~~~p~pW~~ 388 (526)
T PLN03162 309 YTQAPWPRSSRRDGLPYLVPIHTPHIQPRPSMAMAMQPQLQTPHHPISTPLKVWGYPTVDHSNVHMWQQPAVATPSYWQA 388 (526)
T ss_pred hccCCcccCCCCCCCccccccCCCCCCCCCCccCCCCCCcccccccccccceeccCCCCCCcccccccccccCCCCCCCC
Confidence 4431 2221111 145553 222344455557899999999999999999743 568999
Q ss_pred CC--CCCCCCCCCCCCCCCCCCCCCCCCCCCC------CCCCCCCCCCCC---CCCC--------------------CCC
Q 012449 350 AE--SWNWKPYPGMPADAWGCPVMPLPNGPYS------SFPQGASGYHNS---GVDD--------------------NSY 398 (463)
Q Consensus 350 ~~--~w~~~py~~~~a~awG~p~~p~~~~p~~------~~p~~~~g~~~~---~~~~--------------------~~~ 398 (463)
.+ |||+ ||++..|-. |+||||.|...+. ..|+-.|+|..+ |+.| .+.
T Consensus 389 ~Dp~fW~h-~~~~~~a~~-gtpc~p~pm~Rfp~ppv~~G~p~~~P~~p~~~~yy~~d~~a~~~~~~~~~~~~~~~~~~~~ 466 (526)
T PLN03162 389 ADGSYWQH-PATGYDAFS-ARACYPHPMQRVPLGTTHAGLPIMAPGFPDESCYYGDDMLAASMYLCNQSYDSEIGRAAGV 466 (526)
T ss_pred CCcchhhc-ccccCcccc-CCcccCchhhhCCCCCCCCCCccccCCCCchhhcccccchhhcccccccccccccccccch
Confidence 76 7754 888764333 9999997763211 112222233221 1111 112
Q ss_pred CCCCCCccCCCcHHHHHHHHHHHHhCCCCCCCCCCCCCChhHHHHHHHHcCCCCCCCC
Q 012449 399 AMPQNSVDLHPAEEVIDKVVKEAISKPWLPLPLGLKPPSADSVLAELSRQGISTIPPR 456 (463)
Q Consensus 399 ~~p~~~~d~hPs~E~iDaai~dvl~kPWlPLPLGLKpPs~dsVm~EL~rQGi~~iPp~ 456 (463)
...++++++|||||+|||||||||+||||||||||||||+||||+|||||||++|||+
T Consensus 467 ~~~~~~~~~hpSkEsiDAAIgdvLskPWlPlPLGLKpPSldsVm~ELqRQGi~~vpp~ 524 (526)
T PLN03162 467 AACSKPIETHLSKEVLDAAIGEALANPWTPPPLGLKPPSMEGVIAELQRQGINTVPPS 524 (526)
T ss_pred hhcccccccCccHHHHHHHHHHHhhCCCCCCCcCCCCccHHHHHHHHHHcccCCCCCC
Confidence 2245899999999999999999999999999999999999999999999999999996
No 2
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=99.82 E-value=7.3e-21 Score=147.80 Aligned_cols=55 Identities=64% Similarity=0.988 Sum_probs=52.9
Q ss_pred CCcccCCHHHHHHHHHHHHHhCC-CCCCchHHHhhcCCCCCcHHHHHhhhchhhhh
Q 012449 221 KMKVDWTPELHKKFVQAVEQLGV-DQAIPSRILELMKVEGLTRHNVASHLQKYRMH 275 (463)
Q Consensus 221 K~Rl~WT~ELH~rFV~AV~qLG~-dkAtPK~ILelM~V~gLTr~~VkSHLQKYRl~ 275 (463)
|+|+.||+|+|++|++||++||. +.||||.|+++|++++||+.||+|||||||+.
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 68999999999999999999995 99999999999999999999999999999975
No 3
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=97.28 E-value=0.00039 Score=51.16 Aligned_cols=48 Identities=29% Similarity=0.383 Sum_probs=41.4
Q ss_pred cccCCHHHHHHHHHHHHHhCCCCCCchHHHhhcCCCCCcHHHHHhhhchhh
Q 012449 223 KVDWTPELHKKFVQAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYR 273 (463)
Q Consensus 223 Rl~WT~ELH~rFV~AV~qLG~dkAtPK~ILelM~V~gLTr~~VkSHLQKYR 273 (463)
|-.||+|-+.+|++||.++|.+ .-+.|.+.|+ .+-|..++++|.++|+
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~--~W~~Ia~~~~-~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKD--NWKKIAKRMP-GGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTT--HHHHHHHHHS-SSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCc--HHHHHHHHcC-CCCCHHHHHHHHHhhC
Confidence 4689999999999999999965 4588999997 6999999999999985
No 4
>PLN03029 type-a response regulator protein; Provisional
Probab=94.53 E-value=0.04 Score=51.57 Aligned_cols=35 Identities=26% Similarity=0.366 Sum_probs=31.3
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHKAF 40 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr~~ 40 (463)
.+.+|+..||.|||.||++..+|..++.|+.+...
T Consensus 116 ~~~~al~~Ga~dyl~KP~~~~~L~~l~~~~~~~~~ 150 (222)
T PLN03029 116 RITRCLEEGAEEFFLKPVQLSDLNRLKPHMMKTKS 150 (222)
T ss_pred HHHHHHHhCchheEECCCCHHHHHHHHHHHHHHHH
Confidence 34599999999999999999999999999887664
No 5
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=94.08 E-value=0.05 Score=53.50 Aligned_cols=35 Identities=20% Similarity=0.448 Sum_probs=28.7
Q ss_pred HHHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHHH
Q 012449 5 QLFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHKA 39 (463)
Q Consensus 5 ~vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr~ 39 (463)
++|..+|+.||+|||||||..+-|..--+.-.|++
T Consensus 87 ~tI~~alr~Gv~DYLiKPf~~eRl~~aL~~y~~~r 121 (224)
T COG4565 87 ETIKEALRYGVVDYLIKPFTFERLQQALTRYRQKR 121 (224)
T ss_pred HHHHHHHhcCchhheecceeHHHHHHHHHHHHHHH
Confidence 67889999999999999999999987655544443
No 6
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=93.38 E-value=0.088 Score=51.17 Aligned_cols=31 Identities=32% Similarity=0.508 Sum_probs=25.2
Q ss_pred HHHHhhcchhhhhhcCCCHHHHHHHHHHHHH
Q 012449 7 FDNNFQLGAVEFLRKPLSEDKLRNLWQHVVH 37 (463)
Q Consensus 7 v~Kcl~~GA~DyLiKPlr~neLkniWQHV~R 37 (463)
..+++..||+|||.||++..+|..-=+...+
T Consensus 91 aV~AmK~GAvDFLeKP~~~q~Lldav~~Al~ 121 (202)
T COG4566 91 AVQAMKAGAVDFLEKPFSEQDLLDAVERALA 121 (202)
T ss_pred HHHHHHcchhhHHhCCCchHHHHHHHHHHHH
Confidence 3489999999999999999999776554443
No 7
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=92.97 E-value=0.063 Score=51.42 Aligned_cols=37 Identities=19% Similarity=0.332 Sum_probs=30.4
Q ss_pred hHHHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHHHHh
Q 012449 4 NQLFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHKAFN 41 (463)
Q Consensus 4 ~~vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr~~~ 41 (463)
.+.| .++..||.|||.|||...||..==+-+.||...
T Consensus 85 ~d~v-~gl~~GADDYl~KPf~~~EL~ARi~a~lRR~~~ 121 (229)
T COG0745 85 EDRV-LGLEAGADDYLTKPFSPRELLARLRALLRRNAG 121 (229)
T ss_pred HHHH-HHHhCcCCeeeeCCCCHHHHHHHHHHHHCcCcC
Confidence 3444 899999999999999999998766777777654
No 8
>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]
Probab=91.11 E-value=0.19 Score=54.08 Aligned_cols=36 Identities=19% Similarity=0.417 Sum_probs=32.3
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHHHHh
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHKAFN 41 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr~~~ 41 (463)
-+.+||.+|+.|||+||+.+.||...-.+|..+.-.
T Consensus 90 Yak~Am~lGV~dYLLKP~~k~eL~~~L~ki~~kl~~ 125 (475)
T COG4753 90 YAKKAMKLGVKDYLLKPVDKAELEEALKKIIGKLEE 125 (475)
T ss_pred HHHHHHhcCchhheeCcCCHHHHHHHHHHHHHHHHH
Confidence 467999999999999999999999999999877653
No 9
>smart00426 TEA TEA domain.
Probab=90.63 E-value=0.36 Score=40.08 Aligned_cols=46 Identities=22% Similarity=0.280 Sum_probs=30.4
Q ss_pred cCCHHHHHHHHHHHHHhCCCCCCchHH-----------------HhhcCCCCCcHHHHHhhhch
Q 012449 225 DWTPELHKKFVQAVEQLGVDQAIPSRI-----------------LELMKVEGLTRHNVASHLQK 271 (463)
Q Consensus 225 ~WT~ELH~rFV~AV~qLG~dkAtPK~I-----------------LelM~V~gLTr~~VkSHLQK 271 (463)
+|.++|-..|++|+..+=-....+-+| ...-| .--|+.||.||||.
T Consensus 5 vWp~~lE~Af~~aL~~~~~~g~~kik~~~r~k~~gRNelIs~YI~~~tG-k~Rt~KQVsShIQv 67 (68)
T smart00426 5 VWSPDIEQAFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTG-KTRTRKQVSSHIQV 67 (68)
T ss_pred cCcHHHHHHHHHHHHHcCccCcccchhhhcCcccchhHHHHHHHHHHhC-Cccchhhhcchhee
Confidence 799999999999999874211111112 21212 23689999999995
No 10
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=89.88 E-value=0.38 Score=46.05 Aligned_cols=26 Identities=27% Similarity=0.521 Sum_probs=21.4
Q ss_pred hHHHHHHhhcchhhhhhcCCCHHHHHH
Q 012449 4 NQLFDNNFQLGAVEFLRKPLSEDKLRN 30 (463)
Q Consensus 4 ~~vv~Kcl~~GA~DyLiKPlr~neLkn 30 (463)
-..| .++.+||||||-||-..+++-.
T Consensus 94 ATAV-~AvKlGA~~YLaKPAdaDdi~a 119 (182)
T COG4567 94 ATAV-EAVKLGACDYLAKPADADDILA 119 (182)
T ss_pred HHHH-HHHHhhhhhhcCCCCChHHHHH
Confidence 3445 8999999999999999888743
No 11
>PRK10766 DNA-binding transcriptional regulator TorR; Provisional
Probab=88.64 E-value=0.41 Score=42.02 Aligned_cols=33 Identities=18% Similarity=0.289 Sum_probs=27.8
Q ss_pred HHHHhhcchhhhhhcCCCHHHHHHHHHHHHHHH
Q 012449 7 FDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHKA 39 (463)
Q Consensus 7 v~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr~ 39 (463)
..+++..||.|||.||+...+|...=+.++||.
T Consensus 88 ~~~~l~~Ga~d~l~kP~~~~~L~~~i~~~~~r~ 120 (221)
T PRK10766 88 RIVGLEMGADDYVTKPLELRELLVRVKNLLWRI 120 (221)
T ss_pred HHHHHHcCCCcEEeCCCCHHHHHHHHHHHHhhh
Confidence 458899999999999999999987767766663
No 12
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=88.54 E-value=0.44 Score=41.31 Aligned_cols=34 Identities=18% Similarity=0.335 Sum_probs=29.0
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHKA 39 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr~ 39 (463)
.+.+++..||.|||.||+..++|...-+.+.++.
T Consensus 86 ~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~~~~~ 119 (222)
T PRK10643 86 DRVAGLDVGADDYLVKPFALEELHARIRALIRRH 119 (222)
T ss_pred HHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHhhh
Confidence 4568899999999999999999988877776654
No 13
>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]
Probab=88.22 E-value=0.42 Score=51.24 Aligned_cols=32 Identities=28% Similarity=0.503 Sum_probs=27.3
Q ss_pred HHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 7 FDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 7 v~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
...+++.||.|||.|||..++|..+=.+...+
T Consensus 91 AV~A~k~GA~Dfl~KP~~~~~L~~~v~ral~~ 122 (464)
T COG2204 91 AVEALRLGAFDFLEKPFDLDRLLAIVERALEL 122 (464)
T ss_pred HHHHHhcCcceeeeCCCCHHHHHHHHHHHHHH
Confidence 34899999999999999999999986666544
No 14
>PRK09581 pleD response regulator PleD; Reviewed
Probab=88.17 E-value=0.65 Score=45.11 Aligned_cols=29 Identities=17% Similarity=0.413 Sum_probs=24.6
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQH 34 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQH 34 (463)
.+.+|+..||+|||.||+..++|......
T Consensus 242 ~~~~a~~~Ga~d~l~kp~~~~~l~~~i~~ 270 (457)
T PRK09581 242 RLVKALELGVNDYLMRPIDKNELLARVRT 270 (457)
T ss_pred HHHHHHHccchhhhhCCCcHHHHHHHHHH
Confidence 35689999999999999999999865544
No 15
>PRK13856 two-component response regulator VirG; Provisional
Probab=87.71 E-value=0.47 Score=43.01 Aligned_cols=34 Identities=18% Similarity=0.248 Sum_probs=28.7
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHKA 39 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr~ 39 (463)
...+++..||.|||.||+...+|....+.+.|+.
T Consensus 87 ~~~~~l~~Ga~~yl~kP~~~~eL~~~i~~~l~~~ 120 (241)
T PRK13856 87 DKVVALELGATDFIAKPFGTREFLARIRVALRVR 120 (241)
T ss_pred HHHHHHhcCcCeEEeCCCCHHHHHHHHHHHHhhc
Confidence 3458999999999999999999988777777653
No 16
>PRK11173 two-component response regulator; Provisional
Probab=87.51 E-value=0.43 Score=42.84 Aligned_cols=34 Identities=15% Similarity=0.331 Sum_probs=28.9
Q ss_pred HHHHhhcchhhhhhcCCCHHHHHHHHHHHHHHHH
Q 012449 7 FDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHKAF 40 (463)
Q Consensus 7 v~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr~~ 40 (463)
..+++..||.|||.||+...+|...-..++||..
T Consensus 89 ~~~~~~~ga~d~l~kP~~~~eL~~~i~~~l~r~~ 122 (237)
T PRK11173 89 KILGLEIGADDYITKPFNPRELTIRARNLLSRTM 122 (237)
T ss_pred HHHHHHCCCCEEEECCCCHHHHHHHHHHHHhccc
Confidence 4578999999999999999999877777777753
No 17
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=87.05 E-value=0.52 Score=41.50 Aligned_cols=34 Identities=18% Similarity=0.263 Sum_probs=27.2
Q ss_pred HHHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 5 QLFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 5 ~vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
+...+++..||.|||.||++..+|...=+.+.|+
T Consensus 85 ~~~~~~~~~ga~~~l~kP~~~~~l~~~i~~~~~~ 118 (225)
T PRK10529 85 SDKIAALDAGADDYLSKPFGIGELQARLRVALRR 118 (225)
T ss_pred HHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHhh
Confidence 3456899999999999999999987765555554
No 18
>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.
Probab=86.38 E-value=0.64 Score=41.00 Aligned_cols=34 Identities=24% Similarity=0.259 Sum_probs=28.9
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHKA 39 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr~ 39 (463)
.+..++..||.|||.||+...+|...-+.+.|+.
T Consensus 88 ~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~ 121 (227)
T TIGR03787 88 DTVSGLRLGADDYLTKDISLPHLLARITALFRRA 121 (227)
T ss_pred HHHHHHhcCCCEEEECCCCHHHHHHHHHHHHHhh
Confidence 3558899999999999999999988777777654
No 19
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=86.07 E-value=0.61 Score=41.31 Aligned_cols=33 Identities=21% Similarity=0.329 Sum_probs=28.0
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
.+.+++..||.|||.||+...+|...=+.+.|+
T Consensus 90 ~~~~~~~~Ga~~~l~kp~~~~~L~~~i~~~~~~ 122 (229)
T PRK10161 90 DRVRGLETGADDYITKPFSPKELVARIKAVMRR 122 (229)
T ss_pred HHHHHHHcCCCEEEECCCCHHHHHHHHHHHHhc
Confidence 456899999999999999999998776776665
No 20
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=85.71 E-value=0.63 Score=40.37 Aligned_cols=33 Identities=18% Similarity=0.302 Sum_probs=27.7
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
.+.+++..||.|||.||+...+|...-+.+.|+
T Consensus 86 ~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~~~~ 118 (219)
T PRK10336 86 ERVEGLRLGADDYLCKPFALIEVAARLEALMRR 118 (219)
T ss_pred HHHHHHhCCCCeEEECCCCHHHHHHHHHHHHhc
Confidence 456899999999999999999998776666654
No 21
>PRK13435 response regulator; Provisional
Probab=84.59 E-value=0.77 Score=38.36 Aligned_cols=34 Identities=15% Similarity=0.152 Sum_probs=29.1
Q ss_pred HHhhcchhhhhhcCCCHHHHHHHHHHHHHHHHhc
Q 012449 9 NNFQLGAVEFLRKPLSEDKLRNLWQHVVHKAFNA 42 (463)
Q Consensus 9 Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr~~~~ 42 (463)
+++..||.+||.||+...+|...-++++++..+.
T Consensus 92 ~~~~~ga~~~l~kp~~~~~l~~~i~~~~~~~~~~ 125 (145)
T PRK13435 92 PHDFAGALGVIAKPYSPRGVARALSYLSARRVGD 125 (145)
T ss_pred HHHhcCcceeEeCCCCHHHHHHHHHHHHhcCccc
Confidence 5778999999999999999999888888766543
No 22
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=84.07 E-value=0.89 Score=40.10 Aligned_cols=32 Identities=16% Similarity=0.293 Sum_probs=26.1
Q ss_pred HHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 7 FDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 7 v~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
..+++..||.|||.||+...+|...=+.+.|+
T Consensus 87 ~~~~l~~Ga~d~l~kp~~~~eL~~~i~~~~~~ 118 (223)
T PRK10816 87 KVEVLSAGADDYVTKPFHIEEVMARMQALMRR 118 (223)
T ss_pred HHHHHHcCCCeeEeCCCCHHHHHHHHHHHHhc
Confidence 45889999999999999999987765555554
No 23
>PRK09836 DNA-binding transcriptional activator CusR; Provisional
Probab=83.76 E-value=0.87 Score=40.28 Aligned_cols=33 Identities=21% Similarity=0.330 Sum_probs=27.0
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
...+++..||.|||.||+...+|...=+.+.|+
T Consensus 86 ~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~~ 118 (227)
T PRK09836 86 HRVKGLELGADDYLVKPFAFAELLARVRTLLRR 118 (227)
T ss_pred HHHHHHhCCCCEEEeCCCCHHHHHHHHHHHHhc
Confidence 455899999999999999999987765655554
No 24
>PRK10693 response regulator of RpoS; Provisional
Probab=83.68 E-value=0.84 Score=44.74 Aligned_cols=34 Identities=21% Similarity=0.352 Sum_probs=28.0
Q ss_pred HHHHHhhcchhhhhhcCCC-HHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLS-EDKLRNLWQHVVHKA 39 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr-~neLkniWQHV~Rr~ 39 (463)
.+.+|++.||.|||.||++ .++|+...+.+.++.
T Consensus 59 ~~~~al~~Ga~dyl~KP~~~~~~L~~~i~~~l~~~ 93 (303)
T PRK10693 59 DIAKALRLGVQDVLLKPVKDLNRLREMVFACLYPS 93 (303)
T ss_pred HHHHHHHCCCcEEEECCCCcHHHHHHHHHHHhhhh
Confidence 4568999999999999995 899988877766554
No 25
>PRK09468 ompR osmolarity response regulator; Provisional
Probab=83.67 E-value=0.77 Score=41.05 Aligned_cols=33 Identities=21% Similarity=0.320 Sum_probs=27.2
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
...+++..||.|||.||++..+|...=+.+.|+
T Consensus 91 ~~~~~l~~Ga~~~l~kP~~~~~L~~~i~~~~~r 123 (239)
T PRK09468 91 DRIVGLEIGADDYLPKPFNPRELLARIRAVLRR 123 (239)
T ss_pred HHHHHHhcCCCeEEECCCCHHHHHHHHHHHhcc
Confidence 345789999999999999999998776666655
No 26
>PRK14084 two-component response regulator; Provisional
Probab=82.59 E-value=1.1 Score=40.80 Aligned_cols=33 Identities=18% Similarity=0.417 Sum_probs=28.1
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
...+++..||.+||.||+..++|...-+.+.++
T Consensus 86 ~~~~~~~~~~~~yl~KP~~~~~l~~~l~~~~~~ 118 (246)
T PRK14084 86 FAVKAFELNATDYILKPFEQKRIEQAVNKVRAT 118 (246)
T ss_pred HHHHHHhcCCcEEEECCCCHHHHHHHHHHHHHh
Confidence 456899999999999999999998887777654
No 27
>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=82.13 E-value=1.1 Score=38.91 Aligned_cols=33 Identities=21% Similarity=0.321 Sum_probs=26.5
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
.+.+++..||.+||.||+...+|...=..+.++
T Consensus 90 ~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~~ 122 (226)
T TIGR02154 90 DRVRGLETGADDYITKPFSPRELLARIKAVLRR 122 (226)
T ss_pred HHHHHHhcCcceEEeCCCCHHHHHHHHHHHhcc
Confidence 456899999999999999999987665555443
No 28
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=82.01 E-value=1.4 Score=40.44 Aligned_cols=33 Identities=15% Similarity=0.384 Sum_probs=28.0
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
.+.++++.||.+||.||+...+|...=+.+.+.
T Consensus 92 ~~~~al~~Ga~~yl~Kp~~~~~L~~~i~~~~~~ 124 (225)
T PRK10046 92 TVSEAVRCGVFDYLIKPIAYERLGQTLTRFRQR 124 (225)
T ss_pred HHHHHHHcCccEEEECCcCHHHHHHHHHHHHHH
Confidence 456899999999999999999998877766544
No 29
>PLN03162 golden-2 like transcription factor; Provisional
Probab=81.91 E-value=3.4 Score=44.17 Aligned_cols=101 Identities=14% Similarity=0.191 Sum_probs=58.3
Q ss_pred ccccccCC-----CCCCCCCCC-----CCCCCC-CCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCC----CC
Q 012449 334 AAVQMWAP-----PGYPPWQQA-----ESWNWK-PYPGMPADAWGCPVMPL---PNGPYSSFPQGASGYHNSGV----DD 395 (463)
Q Consensus 334 ~~~~~W~~-----p~~~~w~p~-----~~w~~~-py~~~~a~awG~p~~p~---~~~p~~~~p~~~~g~~~~~~----~~ 395 (463)
...|+|+. +..+.|+-+ .+|.-. |+ -|-.|.+.- ..|||.+. ++.+|+.+.+ .-
T Consensus 357 rPLhVWGhPtvd~s~v~mWp~h~~~~p~pW~~~Dp~------fW~h~~~~~~a~~gtpc~p~--pm~Rfp~ppv~~G~p~ 428 (526)
T PLN03162 357 TPLKVWGYPTVDHSNVHMWQQPAVATPSYWQAADGS------YWQHPATGYDAFSARACYPH--PMQRVPLGTTHAGLPI 428 (526)
T ss_pred ccceeccCCCCCCcccccccccccCCCCCCCCCCcc------hhhcccccCccccCCcccCc--hhhhCCCCCCCCCCcc
Confidence 36799995 445788643 244321 21 244444331 15677544 4456655443 11
Q ss_pred CCCCCCCCC---------ccCCCcHHHHHHHHHHHHhCCCCCCCCCCCCCChhHHHH
Q 012449 396 NSYAMPQNS---------VDLHPAEEVIDKVVKEAISKPWLPLPLGLKPPSADSVLA 443 (463)
Q Consensus 396 ~~~~~p~~~---------~d~hPs~E~iDaai~dvl~kPWlPLPLGLKpPs~dsVm~ 443 (463)
|..++|..+ +..++-+.+.|.-||..+--+=..+||-+-| |-++|=+
T Consensus 429 ~~P~~p~~~~yy~~d~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~hp-SkEsiDA 484 (526)
T PLN03162 429 MAPGFPDESCYYGDDMLAASMYLCNQSYDSEIGRAAGVAACSKPIETHL-SKEVLDA 484 (526)
T ss_pred ccCCCCchhhcccccchhhcccccccccccccccccchhhcccccccCc-cHHHHHH
Confidence 333333322 2234667789999999998888889998876 6665533
No 30
>TIGR02875 spore_0_A sporulation transcription factor Spo0A. Spo0A, the stage 0 sporulation protein A, is a transcription factor critical for the initiation of sporulation. It contains a response regulator receiver domain (pfam00072). In Bacillus subtilis, it works together with response regulator Spo0F and the phosphotransferase Spo0B, both of which are missing from at least some sporulating species and thus not part of the endospore forming bacteria minimal gene set. Spo0A, however, is universal among endospore-forming species.
Probab=81.25 E-value=1.1 Score=41.63 Aligned_cols=33 Identities=18% Similarity=0.294 Sum_probs=27.6
Q ss_pred HHHHHHhhcchhhhhhcCCCHHHHHHHHHHHHH
Q 012449 5 QLFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVH 37 (463)
Q Consensus 5 ~vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~R 37 (463)
.+..+++..||.+||.||+..++|....+++++
T Consensus 91 ~~~~~~~~~G~~~~l~KP~~~~~L~~~i~~~~~ 123 (262)
T TIGR02875 91 KITQRAVALGADYYVLKPFDLEILAARIRQLAW 123 (262)
T ss_pred HHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHc
Confidence 355689999999999999999999887766554
No 31
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=80.48 E-value=1.3 Score=38.75 Aligned_cols=33 Identities=21% Similarity=0.204 Sum_probs=26.1
Q ss_pred HHHHHHhhcchhhhhhcCCCHHHHHHHHHHHHH
Q 012449 5 QLFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVH 37 (463)
Q Consensus 5 ~vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~R 37 (463)
..+.+++..||.|||.||+...+|...=+.+.+
T Consensus 84 ~~~~~a~~~Ga~~~l~kp~~~~~l~~~i~~~~~ 116 (223)
T PRK11517 84 DDRVRGLDSGANDYLVKPFSFSELLARVRAQLR 116 (223)
T ss_pred HHHHHHHhcCCCEEEECCCCHHHHHHHHHHHHc
Confidence 346689999999999999999998766444443
No 32
>TIGR01387 cztR_silR_copR heavy metal response regulator. Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system.
Probab=80.45 E-value=1.3 Score=38.33 Aligned_cols=33 Identities=24% Similarity=0.289 Sum_probs=25.9
Q ss_pred HHHHHHhhcchhhhhhcCCCHHHHHHHHHHHHH
Q 012449 5 QLFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVH 37 (463)
Q Consensus 5 ~vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~R 37 (463)
..+.+++..||.||+.||+...+|...=..+.+
T Consensus 83 ~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~ 115 (218)
T TIGR01387 83 ADKVKGLDLGADDYLVKPFSFSELLARVRTLLR 115 (218)
T ss_pred HHHHHHHHcCCCeEEECCCCHHHHHHHHHHHhc
Confidence 345689999999999999999998765444443
No 33
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=80.39 E-value=1.4 Score=38.66 Aligned_cols=33 Identities=21% Similarity=0.364 Sum_probs=26.1
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
.+.+++..||.|||.||++..+|...=+.++|+
T Consensus 85 ~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~~~~ 117 (232)
T PRK10955 85 DRVLGLELGADDYLPKPFNDRELVARIRAILRR 117 (232)
T ss_pred HHHHHHHcCCCEEEcCCCCHHHHHHHHHHHHhc
Confidence 456889999999999999999987665554443
No 34
>CHL00148 orf27 Ycf27; Reviewed
Probab=80.39 E-value=1.5 Score=38.77 Aligned_cols=32 Identities=25% Similarity=0.363 Sum_probs=25.4
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVH 37 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~R 37 (463)
...+++..||.|||.||+...+|...=..+.|
T Consensus 91 ~~~~~~~~Ga~~~l~kp~~~~~L~~~i~~~~~ 122 (240)
T CHL00148 91 DRITGLELGADDYVVKPFSPKELEARIRSVLR 122 (240)
T ss_pred hHHHHHHCCCCEEEeCCCCHHHHHHHHHHHHh
Confidence 34588999999999999999998765444443
No 35
>PRK10701 DNA-binding transcriptional regulator RstA; Provisional
Probab=79.91 E-value=1.4 Score=39.49 Aligned_cols=33 Identities=12% Similarity=0.140 Sum_probs=25.9
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
...+++..||.|||.||+...+|...=..++|+
T Consensus 86 ~~~~~~~~Ga~d~l~kP~~~~~l~~~i~~~l~~ 118 (240)
T PRK10701 86 NHILALEMGACDYILKTTPPAVLLARLRLHLRQ 118 (240)
T ss_pred HHHHHHHcCCCEEEECCCCHHHHHHHHHHHHhc
Confidence 345899999999999999999886654545554
No 36
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=79.67 E-value=4.9 Score=27.51 Aligned_cols=43 Identities=19% Similarity=0.360 Sum_probs=34.2
Q ss_pred ccCCHHHHHHHHHHHHHhC-CCCCCchHHHhhcCCCCCcHHHHHhhhch
Q 012449 224 VDWTPELHKKFVQAVEQLG-VDQAIPSRILELMKVEGLTRHNVASHLQK 271 (463)
Q Consensus 224 l~WT~ELH~rFV~AV~qLG-~dkAtPK~ILelM~V~gLTr~~VkSHLQK 271 (463)
-.||++=...|+.++.++| .+- +.|.+.|+ +-|..+|+.+...
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w---~~Ia~~~~--~rt~~~~~~~~~~ 45 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNW---EKIAKELP--GRTAEQCRERWNN 45 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCH---HHHHHHcC--CCCHHHHHHHHHH
Confidence 4699999999999999999 554 66777775 7788888776443
No 37
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=79.48 E-value=1.3 Score=37.94 Aligned_cols=33 Identities=30% Similarity=0.360 Sum_probs=26.4
Q ss_pred HHHHHHhhcchhhhhhcCCCHHHHHHHHHHHHH
Q 012449 5 QLFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVH 37 (463)
Q Consensus 5 ~vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~R 37 (463)
..+..|+..||.+||.||+...+|...-..+.+
T Consensus 85 ~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~~~ 117 (196)
T PRK10360 85 ALVEQALNAGARGFLSKRCSPDELIAAVHTVAT 117 (196)
T ss_pred HHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHc
Confidence 345689999999999999999998777554443
No 38
>PRK11697 putative two-component response-regulatory protein YehT; Provisional
Probab=79.36 E-value=1.7 Score=39.20 Aligned_cols=33 Identities=18% Similarity=0.323 Sum_probs=27.5
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
....++..||.|||.||+..++|...-+.+.++
T Consensus 86 ~~~~a~~~~~~~yl~KP~~~~~l~~~l~~~~~~ 118 (238)
T PRK11697 86 YAIKAFEEHAFDYLLKPIDPARLAKTLARLRQE 118 (238)
T ss_pred HHHHHHhcCCcEEEECCCCHHHHHHHHHHHHHh
Confidence 456889999999999999999998877776543
No 39
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=79.28 E-value=2 Score=39.71 Aligned_cols=36 Identities=17% Similarity=0.399 Sum_probs=28.3
Q ss_pred HHHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHHHH
Q 012449 5 QLFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHKAF 40 (463)
Q Consensus 5 ~vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr~~ 40 (463)
..+.+++..||.+||.||+...+|...-..++++..
T Consensus 90 ~~~~~al~~Ga~~yl~Kp~~~~~l~~~i~~~~~~~~ 125 (239)
T PRK10430 90 ATIKDSLHYGVVDYLIKPFQASRFEEALTGWRQKKM 125 (239)
T ss_pred HHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHHHHH
Confidence 345689999999999999999998776565555443
No 40
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=78.67 E-value=0.22 Score=44.42 Aligned_cols=34 Identities=26% Similarity=0.193 Sum_probs=30.8
Q ss_pred HHHHhhcchhhhhhcCCCHHHHHHHHHHHHHHHH
Q 012449 7 FDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHKAF 40 (463)
Q Consensus 7 v~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr~~ 40 (463)
+++++..||++|++||++.++++++|+|+++...
T Consensus 108 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 141 (340)
T KOG1601|consen 108 SSSSVSPSASLELTKPDRKNRLKRSRQHVRVKDE 141 (340)
T ss_pred hhcccCCcccccccccccCCCcccCCcccccccc
Confidence 5688999999999999999999999999987654
No 41
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=78.01 E-value=2.2 Score=37.02 Aligned_cols=33 Identities=18% Similarity=0.353 Sum_probs=27.2
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
.+.+++..||.+|+.||+...+|...=+.+.++
T Consensus 86 ~~~~~~~~g~~~~i~kp~~~~~l~~~i~~~~~~ 118 (221)
T PRK15479 86 DRVKGLNVGADDYLPKPFELEELDARLRALLRR 118 (221)
T ss_pred HHHHHHHcCCCeeEeCCCCHHHHHHHHHHHHhh
Confidence 456899999999999999999998765655554
No 42
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=77.48 E-value=1.7 Score=43.88 Aligned_cols=33 Identities=27% Similarity=0.459 Sum_probs=26.8
Q ss_pred HHHHHHhhcchhhhhhcCCCHHHHHHHHHHHHH
Q 012449 5 QLFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVH 37 (463)
Q Consensus 5 ~vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~R 37 (463)
+...+|+..||.|||.||+..++|...=+++++
T Consensus 86 ~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~~~ 118 (445)
T TIGR02915 86 ENAVKAIGLGAYDFYQKPIDPDVLKLIVDRAFH 118 (445)
T ss_pred HHHHHHHHCCccEEEeCCCCHHHHHHHHhhhhh
Confidence 345689999999999999999999776555543
No 43
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=77.00 E-value=1.7 Score=37.87 Aligned_cols=33 Identities=15% Similarity=0.299 Sum_probs=25.7
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
...+++..||.|||.||+...+|...=..+.++
T Consensus 89 ~~~~a~~~Ga~~~l~kp~~~~~l~~~i~~~~~~ 121 (228)
T PRK11083 89 DRLVGLEIGADDYVAKPFSPREVAARVRTILRR 121 (228)
T ss_pred HHHHHhhcCCCeEEECCCCHHHHHHHHHHHHCc
Confidence 345789999999999999999987654544443
No 44
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=76.02 E-value=2.1 Score=38.67 Aligned_cols=30 Identities=10% Similarity=0.084 Sum_probs=25.1
Q ss_pred HHHHHHhhcchhhhhhcCCCHHHHHHHHHH
Q 012449 5 QLFDNNFQLGAVEFLRKPLSEDKLRNLWQH 34 (463)
Q Consensus 5 ~vv~Kcl~~GA~DyLiKPlr~neLkniWQH 34 (463)
..+.++++.||.+||.||.+..+|......
T Consensus 93 ~~~~~a~~~Ga~~yl~K~~~~~~l~~ai~~ 122 (216)
T PRK10840 93 AILSAVLDLDIEGIVLKQGAPTDLPKALAA 122 (216)
T ss_pred HHHHHHHHCCCeEEEECCCCHHHHHHHHHH
Confidence 356689999999999999999998876443
No 45
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=75.34 E-value=18 Score=42.08 Aligned_cols=28 Identities=39% Similarity=0.560 Sum_probs=16.4
Q ss_pred CCCCCCCCChhHHHHHHHHcCCCCCCCC
Q 012449 429 LPLGLKPPSADSVLAELSRQGISTIPPR 456 (463)
Q Consensus 429 LPLGLKpPs~dsVm~EL~rQGi~~iPp~ 456 (463)
||.||||=-+=.|=.-+.|-.-++|=|+
T Consensus 610 lP~gLkpKK~~k~e~~Mrr~nW~kI~p~ 637 (1102)
T KOG1924|consen 610 LPFGLKPKKVYKPEVPMRRFNWSKIVPR 637 (1102)
T ss_pred CCCCCCccccCCCCCccccCCccccCcc
Confidence 7889998555444444455555554443
No 46
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=74.62 E-value=7.8 Score=26.21 Aligned_cols=43 Identities=21% Similarity=0.364 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHHHHhC-CCCCCchHHHhhcCCCCCcHHHHHhhhchh
Q 012449 225 DWTPELHKKFVQAVEQLG-VDQAIPSRILELMKVEGLTRHNVASHLQKY 272 (463)
Q Consensus 225 ~WT~ELH~rFV~AV~qLG-~dkAtPK~ILelM~V~gLTr~~VkSHLQKY 272 (463)
.||.+=+..|+.++.++| .+ =+.|.+.|+ +-|..+|+.|.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~---w~~Ia~~~~--~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNN---WEKIAKELP--GRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCC---HHHHHhHcC--CCCHHHHHHHHHHh
Confidence 499999999999999999 44 367777774 47888888776543
No 47
>COG3437 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]
Probab=74.56 E-value=4.2 Score=42.85 Aligned_cols=36 Identities=25% Similarity=0.313 Sum_probs=28.6
Q ss_pred HHHHHHhhcchhhhhhcCCCHHHHHHHH-HHHHHHHH
Q 012449 5 QLFDNNFQLGAVEFLRKPLSEDKLRNLW-QHVVHKAF 40 (463)
Q Consensus 5 ~vv~Kcl~~GA~DyLiKPlr~neLkniW-QHV~Rr~~ 40 (463)
+-..+|+..||.|||.||++..+|+.-- .|+..|..
T Consensus 102 ~~~~~~~~~g~~dyl~KP~~~~~l~~rv~~~~q~k~~ 138 (360)
T COG3437 102 EDRQRALEAGADDYLSKPISPKELVARVSSHLQLKRN 138 (360)
T ss_pred HHHHHHHHhhHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 3456999999999999999999998765 56655543
No 48
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=74.34 E-value=2.3 Score=36.80 Aligned_cols=32 Identities=13% Similarity=0.060 Sum_probs=26.4
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVH 37 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~R 37 (463)
....++..||.+||.||+...+|...-+.+.+
T Consensus 87 ~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~~~ 118 (204)
T PRK09958 87 YGKHCADAGANGFVSKKEGMNNIIAAIEAAKN 118 (204)
T ss_pred HHHHHHHCCCCEEEecCCCHHHHHHHHHHHHc
Confidence 45688999999999999999998887555543
No 49
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=73.45 E-value=3.1 Score=36.81 Aligned_cols=33 Identities=15% Similarity=0.296 Sum_probs=26.5
Q ss_pred HHHHhhcchhhhhhcCCCHHHHHHHHHHHHHHH
Q 012449 7 FDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHKA 39 (463)
Q Consensus 7 v~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr~ 39 (463)
..+++..||.|||.||+...+|...=+.++++.
T Consensus 96 ~~~~~~~ga~~~l~kp~~~~~L~~~i~~~~~~~ 128 (240)
T PRK10710 96 RLLGLEIGADDYICKPYSPREVVARVKTILRRC 128 (240)
T ss_pred HHHHHhcCCCeEEECCCCHHHHHHHHHHHHhhc
Confidence 457899999999999999999876655555543
No 50
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=72.10 E-value=2.8 Score=36.03 Aligned_cols=30 Identities=20% Similarity=0.206 Sum_probs=24.7
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHV 35 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV 35 (463)
...+++..||.+|+.||+..++|...=+.+
T Consensus 91 ~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~ 120 (210)
T PRK09935 91 YAGRAIQAGANGFVSKCNDQNDIFHAVQMI 120 (210)
T ss_pred HHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence 456899999999999999999987764444
No 51
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=70.69 E-value=5.8 Score=39.84 Aligned_cols=34 Identities=24% Similarity=0.405 Sum_probs=28.3
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHKA 39 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr~ 39 (463)
.+.+++..||.|||.||+...+|...-++++++.
T Consensus 91 ~~~~a~~~ga~~~l~Kp~~~~~L~~~l~~~l~~~ 124 (441)
T PRK10365 91 TAVEALKTGALDYLIKPLDFDNLQATLEKALAHT 124 (441)
T ss_pred HHHHHHHhhhHHHhcCCCCHHHHHHHHHHHHHHH
Confidence 4568999999999999999999988777766543
No 52
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=69.38 E-value=4.3 Score=43.32 Aligned_cols=52 Identities=23% Similarity=0.309 Sum_probs=29.4
Q ss_pred CCCcccCCHHHHHHHHHHHHHhC-CCCCCch----------HHHh----hcCCCCCcHHHHHhhhchh
Q 012449 220 KKMKVDWTPELHKKFVQAVEQLG-VDQAIPS----------RILE----LMKVEGLTRHNVASHLQKY 272 (463)
Q Consensus 220 kK~Rl~WT~ELH~rFV~AV~qLG-~dkAtPK----------~ILe----lM~V~gLTr~~VkSHLQKY 272 (463)
++..-+|+++|...|++|+...- .....-+ -|.+ .-| .--|+.+|.||+|..
T Consensus 46 ~~~~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~~yi~~~tg-~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 46 GDGEGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELISDYIKLKTG-KTRTRKQVSSHIQVL 112 (431)
T ss_dssp GGGS--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHHHHHHHHHS-----SHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHHHHHHHHhC-cccchhHHHHHHHHH
Confidence 46678999999999999998863 1111111 1111 122 347999999999998
No 53
>PRK15115 response regulator GlrR; Provisional
Probab=67.81 E-value=6.1 Score=40.01 Aligned_cols=33 Identities=24% Similarity=0.303 Sum_probs=27.7
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
...+++..||.|||.||+...+|...=+.++++
T Consensus 91 ~~~~a~~~Ga~~~l~KP~~~~~L~~~l~~~~~~ 123 (444)
T PRK15115 91 DAVAATQQGVFSFLTKPVDRDALYKAIDDALEQ 123 (444)
T ss_pred HHHHHHhcChhhhccCCCCHHHHHHHHHHHHHh
Confidence 456899999999999999999988776666654
No 54
>TIGR01818 ntrC nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.
Probab=65.18 E-value=6.6 Score=39.90 Aligned_cols=32 Identities=28% Similarity=0.396 Sum_probs=26.9
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVH 37 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~R 37 (463)
...+|+..||.|||.||+..++|...-.+++.
T Consensus 84 ~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~l~ 115 (463)
T TIGR01818 84 TAVAAYQRGAFEYLPKPFDLDEAVTLVERALA 115 (463)
T ss_pred HHHHHHHcCcceeecCCCCHHHHHHHHHHHHH
Confidence 45689999999999999999998887666554
No 55
>PRK09581 pleD response regulator PleD; Reviewed
Probab=65.16 E-value=6.2 Score=38.47 Aligned_cols=33 Identities=21% Similarity=0.243 Sum_probs=26.7
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
.+.+++..||.|||.||++.++|...-..++|.
T Consensus 90 ~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~~~~ 122 (457)
T PRK09581 90 DRVRGLEAGADDFLTKPINDVALFARVKSLTRL 122 (457)
T ss_pred HHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHH
Confidence 456899999999999999999997665555543
No 56
>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein. Members of this protein family belong to the MinD/ParA family of P-loop NTPases, and in particular show homology to the CpaE family of pilus assembly proteins (see PubMed:12370432). Nearly all members are found, not only in a gene context consistent with pilus biogenesis or a pilus-like secretion apparatus, but also near a DEAD/DEAH-box helicase, suggesting an involvement in DNA transfer activity. The model describes a clade restricted to the Actinobacteria.
Probab=64.96 E-value=5.6 Score=39.16 Aligned_cols=31 Identities=23% Similarity=0.243 Sum_probs=27.0
Q ss_pred HHHHHHhhcchhhhhhcCCCHHHHHHHHHHH
Q 012449 5 QLFDNNFQLGAVEFLRKPLSEDKLRNLWQHV 35 (463)
Q Consensus 5 ~vv~Kcl~~GA~DyLiKPlr~neLkniWQHV 35 (463)
+++.++++.||.|||.+|+..+||..+-..+
T Consensus 55 ~~~~~a~~~Ga~~~l~~P~~~~~l~~~l~~~ 85 (322)
T TIGR03815 55 ALWRAAAAVGAEHVAVLPEAEGWLVELLADL 85 (322)
T ss_pred HHHHHHHHhChhheeeCCCCHHHHHHHHHhh
Confidence 5677999999999999999999998776555
No 57
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=64.25 E-value=6.1 Score=40.43 Aligned_cols=33 Identities=24% Similarity=0.412 Sum_probs=28.0
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVHK 38 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~Rr 38 (463)
.+.+++..||.|||.||+...+|...-++++.+
T Consensus 89 ~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~l~~ 121 (469)
T PRK10923 89 AAVSAYQQGAFDYLPKPFDIDEAVALVERAISH 121 (469)
T ss_pred HHHHHHhcCcceEEecCCcHHHHHHHHHHHHHH
Confidence 456899999999999999999998877776653
No 58
>PRK10403 transcriptional regulator NarP; Provisional
Probab=63.09 E-value=5.4 Score=34.04 Aligned_cols=32 Identities=16% Similarity=0.007 Sum_probs=26.2
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVH 37 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~R 37 (463)
.+..++..||.+|+.||+...+|...-+.+.+
T Consensus 94 ~~~~~~~~g~~~~i~kp~~~~~l~~~i~~~~~ 125 (215)
T PRK10403 94 DVFALIDAGADGYLLKDSDPEVLLEAIRAGAK 125 (215)
T ss_pred HHHHHHHcCCCeEEecCCCHHHHHHHHHHHhC
Confidence 34578899999999999999998887666543
No 59
>PRK09483 response regulator; Provisional
Probab=59.56 E-value=7.1 Score=34.08 Aligned_cols=28 Identities=21% Similarity=0.253 Sum_probs=23.1
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQ 33 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQ 33 (463)
.+.+++..||.+||.||+...+|...=.
T Consensus 89 ~~~~~~~~g~~~~l~k~~~~~~l~~~i~ 116 (217)
T PRK09483 89 LPAKVMQAGAAGYLSKGAAPQEVVSAIR 116 (217)
T ss_pred HHHHHHHcCCCEEEeCCCCHHHHHHHHH
Confidence 4568899999999999999998865533
No 60
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=58.87 E-value=16 Score=30.64 Aligned_cols=32 Identities=28% Similarity=0.577 Sum_probs=24.6
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVH 37 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~R 37 (463)
...+++..||.+|+.||+...+|...-+.+.+
T Consensus 89 ~~~~~~~~g~~~~l~~p~~~~~l~~~l~~~~~ 120 (202)
T PRK09390 89 LAVEAMKLGAVDFIEKPFEDERLIGAIERALA 120 (202)
T ss_pred HHHHHHHcChHHHhhCCCCHHHHHHHHHHHHH
Confidence 45578999999999999999887665444443
No 61
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=57.95 E-value=68 Score=32.63 Aligned_cols=26 Identities=19% Similarity=0.155 Sum_probs=20.6
Q ss_pred CCcHHHHHhhhchhhhhhcccCCccc
Q 012449 259 GLTRHNVASHLQKYRMHRRHILPKED 284 (463)
Q Consensus 259 gLTr~~VkSHLQKYRl~~k~~l~~e~ 284 (463)
-||-.|||.-.|.-|...|+....+.
T Consensus 142 qLTETQVKIWFQNRRnKwKRq~aad~ 167 (268)
T KOG0485|consen 142 QLTETQVKIWFQNRRNKWKRQYAADL 167 (268)
T ss_pred hhhhhhhhhhhhhhhHHHHHHHhhhh
Confidence 58999999999999887776555444
No 62
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=57.33 E-value=6.8 Score=42.61 Aligned_cols=27 Identities=22% Similarity=0.413 Sum_probs=23.6
Q ss_pred HHHHHHhhcchhhhhhcCCCHHHHHHH
Q 012449 5 QLFDNNFQLGAVEFLRKPLSEDKLRNL 31 (463)
Q Consensus 5 ~vv~Kcl~~GA~DyLiKPlr~neLkni 31 (463)
....+|++.||.|||.||+...+|...
T Consensus 754 ~~~~~~~~~G~~~~l~KP~~~~~L~~~ 780 (919)
T PRK11107 754 GERERLLSAGMDDYLAKPIDEAMLKQV 780 (919)
T ss_pred HHHHHHHHcCCCeEeeCCCCHHHHHHH
Confidence 456689999999999999999998665
No 63
>PRK15347 two component system sensor kinase SsrA; Provisional
Probab=56.45 E-value=8.5 Score=41.99 Aligned_cols=31 Identities=16% Similarity=0.232 Sum_probs=26.0
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVV 36 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~ 36 (463)
...+|+..||.|||.||+..++|...-..+.
T Consensus 780 ~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~ 810 (921)
T PRK15347 780 EIHRCKKAGMNHYLTKPVTLAQLARALELAA 810 (921)
T ss_pred HHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence 4568999999999999999999987755443
No 64
>COG3706 PleD Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]
Probab=55.58 E-value=6.5 Score=42.17 Aligned_cols=24 Identities=38% Similarity=0.780 Sum_probs=20.6
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLR 29 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLk 29 (463)
.+.+++..||.|||.|||...+|.
T Consensus 220 ~~~~Af~~G~~Dyi~kPi~~~~l~ 243 (435)
T COG3706 220 LVVRAFELGVNDYITKPIEEGELR 243 (435)
T ss_pred HHHHHHHcCCcceEecCCCHHHHH
Confidence 456999999999999999977664
No 65
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=55.38 E-value=7 Score=39.59 Aligned_cols=30 Identities=23% Similarity=0.376 Sum_probs=24.7
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHV 35 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV 35 (463)
.+..++..||.|||.||+...+|...=+++
T Consensus 90 ~~~~a~~~Ga~d~l~KP~~~~~L~~~i~~~ 119 (457)
T PRK11361 90 TAVEALRCGAFDYVIKPFDLDELNLIVQRA 119 (457)
T ss_pred HHHHHHHCCccEEEecccCHHHHHHHHhhh
Confidence 456899999999999999999987765444
No 66
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=55.28 E-value=8.8 Score=32.31 Aligned_cols=30 Identities=20% Similarity=0.255 Sum_probs=24.1
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHV 35 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV 35 (463)
....++..||.+||.||+...+|...=+.+
T Consensus 91 ~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~ 120 (211)
T PRK15369 91 MASRTLAAGALGYVLKKSPQQILLAAIQTV 120 (211)
T ss_pred HHHHHHHhCCCEEEeCCCCHHHHHHHHHHH
Confidence 455789999999999999998887664443
No 67
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=51.34 E-value=12 Score=41.18 Aligned_cols=33 Identities=15% Similarity=0.219 Sum_probs=27.6
Q ss_pred HHHHHHhhcchhhhhhcCCCHHHHHHHHHHHHH
Q 012449 5 QLFDNNFQLGAVEFLRKPLSEDKLRNLWQHVVH 37 (463)
Q Consensus 5 ~vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~R 37 (463)
....+|+..|+.+||.||+..++|...=.++.+
T Consensus 767 ~~~~~~~~~g~~~~l~KP~~~~~L~~~i~~~~~ 799 (914)
T PRK11466 767 ETLRQRTSSLFRGIIPKPVPREVLGQLLAHYLQ 799 (914)
T ss_pred hhHHHHHhcCcCCEEeCCCCHHHHHHHHHHHhh
Confidence 445689999999999999999999887666553
No 68
>PF07830 PP2C_C: Protein serine/threonine phosphatase 2C, C-terminal domain; InterPro: IPR012911 Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain []. ; GO: 0000287 magnesium ion binding, 0004721 phosphoprotein phosphatase activity, 0030145 manganese ion binding; PDB: 2P8E_A 3FXL_A 3FXO_A 1A6Q_A 3FXK_A 3FXM_A 3FXJ_A.
Probab=50.89 E-value=23 Score=30.31 Aligned_cols=39 Identities=26% Similarity=0.404 Sum_probs=22.6
Q ss_pred HHHHHHHHHHhCCCCCCCCCCCCCChhHHHHHHHHcCCCCCCCC
Q 012449 413 VIDKVVKEAISKPWLPLPLGLKPPSADSVLAELSRQGISTIPPR 456 (463)
Q Consensus 413 ~iDaai~dvl~kPWlPLPLGLKpPs~dsVm~EL~rQGi~~iPp~ 456 (463)
.|.+-|.|+|.+-. .-..|++..||..|+..-|++.||.
T Consensus 27 ~l~~rv~ei~~~~~-----~~~~~~l~~V~~~L~~e~ip~LPPG 65 (81)
T PF07830_consen 27 YLEQRVEEIIEKSS-----EEENPDLVYVMRTLASEDIPGLPPG 65 (81)
T ss_dssp HHHHHHHHHT---------------HHHHHHHHHHTT-SS--TT
T ss_pred HHHHHHHHHHHHhc-----ccCCCCHHHHHHHHHhccCCCCcCC
Confidence 45566788998822 3567899999999999999999996
No 69
>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS. This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (pfam02518), HAMP (pfam00672), phosphoacceptor (pfam00512), and phosphotransfer (pfam01627) domains and a response regulator receiver domain (pfam00072).
Probab=49.69 E-value=12 Score=41.30 Aligned_cols=32 Identities=22% Similarity=0.366 Sum_probs=26.4
Q ss_pred HHHHHHhhcchhhhhhcCCCHHHHHHHHHHHH
Q 012449 5 QLFDNNFQLGAVEFLRKPLSEDKLRNLWQHVV 36 (463)
Q Consensus 5 ~vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~ 36 (463)
+...+|+..|+.+||.||++..+|...-..+.
T Consensus 790 ~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~ 821 (968)
T TIGR02956 790 EDVAQYLAAGFDGFLAKPVVEEQLTAMIAVIL 821 (968)
T ss_pred HHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHh
Confidence 34568999999999999999999987755443
No 70
>PRK10651 transcriptional regulator NarL; Provisional
Probab=48.80 E-value=14 Score=31.66 Aligned_cols=31 Identities=19% Similarity=0.216 Sum_probs=24.4
Q ss_pred HHHHHhhcchhhhhhcCCCHHHHHHHHHHHH
Q 012449 6 LFDNNFQLGAVEFLRKPLSEDKLRNLWQHVV 36 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr~neLkniWQHV~ 36 (463)
.+..++..||.+|+.||+...+|...=+.+.
T Consensus 94 ~~~~~~~~g~~~~i~k~~~~~~l~~~i~~~~ 124 (216)
T PRK10651 94 DVVTALKRGADGYLLKDMEPEDLLKALQQAA 124 (216)
T ss_pred HHHHHHHcCCCEEEeCCCCHHHHHHHHHHHH
Confidence 4558899999999999999988776644443
No 71
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=44.24 E-value=24 Score=28.48 Aligned_cols=50 Identities=16% Similarity=0.296 Sum_probs=34.1
Q ss_pred cCCHHHHHHHHHHHHHh---C-C-CCCCch-----HHHhhcCC---CCCcHHHHHhhhchhhh
Q 012449 225 DWTPELHKKFVQAVEQL---G-V-DQAIPS-----RILELMKV---EGLTRHNVASHLQKYRM 274 (463)
Q Consensus 225 ~WT~ELH~rFV~AV~qL---G-~-dkAtPK-----~ILelM~V---~gLTr~~VkSHLQKYRl 274 (463)
.||++..+.||+.+-+. | . .....+ .|.+.|+- -.+|..||++|++..|.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~ 63 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKK 63 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHH
Confidence 59999999999988653 4 2 223333 35555553 35799999999876554
No 72
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=40.93 E-value=18 Score=39.31 Aligned_cols=30 Identities=23% Similarity=0.292 Sum_probs=25.0
Q ss_pred HHHHhhcchhhhhhcCCCHHHHHHHHHHHH
Q 012449 7 FDNNFQLGAVEFLRKPLSEDKLRNLWQHVV 36 (463)
Q Consensus 7 v~Kcl~~GA~DyLiKPlr~neLkniWQHV~ 36 (463)
..+|+..||.|||.||++..+|...-.+++
T Consensus 614 ~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~ 643 (779)
T PRK11091 614 KKEYLDAGMDDVLSKPLSVPALTAMIKKFW 643 (779)
T ss_pred HHHHHHCCCCEEEECCCCHHHHHHHHHHHh
Confidence 458999999999999999999877755544
No 73
>PRK12555 chemotaxis-specific methylesterase; Provisional
Probab=40.14 E-value=19 Score=35.57 Aligned_cols=18 Identities=17% Similarity=0.233 Sum_probs=16.1
Q ss_pred HHHHHhhcchhhhhhcCC
Q 012449 6 LFDNNFQLGAVEFLRKPL 23 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPl 23 (463)
.+.+|+..||.|||.||+
T Consensus 89 ~~~~al~~Ga~d~l~KP~ 106 (337)
T PRK12555 89 RVFEAMGAGALDAVDTPT 106 (337)
T ss_pred HHHHHHhcCceEEEECCC
Confidence 355899999999999999
No 74
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=39.93 E-value=21 Score=40.84 Aligned_cols=28 Identities=25% Similarity=0.255 Sum_probs=23.8
Q ss_pred HHHHHHhhcchhhhhhcCCCHHHHHHHH
Q 012449 5 QLFDNNFQLGAVEFLRKPLSEDKLRNLW 32 (463)
Q Consensus 5 ~vv~Kcl~~GA~DyLiKPlr~neLkniW 32 (463)
....+|++.||.|||.||+...+|...=
T Consensus 1043 ~~~~~~~~~G~~~~l~KP~~~~~L~~~l 1070 (1197)
T PRK09959 1043 NEREKGLSCGMNLCLFKPLTLDVLKTHL 1070 (1197)
T ss_pred HHHHHHHHCCCCEEEeCCCCHHHHHHHH
Confidence 3456899999999999999999987653
No 75
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=38.37 E-value=30 Score=31.06 Aligned_cols=57 Identities=14% Similarity=0.296 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHhCCC-----------CCCchHHHhhcCCCCCcHHHHHhhhchhhhhhcccCCccc-cccC
Q 012449 229 ELHKKFVQAVEQLGVD-----------QAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHILPKED-DRKW 288 (463)
Q Consensus 229 ELH~rFV~AV~qLG~d-----------kAtPK~ILelM~V~gLTr~~VkSHLQKYRl~~k~~l~~e~-~~~w 288 (463)
++...+.+++.+|... .-+.+.|-+.| |+|...|+++|.+=|..++..+..+. .+.|
T Consensus 120 ~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~l---gis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~ 188 (189)
T PRK12515 120 DTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIV---GIPESTVKTRMFYARKKLAELLKAAGVERGW 188 (189)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH---CcCHHHHHHHHHHHHHHHHHHHHHhccccCC
Confidence 3455566667666522 34445555555 55778888888888887777666554 5566
No 76
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=38.02 E-value=23 Score=38.23 Aligned_cols=52 Identities=23% Similarity=0.369 Sum_probs=34.5
Q ss_pred cccCCHHHHHHHHHHHHHhCCCCCCchH--------------HHhhcCC---CCCcHHHHHhhhchhhhh
Q 012449 223 KVDWTPELHKKFVQAVEQLGVDQAIPSR--------------ILELMKV---EGLTRHNVASHLQKYRMH 275 (463)
Q Consensus 223 Rl~WT~ELH~rFV~AV~qLG~dkAtPK~--------------ILelM~V---~gLTr~~VkSHLQKYRl~ 275 (463)
-=+|+++.-+.|.+|+...- ..-+=|- |-..++. +--||.||.||.|.....
T Consensus 76 egvWSpdIEqsFqEALaiyp-pcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarr 144 (455)
T KOG3841|consen 76 EGVWSPDIEQSFQEALAIYP-PCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARR 144 (455)
T ss_pred ccccChhHHHHHHHHHhhcC-CCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHH
Confidence 34899999999999998752 0011122 2222222 457999999999986544
No 77
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=36.17 E-value=46 Score=29.91 Aligned_cols=50 Identities=22% Similarity=0.357 Sum_probs=39.5
Q ss_pred ccCCHHHHHHHHHHHHHhCCCCCCchHHHhhcCCCCCcHHHHHhhhchhhhhhcccCCc
Q 012449 224 VDWTPELHKKFVQAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHILPK 282 (463)
Q Consensus 224 l~WT~ELH~rFV~AV~qLG~dkAtPK~ILelM~V~gLTr~~VkSHLQKYRl~~k~~l~~ 282 (463)
+-=..|+|++....|..||..+.|-..+++-+ ++-||..|+--+..+..+
T Consensus 83 vyI~~e~h~~l~~Iv~~ig~~~~si~~yidNI---------L~~Hle~~~eeI~~l~~~ 132 (136)
T PF11888_consen 83 VYISRETHERLSRIVRVIGERKMSISGYIDNI---------LRHHLEEYREEINELYEK 132 (136)
T ss_pred eEECHHHHHHHHHHHHHHCCCCCcHHHHHHHH---------HHHHHHHHHHHHHHHHHH
Confidence 77789999999999999998777777666644 567999999877665443
No 78
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=34.39 E-value=39 Score=34.25 Aligned_cols=60 Identities=27% Similarity=0.383 Sum_probs=42.7
Q ss_pred ccCCCCCcccCCH----HHHHHHHHHHHHhCCCCCCchHHHhhcCCCCCcHHHHHhhhchhhhhhcccCC
Q 012449 216 KANRKKMKVDWTP----ELHKKFVQAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHILP 281 (463)
Q Consensus 216 ~~~~kK~Rl~WT~----ELH~rFV~AV~qLG~dkAtPK~ILelM~V~gLTr~~VkSHLQKYRl~~k~~l~ 281 (463)
..+.||+|-..+. .|.+||-..= -| |.|.+- ||--.-|||..+||.-.|.=|...|+++.
T Consensus 119 ~KK~RKPRTIYSS~QLqaL~rRFQkTQ-YL----ALPERA-eLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQALNRRFQQTQ-YL----ALPERA-ELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cccccCCcccccHHHHHHHHHHHhhcc-hh----cCcHHH-HHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 4467788888875 6888886642 22 444432 23334599999999999999998888765
No 79
>PRK00742 chemotaxis-specific methylesterase; Provisional
Probab=33.13 E-value=38 Score=33.69 Aligned_cols=19 Identities=37% Similarity=0.679 Sum_probs=16.6
Q ss_pred HHHHHhhcchhhhhhcCCC
Q 012449 6 LFDNNFQLGAVEFLRKPLS 24 (463)
Q Consensus 6 vv~Kcl~~GA~DyLiKPlr 24 (463)
...+++..||.|||.||+.
T Consensus 92 ~~~~al~~Ga~d~l~kP~~ 110 (354)
T PRK00742 92 ITLRALELGAVDFVTKPFL 110 (354)
T ss_pred HHHHHHhCCCcEEEeCCcc
Confidence 4568999999999999994
No 80
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=32.49 E-value=33 Score=32.54 Aligned_cols=25 Identities=12% Similarity=0.012 Sum_probs=20.4
Q ss_pred HHHHh-hcchhhhhhcCCCHHHHHHH
Q 012449 7 FDNNF-QLGAVEFLRKPLSEDKLRNL 31 (463)
Q Consensus 7 v~Kcl-~~GA~DyLiKPlr~neLkni 31 (463)
+.+++ +.||.+||.||...++|..-
T Consensus 83 ~~~~~~~~Ga~gyl~K~~~~~eL~~a 108 (207)
T PRK11475 83 LIGSLSPSPLDGVLSKASTLEILQQE 108 (207)
T ss_pred HHHHHHHcCCeEEEecCCCHHHHHHH
Confidence 44555 79999999999999988755
No 81
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=31.52 E-value=54 Score=28.44 Aligned_cols=51 Identities=14% Similarity=0.061 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHhCCC-----------CCCchHHHhhcCCCCCcHHHHHhhhchhhhhhcccCCcc
Q 012449 230 LHKKFVQAVEQLGVD-----------QAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHILPKE 283 (463)
Q Consensus 230 LH~rFV~AV~qLG~d-----------kAtPK~ILelM~V~gLTr~~VkSHLQKYRl~~k~~l~~e 283 (463)
+-..+..|+++|... .-+.+.|-+.| |++...|++||.+-|..++..+.++
T Consensus 96 ~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~l---gis~~tV~~~l~Rar~~Lr~~l~~~ 157 (160)
T PRK09642 96 QKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQE---KIEVKTVEMKLYRARKWIKKHWKEE 157 (160)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHH---CCCHHHHHHHHHHHHHHHHHHHhhh
Confidence 344566666666522 33445555555 6678889999999888888776543
No 82
>cd03412 CbiK_N Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases and is a homomeric enzyme that does not require ATP for its enzymatic activity.
Probab=25.51 E-value=53 Score=28.99 Aligned_cols=22 Identities=23% Similarity=0.551 Sum_probs=19.9
Q ss_pred CCCCCChhHHHHHHHHcCCCCC
Q 012449 432 GLKPPSADSVLAELSRQGISTI 453 (463)
Q Consensus 432 GLKpPs~dsVm~EL~rQGi~~i 453 (463)
|++-|+++.+|.+|.++|+..|
T Consensus 52 ~~~~p~~~eaL~~l~~~G~~~V 73 (127)
T cd03412 52 GIEVDTPEEALAKLAADGYTEV 73 (127)
T ss_pred CCCCCCHHHHHHHHHHCCCCEE
Confidence 5788999999999999999864
No 83
>cd03409 Chelatase_Class_II Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the cobaltochelatases, CbiK and CbiX. HemH and SirB are involved in heme and siroheme biosynthesis, respectively, while the cobaltochelatases are associated with cobalamin biosynthesis. Excluded from this family are the ATP-dependent heterotrimeric chelatases (class I) and the multifunctional homodimeric enzymes with dehydrogenase and chelatase activities (class III).
Probab=25.37 E-value=72 Score=25.66 Aligned_cols=19 Identities=21% Similarity=0.473 Sum_probs=17.0
Q ss_pred CCCChhHHHHHHHHcCCCC
Q 012449 434 KPPSADSVLAELSRQGIST 452 (463)
Q Consensus 434 KpPs~dsVm~EL~rQGi~~ 452 (463)
-.|+++.++.+|.++|+..
T Consensus 43 ~~P~i~~~l~~l~~~g~~~ 61 (101)
T cd03409 43 LGPDTEEAIRELAEEGYQR 61 (101)
T ss_pred CCCCHHHHHHHHHHcCCCe
Confidence 4789999999999999875
No 84
>COG3360 Uncharacterized conserved protein [Function unknown]
Probab=24.08 E-value=35 Score=28.92 Aligned_cols=15 Identities=27% Similarity=0.483 Sum_probs=13.2
Q ss_pred cHHHHHHHHHHHHhC
Q 012449 410 AEEVIDKVVKEAISK 424 (463)
Q Consensus 410 s~E~iDaai~dvl~k 424 (463)
|++|||+||.++|.+
T Consensus 15 Sp~S~d~Ai~~Ai~R 29 (71)
T COG3360 15 SPTSIDAAIANAIAR 29 (71)
T ss_pred CCccHHHHHHHHHHH
Confidence 679999999999864
No 85
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=23.06 E-value=27 Score=27.46 Aligned_cols=20 Identities=35% Similarity=0.858 Sum_probs=17.0
Q ss_pred CCCCCCChhHHHHHHHHcCC
Q 012449 431 LGLKPPSADSVLAELSRQGI 450 (463)
Q Consensus 431 LGLKpPs~dsVm~EL~rQGi 450 (463)
||.+||++-..+..|.++|.
T Consensus 32 L~vs~~tvt~ml~~L~~~Gl 51 (60)
T PF01325_consen 32 LGVSPPTVTEMLKRLAEKGL 51 (60)
T ss_dssp HTS-HHHHHHHHHHHHHTTS
T ss_pred HCCChHHHHHHHHHHHHCCC
Confidence 68999999999999999986
No 86
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=22.60 E-value=1.2e+02 Score=20.58 Aligned_cols=29 Identities=17% Similarity=0.206 Sum_probs=19.3
Q ss_pred CCCchHHHhhcCCCCCcHHHHHhhhchhhhhh
Q 012449 245 QAIPSRILELMKVEGLTRHNVASHLQKYRMHR 276 (463)
Q Consensus 245 kAtPK~ILelM~V~gLTr~~VkSHLQKYRl~~ 276 (463)
.-+.+.|-+.|| ++...|.+++++.+..+
T Consensus 26 ~~~~~~ia~~~~---~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 26 GLSYEEIAEILG---ISRSTVRQRLHRALKKL 54 (55)
T ss_pred CCCHHHHHHHHC---cCHHHHHHHHHHHHHHc
Confidence 346677777774 56777777777665543
No 87
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=21.80 E-value=1.8e+02 Score=21.80 Aligned_cols=41 Identities=20% Similarity=0.286 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHHHhCCCCCCchHHHhhcCCCCCcHHHHHhhhch
Q 012449 226 WTPELHKKFVQAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQK 271 (463)
Q Consensus 226 WT~ELH~rFV~AV~qLG~dkAtPK~ILelM~V~gLTr~~VkSHLQK 271 (463)
||.|=-++.+++|.+.|. .-+.|-+.|+ .-|..+|+.+..+
T Consensus 1 WT~eEd~~L~~~~~~~g~---~W~~Ia~~l~--~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN---DWKKIAEHLG--NRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS----HHHHHHHST--TS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc---CHHHHHHHHC--cCCHHHHHHHHHH
Confidence 999999999999999985 3688999985 5788888876655
No 88
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=21.59 E-value=1.4e+02 Score=31.16 Aligned_cols=57 Identities=23% Similarity=0.263 Sum_probs=39.4
Q ss_pred ccCCCCCcccCCH----HHHHHHHHHHHHhCCCCCCchHHHhhcCCCCCcHHHHHhhhchhhhhhcc
Q 012449 216 KANRKKMKVDWTP----ELHKKFVQAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRH 278 (463)
Q Consensus 216 ~~~~kK~Rl~WT~----ELH~rFV~AV~qLG~dkAtPK~ILelM~V~gLTr~~VkSHLQKYRl~~k~ 278 (463)
...+||+|+-.|. ||-|||-..=..=+.+ +..|-. .-.||-.|||.=.|..|=..||
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPE----RE~LA~--~LrLT~TQVKIWFQNrRYK~KR 210 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPE----REHLAS--SLRLTPTQVKIWFQNRRYKTKR 210 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHh----HHHHHH--hcCCCchheeeeeecchhhhhh
Confidence 5578899999986 9999997643333322 222221 2389999999999988865544
No 89
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=21.50 E-value=87 Score=28.12 Aligned_cols=49 Identities=20% Similarity=0.169 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHhCCC-----------CCCchHHHhhcCCCCCcHHHHHhhhchhhhhhcccC
Q 012449 229 ELHKKFVQAVEQLGVD-----------QAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHIL 280 (463)
Q Consensus 229 ELH~rFV~AV~qLG~d-----------kAtPK~ILelM~V~gLTr~~VkSHLQKYRl~~k~~l 280 (463)
++++.|.+|+..|... .-+.+.|-+.| |+|...|++||++=|..+++.+
T Consensus 127 ~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l---gis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 127 EIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVM---QCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred HHHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHHH---CCCHHHHHHHHHHHHHHHHHHH
Confidence 4566788888887632 12233333333 4456667777777766666544
No 90
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=21.18 E-value=1.5e+02 Score=25.42 Aligned_cols=47 Identities=23% Similarity=0.274 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHhCCCCCCchHHHhhcCCC-----------CCcHHHHHhhhchhhhhhc
Q 012449 228 PELHKKFVQAVEQLGVDQAIPSRILELMKVE-----------GLTRHNVASHLQKYRMHRR 277 (463)
Q Consensus 228 ~ELH~rFV~AV~qLG~dkAtPK~ILelM~V~-----------gLTr~~VkSHLQKYRl~~k 277 (463)
.+++..+.+|+++|.... +.|+.+.-+. |+|...|+++|.+=|..++
T Consensus 99 ~~~~~~l~~~i~~L~~~~---r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 99 EDELQALEGCLEKLPERQ---RELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred HHHHHHHHHHHHHCCHHH---HHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 456667788888887332 3344433333 4455556666555554443
No 91
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.93 E-value=2.9e+02 Score=30.73 Aligned_cols=108 Identities=16% Similarity=0.249 Sum_probs=0.0
Q ss_pred HHhhhchhhhh-hcccCCccccccCchhhhhhhccc-CCCCCCcCCCCCCCCCCCCCCCCCcccCCCCcccccccccCCC
Q 012449 265 VASHLQKYRMH-RRHILPKEDDRKWPHARDQMLRNY-YPHKPIMAFPPYHSNHLVPTGPVYPVWGAPSNHLAAVQMWAPP 342 (463)
Q Consensus 265 VkSHLQKYRl~-~k~~l~~e~~~~w~~~R~~~~~ny-~~~~p~~~f~p~~s~h~~p~~~~~~vwG~p~~~~~~~~~W~~p 342 (463)
.+.|-|.||.+ .++...|.....-+..+...+-++ -......++.|+.+++. |+.+.+.++ .+
T Consensus 367 n~p~~~~y~~r~~~~gf~rp~s~~~q~pP~~~q~~~~p~~~~~s~p~pq~qNyp-pp~p~f~m~--------------~~ 431 (483)
T KOG2236|consen 367 NQPAPQMYRGRDQNRGFKRPRSNHGQKPPQSAQNSFHPSSSDNSGPSPQQQNYP-PPSPSFPMF--------------QP 431 (483)
T ss_pred cCCcccccCCcccccCCCCcccccCCCCCcccccccCccccCCCCCCcccCCCC-CCCCCCCcc--------------CC
Q ss_pred CCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 012449 343 GYPPWQQAESWNWK-PYPGMPADAWGCPVMPLPNGPYSSFPQGASGYHN 390 (463)
Q Consensus 343 ~~~~w~p~~~w~~~-py~~~~a~awG~p~~p~~~~p~~~~p~~~~g~~~ 390 (463)
..+.=.|+...-|. ||.+|..-- |++-++.+|..+++.+.+-+..
T Consensus 432 hP~~~~p~~~~g~~~P~~~mpp~~---P~~~~pppP~~pp~p~~~~~q~ 477 (483)
T KOG2236|consen 432 HPPESNPPANFGQANPFNQMPPAY---PHQQSPPPPPPPPPPNSPMNQM 477 (483)
T ss_pred CCCCCCCcccccccCccccCCCCC---ccccCCCCCCCCCCCCChhhcc
No 92
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=20.83 E-value=1e+02 Score=25.18 Aligned_cols=34 Identities=15% Similarity=0.301 Sum_probs=28.2
Q ss_pred hHHHHHHhhcchhhhhhcCC--CHHHHHHHHHHHHH
Q 012449 4 NQLFDNNFQLGAVEFLRKPL--SEDKLRNLWQHVVH 37 (463)
Q Consensus 4 ~~vv~Kcl~~GA~DyLiKPl--r~neLkniWQHV~R 37 (463)
-+++.+|++.|--=|+.||+ +.+|++.|.+-.-+
T Consensus 76 ~~~~~~~l~~g~~v~~EKP~~~~~~~~~~l~~~a~~ 111 (120)
T PF01408_consen 76 AEIAKKALEAGKHVLVEKPLALTLEEAEELVEAAKE 111 (120)
T ss_dssp HHHHHHHHHTTSEEEEESSSSSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCEEEEEcCCcCCHHHHHHHHHHHHH
Confidence 46788999999999999999 88899888665443
No 93
>PLN02878 homogentisate phytyltransferase
Probab=20.23 E-value=42 Score=34.38 Aligned_cols=16 Identities=38% Similarity=0.748 Sum_probs=13.2
Q ss_pred HHHhCCCCCCCCCCCC
Q 012449 420 EAISKPWLPLPLGLKP 435 (463)
Q Consensus 420 dvl~kPWlPLPLGLKp 435 (463)
|.|+||++|+|=|-=.
T Consensus 51 DkINkP~rPIpSG~iS 66 (280)
T PLN02878 51 DKVNKPYLPLASGEFS 66 (280)
T ss_pred cccCCCCCCCCCCCCC
Confidence 4689999999999543
Done!