Query 041805
Match_columns 215
No_of_seqs 199 out of 1623
Neff 8.7
Searched_HMMs 46136
Date Fri Mar 29 10:50:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041805.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041805hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03210 Resistant to P. syrin 100.0 7.8E-39 1.7E-43 309.5 19.1 214 1-215 348-635 (1153)
2 KOG4658 Apoptotic ATPase [Sign 100.0 1.1E-39 2.4E-44 305.0 10.1 156 1-156 314-496 (889)
3 PF00931 NB-ARC: NB-ARC domain 99.9 1.7E-22 3.6E-27 168.5 2.8 121 1-121 154-284 (287)
4 PF07725 LRR_3: Leucine Rich R 98.6 2.7E-08 5.9E-13 48.6 1.6 20 192-211 1-20 (20)
5 PRK04841 transcriptional regul 98.2 1.5E-05 3.2E-10 76.5 12.3 147 3-158 185-335 (903)
6 PF00560 LRR_1: Leucine Rich R 97.1 0.00021 4.5E-09 36.0 1.2 22 192-213 1-22 (22)
7 PRK00080 ruvB Holliday junctio 96.7 0.0076 1.7E-07 51.4 7.6 132 1-140 177-314 (328)
8 TIGR00635 ruvB Holliday juncti 96.7 0.018 4E-07 48.3 9.8 132 1-142 156-295 (305)
9 PF13504 LRR_7: Leucine rich r 96.3 0.0023 4.9E-08 30.0 1.2 17 191-207 1-17 (17)
10 PF12799 LRR_4: Leucine Rich r 95.1 0.013 2.9E-07 34.7 1.6 25 183-207 15-40 (44)
11 smart00369 LRR_TYP Leucine-ric 95.1 0.015 3.2E-07 30.1 1.5 21 190-210 1-21 (26)
12 smart00370 LRR Leucine-rich re 95.1 0.015 3.2E-07 30.1 1.5 21 190-210 1-21 (26)
13 COG3903 Predicted ATPase [Gene 94.5 0.086 1.9E-06 46.0 5.7 155 2-158 139-317 (414)
14 smart00364 LRR_BAC Leucine-ric 91.5 0.13 2.7E-06 26.9 1.4 18 191-208 2-19 (26)
15 KOG0617 Ras suppressor protein 91.4 0.043 9.3E-07 42.8 -0.6 32 183-214 47-79 (264)
16 PF13855 LRR_8: Leucine rich r 91.2 0.2 4.3E-06 31.4 2.4 32 183-214 15-49 (61)
17 PF12799 LRR_4: Leucine Rich r 91.2 0.12 2.6E-06 30.5 1.2 25 191-215 1-25 (44)
18 smart00365 LRR_SD22 Leucine-ri 89.8 0.26 5.6E-06 25.7 1.6 18 190-207 1-18 (26)
19 COG3899 Predicted ATPase [Gene 89.2 2.4 5.2E-05 41.1 8.9 151 1-154 216-385 (849)
20 COG2909 MalT ATP-dependent tra 84.5 14 0.00031 35.6 10.9 143 4-158 194-341 (894)
21 PF13516 LRR_6: Leucine Rich r 84.3 0.57 1.2E-05 23.5 1.0 16 190-205 1-16 (24)
22 TIGR03015 pepcterm_ATPase puta 82.4 7.2 0.00016 31.8 7.5 52 1-52 189-242 (269)
23 smart00368 LRR_RI Leucine rich 81.1 1.2 2.6E-05 23.4 1.5 14 191-204 2-15 (28)
24 PF13855 LRR_8: Leucine rich r 75.0 2.7 5.9E-05 26.0 2.2 21 183-203 39-61 (61)
25 PF13730 HTH_36: Helix-turn-he 73.9 7 0.00015 23.6 3.8 49 85-133 2-55 (55)
26 KOG0617 Ras suppressor protein 71.6 1.7 3.8E-05 34.0 0.7 31 183-213 70-101 (264)
27 KOG0472 Leucine-rich repeat pr 65.1 2.2 4.8E-05 37.7 0.1 26 189-214 503-528 (565)
28 PLN03150 hypothetical protein; 61.3 5.1 0.00011 37.4 1.8 31 183-213 457-489 (623)
29 KOG0444 Cytoskeletal regulator 56.5 4.8 0.0001 37.8 0.8 27 183-209 117-144 (1255)
30 PRK00411 cdc6 cell division co 55.5 1.4E+02 0.003 25.8 13.0 129 1-136 204-358 (394)
31 PF12802 MarR_2: MarR family; 53.6 20 0.00043 21.9 3.1 53 85-137 2-55 (62)
32 PF14580 LRR_9: Leucine-rich r 52.6 10 0.00022 29.4 1.9 28 183-210 56-83 (175)
33 KOG3665 ZYG-1-like serine/thre 52.4 7.5 0.00016 36.9 1.4 25 190-215 172-196 (699)
34 KOG4658 Apoptotic ATPase [Sign 52.3 7.4 0.00016 38.0 1.3 33 183-215 586-619 (889)
35 PLN03150 hypothetical protein; 49.2 9.7 0.00021 35.6 1.6 32 183-214 433-466 (623)
36 KOG4237 Extracellular matrix p 47.4 8.4 0.00018 34.0 0.8 24 183-206 81-106 (498)
37 KOG0472 Leucine-rich repeat pr 47.0 6.4 0.00014 35.0 -0.0 31 183-213 266-297 (565)
38 PF14580 LRR_9: Leucine-rich r 44.5 9.6 0.00021 29.6 0.6 24 183-206 78-103 (175)
39 PLN00113 leucine-rich repeat r 40.3 16 0.00035 35.7 1.6 31 183-213 203-235 (968)
40 KOG0618 Serine/threonine phosp 40.3 3.7 7.9E-05 39.9 -2.6 25 183-207 375-399 (1081)
41 PRK15387 E3 ubiquitin-protein 40.0 22 0.00048 34.3 2.4 25 89-113 48-72 (788)
42 smart00367 LRR_CC Leucine-rich 39.6 20 0.00044 18.0 1.3 13 190-202 1-13 (26)
43 PF03861 ANTAR: ANTAR domain; 38.2 38 0.00083 20.7 2.6 30 3-35 27-56 (56)
44 KOG0444 Cytoskeletal regulator 37.8 21 0.00046 33.8 1.8 20 120-140 142-161 (1255)
45 PLN00113 leucine-rich repeat r 36.6 19 0.00042 35.1 1.5 32 183-214 179-212 (968)
46 TIGR01610 phage_O_Nterm phage 35.9 1.4E+02 0.003 20.3 5.4 64 81-144 18-89 (95)
47 PRK15386 type III secretion pr 34.5 17 0.00036 32.4 0.7 21 191-211 94-115 (426)
48 KOG4579 Leucine-rich repeat (L 34.5 4.8 0.0001 30.5 -2.3 29 183-211 91-120 (177)
49 smart00346 HTH_ICLR helix_turn 34.4 1.3E+02 0.0029 19.6 6.6 63 94-156 11-74 (91)
50 PF02082 Rrf2: Transcriptional 33.9 73 0.0016 21.0 3.6 53 91-143 11-67 (83)
51 COG3355 Predicted transcriptio 33.4 1.5E+02 0.0033 21.7 5.4 61 74-137 14-76 (126)
52 PF05843 Suf: Suppressor of fo 33.1 2.8E+02 0.0061 22.9 7.8 98 6-104 17-120 (280)
53 PLN03210 Resistant to P. syrin 31.5 36 0.00078 34.3 2.5 28 183-210 793-822 (1153)
54 KOG4194 Membrane glycoprotein 31.3 27 0.00058 32.8 1.4 21 189-209 315-335 (873)
55 PF09114 MotA_activ: Transcrip 31.1 1.2E+02 0.0025 20.9 4.1 66 74-141 2-70 (96)
56 PF00486 Trans_reg_C: Transcri 30.9 67 0.0014 20.3 3.0 35 86-120 6-42 (77)
57 KOG0618 Serine/threonine phosp 30.6 25 0.00054 34.5 1.1 32 183-214 397-430 (1081)
58 KOG3926 F-box proteins [Amino 30.5 1.1E+02 0.0024 25.7 4.7 76 32-115 155-232 (332)
59 PF14050 Nudc_N: N-terminal co 30.1 56 0.0012 20.7 2.3 30 27-56 3-32 (62)
60 COG2033 Desulfoferrodoxin [Ene 28.9 17 0.00038 26.3 -0.1 17 197-213 109-125 (126)
61 PF13412 HTH_24: Winged helix- 28.8 96 0.0021 17.8 3.2 44 90-134 5-48 (48)
62 smart00862 Trans_reg_C Transcr 28.1 1.1E+02 0.0024 19.3 3.7 31 86-116 6-38 (78)
63 PRK13342 recombination factor 27.4 4.3E+02 0.0093 23.2 9.4 47 1-47 148-195 (413)
64 PF13545 HTH_Crp_2: Crp-like h 26.1 48 0.001 21.1 1.6 41 105-146 30-70 (76)
65 PRK15387 E3 ubiquitin-protein 26.1 58 0.0013 31.5 2.7 29 183-213 236-264 (788)
66 PF04089 BRICHOS: BRICHOS doma 25.8 42 0.00092 22.8 1.4 18 26-43 77-94 (97)
67 PRK07471 DNA polymerase III su 25.4 4.5E+02 0.0098 22.8 8.0 42 1-48 197-238 (365)
68 PF09840 DUF2067: Uncharacteri 24.6 2.7E+02 0.0058 21.9 5.8 48 96-143 131-179 (190)
69 COG4886 Leucine-rich repeat (L 24.5 35 0.00076 29.4 0.9 20 189-208 161-180 (394)
70 PRK11920 rirA iron-responsive 23.7 1.3E+02 0.0028 22.6 3.8 48 90-137 10-58 (153)
71 KOG0531 Protein phosphatase 1, 23.2 35 0.00076 30.0 0.7 20 189-208 116-135 (414)
72 PRK15370 E3 ubiquitin-protein 23.2 51 0.0011 31.7 1.8 20 89-108 45-64 (754)
73 PRK15370 E3 ubiquitin-protein 23.2 56 0.0012 31.5 2.0 27 183-210 213-239 (754)
74 PF01978 TrmB: Sugar-specific 22.5 70 0.0015 20.1 1.9 52 85-137 5-56 (68)
75 COG3636 Predicted transcriptio 22.4 2.8E+02 0.0061 19.4 6.5 43 4-48 17-59 (100)
76 smart00419 HTH_CRP helix_turn_ 21.2 1.2E+02 0.0027 16.9 2.6 23 121-144 26-48 (48)
77 KOG4194 Membrane glycoprotein 21.0 31 0.00066 32.4 -0.1 27 188-214 290-320 (873)
78 cd00383 trans_reg_C Effector d 20.7 1.7E+02 0.0036 19.2 3.6 32 86-117 24-57 (95)
79 PF03849 Tfb2: Transcription f 20.4 3.6E+02 0.0079 23.5 6.4 69 83-152 25-99 (366)
80 PRK06893 DNA replication initi 20.2 2.4E+02 0.0051 22.5 4.9 40 1-42 158-197 (229)
No 1
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=100.00 E-value=7.8e-39 Score=309.51 Aligned_cols=214 Identities=42% Similarity=0.673 Sum_probs=195.4
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCCchHHHHHHHHHHHhcCCchhHHhhhcccCCCCHHHHHHHHHHHhcCCchhHHHHHH
Q 041805 1 MEALEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVLGCFLYEREKEVWESAINKLQRILHPSILEVLK 80 (215)
Q Consensus 1 v~~L~~~ea~~Lf~~~af~~~~~~~~~~~~~~~iv~~c~GlPLal~~ig~~L~~k~~~~w~~~l~~l~~~~~~~i~~~l~ 80 (215)
|++|+++|||+||+++||+...+++++.+++++||++|+|+||||+++|+.|++++..+|+.++++++...+.+|..+|+
T Consensus 348 v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~k~~~~W~~~l~~L~~~~~~~I~~~L~ 427 (1153)
T PLN03210 348 VCLPSNELALEMFCRSAFKKNSPPDGFMELASEVALRAGNLPLGLNVLGSYLRGRDKEDWMDMLPRLRNGLDGKIEKTLR 427 (1153)
T ss_pred ecCCCHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcCCCHHHHHHHHHHHHhCccHHHHHHHH
Confidence 56889999999999999988777778999999999999999999999999999999999999999999888889999999
Q ss_pred HhhcCccH-HHHHHHHHHhhccCCCCHHHHHHHHHHcCCchhhhHHHHHhccCceeccCCeEEecHHHHHHHHHHHhhcc
Q 041805 81 ISYDGLDN-KEKNIFLDVACFFQGEDVNLVMKFLNASGFYPKLGRSVLVDKSLIVKSNNNKITMHDLLQELGRDIVSKES 159 (215)
Q Consensus 81 ~Sy~~L~~-~~k~~fl~~a~fp~~~~~~~l~~~w~~~g~~~~~~l~~L~~~~Ll~~~~~~~~~mHdlvr~~a~~i~~~e~ 159 (215)
+||++|++ ..|.||++||+||.+.+.+.+..++...|+.++..++.|+++||++.. +++++|||++|+||++++++++
T Consensus 428 ~SYd~L~~~~~k~~Fl~ia~ff~~~~~~~v~~~l~~~~~~~~~~l~~L~~ksLi~~~-~~~~~MHdLl~~~~r~i~~~~~ 506 (1153)
T PLN03210 428 VSYDGLNNKKDKAIFRHIACLFNGEKVNDIKLLLANSDLDVNIGLKNLVDKSLIHVR-EDIVEMHSLLQEMGKEIVRAQS 506 (1153)
T ss_pred HhhhccCccchhhhhheehhhcCCCCHHHHHHHHHhcCCCchhChHHHHhcCCEEEc-CCeEEhhhHHHHHHHHHHHhhc
Confidence 99999987 699999999999999988888887777888888899999999999987 6789999999999999999998
Q ss_pred CCCCCccccccccchhHhhhCCC---------------------------------------------------------
Q 041805 160 NNPGNCSLLWHHEDIYEVLTYNM--------------------------------------------------------- 182 (215)
Q Consensus 160 ~~~~~~~~l~~~~~~~~~l~~~~--------------------------------------------------------- 182 (215)
.+|++++++|.++|+++++..+.
T Consensus 507 ~~~~~r~~l~~~~di~~vl~~~~g~~~v~~i~l~~~~~~~~~i~~~aF~~m~~L~~L~~~~~~~~~~~~~~~~lp~~~~~ 586 (1153)
T PLN03210 507 NEPGEREFLVDAKDICDVLEDNTGTKKVLGITLDIDEIDELHIHENAFKGMRNLLFLKFYTKKWDQKKEVRWHLPEGFDY 586 (1153)
T ss_pred CCCCcceeEeCHHHHHHHHHhCcccceeeEEEeccCccceeeecHHHHhcCccccEEEEecccccccccceeecCcchhh
Confidence 88999999999988887764321
Q ss_pred ----------------CCCCCCCCCCceEEEcCCCCccccccccccCCC
Q 041805 183 ----------------SLPSNISAKKLVFLEMPNSSIEQLWDGMKVCET 215 (215)
Q Consensus 183 ----------------~lP~~~~~~~L~~L~L~~s~i~~L~~~~~~l~~ 215 (215)
++|+.|.+++|++|+|++|+|++||++++.|++
T Consensus 587 lp~~Lr~L~~~~~~l~~lP~~f~~~~L~~L~L~~s~l~~L~~~~~~l~~ 635 (1153)
T PLN03210 587 LPPKLRLLRWDKYPLRCMPSNFRPENLVKLQMQGSKLEKLWDGVHSLTG 635 (1153)
T ss_pred cCcccEEEEecCCCCCCCCCcCCccCCcEEECcCccccccccccccCCC
Confidence 678888889999999999999999999987764
No 2
>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]
Probab=100.00 E-value=1.1e-39 Score=304.96 Aligned_cols=156 Identities=30% Similarity=0.434 Sum_probs=140.0
Q ss_pred CCCCCHHHHHHHHHHhhcCCC-CCCchHHHHHHHHHHHhcCCchhHHhhhcccCCC-CHHHHHHHHHHHhcC-------C
Q 041805 1 MEALEYHLALERFSRHAFKQN-HPDVGYEELSSKAMKYAQGVPLALKVLGCFLYER-EKEVWESAINKLQRI-------L 71 (215)
Q Consensus 1 v~~L~~~ea~~Lf~~~af~~~-~~~~~~~~~~~~iv~~c~GlPLal~~ig~~L~~k-~~~~w~~~l~~l~~~-------~ 71 (215)
+.+|+++|||+||++.||+.. ...+.++++|++||++|+|||||++++|+.|+.| +..+|+.+.+.+... .
T Consensus 314 v~~L~~~eaW~LF~~~v~~~~~~~~~~i~~lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~~~ 393 (889)
T KOG4658|consen 314 VECLTPEEAWDLFQKKVGPNTLGSHPDIEELAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFSGM 393 (889)
T ss_pred ccccCccccHHHHHHhhccccccccccHHHHHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCCch
Confidence 578999999999999998764 3445589999999999999999999999999997 678999999987664 1
Q ss_pred chhHHHHHHHhhcCccHHHHHHHHHHhhccCCC--CHHHHHHHHHHcCCch------------hhhHHHHHhccCceecc
Q 041805 72 HPSILEVLKISYDGLDNKEKNIFLDVACFFQGE--DVNLVMKFLNASGFYP------------KLGRSVLVDKSLIVKSN 137 (215)
Q Consensus 72 ~~~i~~~l~~Sy~~L~~~~k~~fl~~a~fp~~~--~~~~l~~~w~~~g~~~------------~~~l~~L~~~~Ll~~~~ 137 (215)
+..|..+|++|||.||++.|.||+|||+||+|+ +++.++.+|+|+||+. ..|+.+|+++||+....
T Consensus 394 ~~~i~~iLklSyd~L~~~lK~CFLycalFPED~~I~~e~Li~yWiaEGfi~~~~~~~~~~d~G~~~i~~LV~~~Ll~~~~ 473 (889)
T KOG4658|consen 394 EESILPILKLSYDNLPEELKSCFLYCALFPEDYEIKKEKLIEYWIAEGFIDPLDGGETAEDVGYDYIEELVRASLLIEER 473 (889)
T ss_pred hhhhHHhhhccHhhhhHHHHHHHHhhccCCcccccchHHHHHHHHhccCcCccccccchhcchHHHHHHHHHHHHHhhcc
Confidence 467999999999999999999999999999998 8999999999999874 45799999999999875
Q ss_pred C----CeEEecHHHHHHHHHHHh
Q 041805 138 N----NKITMHDLLQELGRDIVS 156 (215)
Q Consensus 138 ~----~~~~mHdlvr~~a~~i~~ 156 (215)
. ..|+|||+||+||.+++.
T Consensus 474 ~~~~~~~~kmHDvvRe~al~ias 496 (889)
T KOG4658|consen 474 DEGRKETVKMHDVVREMALWIAS 496 (889)
T ss_pred cccceeEEEeeHHHHHHHHHHhc
Confidence 3 459999999999999999
No 3
>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=99.85 E-value=1.7e-22 Score=168.52 Aligned_cols=121 Identities=28% Similarity=0.518 Sum_probs=100.0
Q ss_pred CCCCCHHHHHHHHHHhhcCCC-CCCchHHHHHHHHHHHhcCCchhHHhhhcccCCC-CHHHHHHHHHHHhcCC------c
Q 041805 1 MEALEYHLALERFSRHAFKQN-HPDVGYEELSSKAMKYAQGVPLALKVLGCFLYER-EKEVWESAINKLQRIL------H 72 (215)
Q Consensus 1 v~~L~~~ea~~Lf~~~af~~~-~~~~~~~~~~~~iv~~c~GlPLal~~ig~~L~~k-~~~~w~~~l~~l~~~~------~ 72 (215)
|++|+++||++||++.++... ...+...+.+++|+++|+|+||||+++|+.|+.+ +..+|+.+++++.... .
T Consensus 154 l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~ 233 (287)
T PF00931_consen 154 LEPLSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSLRESRDYD 233 (287)
T ss_dssp CSS--HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCSSGSC
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 578999999999999997655 3445567789999999999999999999999654 5678999998865532 4
Q ss_pred hhHHHHHHHhhcCccHHHHHHHHHHhhccCCC--CHHHHHHHHHHcCCchh
Q 041805 73 PSILEVLKISYDGLDNKEKNIFLDVACFFQGE--DVNLVMKFLNASGFYPK 121 (215)
Q Consensus 73 ~~i~~~l~~Sy~~L~~~~k~~fl~~a~fp~~~--~~~~l~~~w~~~g~~~~ 121 (215)
..+..++.+||+.||++.|+||+|||+||.++ +.+.++.+|+++|++..
T Consensus 234 ~~~~~~l~~s~~~L~~~~~~~f~~L~~f~~~~~i~~~~li~lW~~e~~i~~ 284 (287)
T PF00931_consen 234 RSVFSALELSYDSLPDELRRCFLYLSIFPEGVPIPRERLIRLWVAEGFISS 284 (287)
T ss_dssp HHHHHHHHHHHHSSHTCCHHHHHHGGGSGTTS-EEHHHHHHHHTT-HHTC-
T ss_pred ccccccceechhcCCccHHHHHhhCcCCCCCceECHHHHHHHHHHCCCCcc
Confidence 77999999999999999999999999999987 79999999999998864
No 4
>PF07725 LRR_3: Leucine Rich Repeat; InterPro: IPR011713 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. This entry includes some LRRs that fail to be detected by the IPR001611 from INTERPRO model.
Probab=98.58 E-value=2.7e-08 Score=48.64 Aligned_cols=20 Identities=55% Similarity=1.036 Sum_probs=18.9
Q ss_pred CceEEEcCCCCccccccccc
Q 041805 192 KLVFLEMPNSSIEQLWDGMK 211 (215)
Q Consensus 192 ~L~~L~L~~s~i~~L~~~~~ 211 (215)
+|++|+|++|+|++||+|+|
T Consensus 1 ~LVeL~m~~S~lekLW~G~k 20 (20)
T PF07725_consen 1 NLVELNMPYSKLEKLWEGVK 20 (20)
T ss_pred CcEEEECCCCChHHhcCccC
Confidence 68999999999999999986
No 5
>PRK04841 transcriptional regulator MalT; Provisional
Probab=98.22 E-value=1.5e-05 Score=76.45 Aligned_cols=147 Identities=14% Similarity=0.181 Sum_probs=100.3
Q ss_pred CCCHHHHHHHHHHhhcCCCCCCchHHHHHHHHHHHhcCCchhHHhhhcccCCCCHHHHHHHHHHHhcCCchhHHHHHHHh
Q 041805 3 ALEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVLGCFLYEREKEVWESAINKLQRILHPSILEVLKIS 82 (215)
Q Consensus 3 ~L~~~ea~~Lf~~~af~~~~~~~~~~~~~~~iv~~c~GlPLal~~ig~~L~~k~~~~w~~~l~~l~~~~~~~i~~~l~~S 82 (215)
+++.+|+.++|.... +..- + .+...+|.+.|+|.|+++..++..+...+.. .......+...+...+...|.-.
T Consensus 185 ~f~~~e~~~ll~~~~-~~~~-~---~~~~~~l~~~t~Gwp~~l~l~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~ 258 (903)
T PRK04841 185 AFDHQEAQQFFDQRL-SSPI-E---AAESSRLCDDVEGWATALQLIALSARQNNSS-LHDSARRLAGINASHLSDYLVEE 258 (903)
T ss_pred CCCHHHHHHHHHhcc-CCCC-C---HHHHHHHHHHhCChHHHHHHHHHHHhhCCCc-hhhhhHhhcCCCchhHHHHHHHH
Confidence 789999999998765 3221 2 2445789999999999999988776543210 11112222222234566655444
Q ss_pred -hcCccHHHHHHHHHHhhccCCCCHHHHHHHHHHcCCchhhhHHHHHhccCcee-cc-C-CeEEecHHHHHHHHHHHhhc
Q 041805 83 -YDGLDNKEKNIFLDVACFFQGEDVNLVMKFLNASGFYPKLGRSVLVDKSLIVK-SN-N-NKITMHDLLQELGRDIVSKE 158 (215)
Q Consensus 83 -y~~L~~~~k~~fl~~a~fp~~~~~~~l~~~w~~~g~~~~~~l~~L~~~~Ll~~-~~-~-~~~~mHdlvr~~a~~i~~~e 158 (215)
++.||++.++.++..|+++ .++.+.+..+... -.....++.|.+.+++.. .+ + ..|++|+++|++.+.....+
T Consensus 259 v~~~l~~~~~~~l~~~a~~~-~~~~~l~~~l~~~--~~~~~~L~~l~~~~l~~~~~~~~~~~yr~H~L~r~~l~~~l~~~ 335 (903)
T PRK04841 259 VLDNVDLETRHFLLRCSVLR-SMNDALIVRVTGE--ENGQMRLEELERQGLFIQRMDDSGEWFRYHPLFASFLRHRCQWE 335 (903)
T ss_pred HHhcCCHHHHHHHHHhcccc-cCCHHHHHHHcCC--CcHHHHHHHHHHCCCeeEeecCCCCEEehhHHHHHHHHHHHHhc
Confidence 8899999999999999987 6666655544431 123678999999999764 22 2 36999999999998876433
No 6
>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....
Probab=97.15 E-value=0.00021 Score=35.96 Aligned_cols=22 Identities=9% Similarity=0.300 Sum_probs=19.4
Q ss_pred CceEEEcCCCCccccccccccC
Q 041805 192 KLVFLEMPNSSIEQLWDGMKVC 213 (215)
Q Consensus 192 ~L~~L~L~~s~i~~L~~~~~~l 213 (215)
+|++|||++|+|+.+|.++++|
T Consensus 1 ~L~~Ldls~n~l~~ip~~~~~l 22 (22)
T PF00560_consen 1 NLEYLDLSGNNLTSIPSSFSNL 22 (22)
T ss_dssp TESEEEETSSEESEEGTTTTT-
T ss_pred CccEEECCCCcCEeCChhhcCC
Confidence 5899999999999999998765
No 7
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=96.67 E-value=0.0076 Score=51.44 Aligned_cols=132 Identities=14% Similarity=0.075 Sum_probs=86.4
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCCchHHHHHHHHHHHhcCCchhHHhhhcccCCCCHHHHHHHHHHHhcCCc---hhHHH
Q 041805 1 MEALEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVLGCFLYEREKEVWESAINKLQRILH---PSILE 77 (215)
Q Consensus 1 v~~L~~~ea~~Lf~~~af~~~~~~~~~~~~~~~iv~~c~GlPLal~~ig~~L~~k~~~~w~~~l~~l~~~~~---~~i~~ 77 (215)
++++++++..+++.+.+-.... .--.+....|++.|+|.|-.+..+...+ ..|..... -..... .....
T Consensus 177 l~~~~~~e~~~il~~~~~~~~~--~~~~~~~~~ia~~~~G~pR~a~~~l~~~-----~~~a~~~~-~~~I~~~~v~~~l~ 248 (328)
T PRK00080 177 LEFYTVEELEKIVKRSARILGV--EIDEEGALEIARRSRGTPRIANRLLRRV-----RDFAQVKG-DGVITKEIADKALD 248 (328)
T ss_pred cCCCCHHHHHHHHHHHHHHcCC--CcCHHHHHHHHHHcCCCchHHHHHHHHH-----HHHHHHcC-CCCCCHHHHHHHHH
Confidence 4689999999999988732221 1224567899999999996554444322 12211110 000111 23445
Q ss_pred HHHHhhcCccHHHHHHHH-HHhhccCCC-CHHHHHHHHHHcCCchhhhHH-HHHhccCceeccCCe
Q 041805 78 VLKISYDGLDNKEKNIFL-DVACFFQGE-DVNLVMKFLNASGFYPKLGRS-VLVDKSLIVKSNNNK 140 (215)
Q Consensus 78 ~l~~Sy~~L~~~~k~~fl-~~a~fp~~~-~~~~l~~~w~~~g~~~~~~l~-~L~~~~Ll~~~~~~~ 140 (215)
.+...|..|++..+..+. ....|+.+. +.+.+...+.......+..++ .|++.+|++....|+
T Consensus 249 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~~~~~gr 314 (328)
T PRK00080 249 MLGVDELGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTPRGR 314 (328)
T ss_pred HhCCCcCCCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHHhhHHHHHcCCcccCCchH
Confidence 567788999998888876 777787665 888887777665555666778 999999998665554
No 8
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=96.66 E-value=0.018 Score=48.35 Aligned_cols=132 Identities=18% Similarity=0.109 Sum_probs=84.6
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCCchHHHHHHHHHHHhcCCchhHHhhhcccCCCCHHHHHHHHHHHhc--CCc---hhH
Q 041805 1 MEALEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVLGCFLYEREKEVWESAINKLQR--ILH---PSI 75 (215)
Q Consensus 1 v~~L~~~ea~~Lf~~~af~~~~~~~~~~~~~~~iv~~c~GlPLal~~ig~~L~~k~~~~w~~~l~~l~~--~~~---~~i 75 (215)
+++++++|..+++.+.+-.... .--.+....|++.|+|.|-.+..++..+ |..+ ..... ... ...
T Consensus 156 l~~l~~~e~~~il~~~~~~~~~--~~~~~al~~ia~~~~G~pR~~~~ll~~~-------~~~a-~~~~~~~it~~~v~~~ 225 (305)
T TIGR00635 156 LEFYTVEELAEIVSRSAGLLNV--EIEPEAALEIARRSRGTPRIANRLLRRV-------RDFA-QVRGQKIINRDIALKA 225 (305)
T ss_pred eCCCCHHHHHHHHHHHHHHhCC--CcCHHHHHHHHHHhCCCcchHHHHHHHH-------HHHH-HHcCCCCcCHHHHHHH
Confidence 4689999999999988732221 1224566789999999997655444322 1111 00000 011 122
Q ss_pred HHHHHHhhcCccHHHHHHHH-HHhhccCC-CCHHHHHHHHHHcCCchhhhHH-HHHhccCceeccCCeEE
Q 041805 76 LEVLKISYDGLDNKEKNIFL-DVACFFQG-EDVNLVMKFLNASGFYPKLGRS-VLVDKSLIVKSNNNKIT 142 (215)
Q Consensus 76 ~~~l~~Sy~~L~~~~k~~fl-~~a~fp~~-~~~~~l~~~w~~~g~~~~~~l~-~L~~~~Ll~~~~~~~~~ 142 (215)
...+..+|..+++..+..+. .++.+..+ .+.+.+...+.......+..++ .|++++|+.....|++.
T Consensus 226 l~~l~~~~~~l~~~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~~~~~g~~~ 295 (305)
T TIGR00635 226 LEMLMIDELGLDEIDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRGRIA 295 (305)
T ss_pred HHHhCCCCCCCCHHHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhHHHHHcCCcccCCchhhh
Confidence 23356678999998887776 55777654 4777777777766666677788 69999999866566543
No 9
>PF13504 LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OOK_G 1QYY_G 1SQ0_B 1P9A_G 1GWB_A 1P8V_A 1M0Z_A 1U0N_D ....
Probab=96.29 E-value=0.0023 Score=30.02 Aligned_cols=17 Identities=24% Similarity=0.321 Sum_probs=11.8
Q ss_pred CCceEEEcCCCCccccc
Q 041805 191 KKLVFLEMPNSSIEQLW 207 (215)
Q Consensus 191 ~~L~~L~L~~s~i~~L~ 207 (215)
.+|++|+|++|+|+.||
T Consensus 1 ~~L~~L~l~~n~L~~lP 17 (17)
T PF13504_consen 1 PNLRTLDLSNNRLTSLP 17 (17)
T ss_dssp TT-SEEEETSS--SSE-
T ss_pred CccCEEECCCCCCCCCc
Confidence 37999999999999987
No 10
>PF12799 LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_A 1XEU_A 2OMX_A 2OMU_A 2UZY_A 2WQU_D 1D0B_A 2WQW_A 1OTO_A 2WQV_B ....
Probab=95.12 E-value=0.013 Score=34.70 Aligned_cols=25 Identities=24% Similarity=0.339 Sum_probs=19.5
Q ss_pred CCCC-CCCCCCceEEEcCCCCccccc
Q 041805 183 SLPS-NISAKKLVFLEMPNSSIEQLW 207 (215)
Q Consensus 183 ~lP~-~~~~~~L~~L~L~~s~i~~L~ 207 (215)
++|. -.++++|++|+|++|+|+.++
T Consensus 15 ~l~~~l~~l~~L~~L~l~~N~i~~i~ 40 (44)
T PF12799_consen 15 DLPPELSNLPNLETLNLSNNPISDIS 40 (44)
T ss_dssp SHGGHGTTCTTSSEEEETSSCCSBEG
T ss_pred ccCchHhCCCCCCEEEecCCCCCCCc
Confidence 6677 347889999999999888654
No 11
>smart00369 LRR_TYP Leucine-rich repeats, typical (most populated) subfamily.
Probab=95.06 E-value=0.015 Score=30.15 Aligned_cols=21 Identities=24% Similarity=0.308 Sum_probs=18.7
Q ss_pred CCCceEEEcCCCCcccccccc
Q 041805 190 AKKLVFLEMPNSSIEQLWDGM 210 (215)
Q Consensus 190 ~~~L~~L~L~~s~i~~L~~~~ 210 (215)
+.+|++|+|++|+|+.+|.++
T Consensus 1 L~~L~~L~L~~N~l~~lp~~~ 21 (26)
T smart00369 1 LPNLRELDLSNNQLSSLPPGA 21 (26)
T ss_pred CCCCCEEECCCCcCCcCCHHH
Confidence 468999999999999999875
No 12
>smart00370 LRR Leucine-rich repeats, outliers.
Probab=95.06 E-value=0.015 Score=30.15 Aligned_cols=21 Identities=24% Similarity=0.308 Sum_probs=18.7
Q ss_pred CCCceEEEcCCCCcccccccc
Q 041805 190 AKKLVFLEMPNSSIEQLWDGM 210 (215)
Q Consensus 190 ~~~L~~L~L~~s~i~~L~~~~ 210 (215)
+.+|++|+|++|+|+.+|.++
T Consensus 1 L~~L~~L~L~~N~l~~lp~~~ 21 (26)
T smart00370 1 LPNLRELDLSNNQLSSLPPGA 21 (26)
T ss_pred CCCCCEEECCCCcCCcCCHHH
Confidence 468999999999999999875
No 13
>COG3903 Predicted ATPase [General function prediction only]
Probab=94.55 E-value=0.086 Score=46.02 Aligned_cols=155 Identities=19% Similarity=0.231 Sum_probs=103.3
Q ss_pred CCCCH-HHHHHHHHHhhcCCC---CCCchHHHHHHHHHHHhcCCchhHHhhhcccCCCCHHHHHHHHHH----HhcC---
Q 041805 2 EALEY-HLALERFSRHAFKQN---HPDVGYEELSSKAMKYAQGVPLALKVLGCFLYEREKEVWESAINK----LQRI--- 70 (215)
Q Consensus 2 ~~L~~-~ea~~Lf~~~af~~~---~~~~~~~~~~~~iv~~c~GlPLal~~ig~~L~~k~~~~w~~~l~~----l~~~--- 70 (215)
++|+. +++.++|...+--.. ............|.++..|.|++|...+++.+.-...+-...++. ++..
T Consensus 139 ~~L~~~d~a~~lf~~ra~~~~~~f~l~~~~~a~v~~icr~ldg~~laielaaarv~sl~~~~i~~~L~drf~ll~~~~r~ 218 (414)
T COG3903 139 PSLSLFDEAIELFVCRAVLVALSFWLTDDNAAAVAEICRRLDGIPLAIELAAARVRSLSPDEIAAGLRDRFRLLTGGARL 218 (414)
T ss_pred CccccCCchhHHHHHHHHHhccceeecCCchHHHHHHHHHhhcchHHHHHHHHHHHhcCHHHHHHHHhhHHHHHhccccc
Confidence 34443 378888887762111 112234567789999999999999999998887543333333222 2222
Q ss_pred ---CchhHHHHHHHhhcCccHHHHHHHHHHhhccCCCCHHHHHHHHHHcCCc-------hhhhHHHHHhccCceecc---
Q 041805 71 ---LHPSILEVLKISYDGLDNKEKNIFLDVACFFQGEDVNLVMKFLNASGFY-------PKLGRSVLVDKSLIVKSN--- 137 (215)
Q Consensus 71 ---~~~~i~~~l~~Sy~~L~~~~k~~fl~~a~fp~~~~~~~l~~~w~~~g~~-------~~~~l~~L~~~~Ll~~~~--- 137 (215)
..+.....+.+||.-|..-.+-.|..++.|...++.+ ...|.+.|-. ....+..|++++++...+
T Consensus 219 a~~~~qtl~asl~ws~~lLtgwe~~~~~rLa~~~g~f~~~--l~~~~a~g~~~~~~~y~~~~a~~ll~~kslv~a~~~~~ 296 (414)
T COG3903 219 AVLRQQTLRASLDWSYALLTGWERALFGRLAVFVGGFDLG--LALAVAAGADVDVPRYLVLLALTLLVDKSLVVALDLLG 296 (414)
T ss_pred chhHHHhccchhhhhhHhhhhHHHHHhcchhhhhhhhccc--HHHHHhcCCccccchHHHHHHHHHHhhccchhhhhhhh
Confidence 2366889999999999999999999999999888555 2234443332 233467789999987654
Q ss_pred CCeEEecHHHHHHHHHHHhhc
Q 041805 138 NNKITMHDLLQELGRDIVSKE 158 (215)
Q Consensus 138 ~~~~~mHdlvr~~a~~i~~~e 158 (215)
.-+|+.-+-+|.|+.....+.
T Consensus 297 ~a~~Rl~eT~r~YalaeL~r~ 317 (414)
T COG3903 297 RARYRLLETGRRYALAELHRS 317 (414)
T ss_pred HHHHHHHHHHHHHHHHHHHhh
Confidence 223777777777777665443
No 14
>smart00364 LRR_BAC Leucine-rich repeats, bacterial type.
Probab=91.51 E-value=0.13 Score=26.87 Aligned_cols=18 Identities=22% Similarity=0.266 Sum_probs=16.6
Q ss_pred CCceEEEcCCCCcccccc
Q 041805 191 KKLVFLEMPNSSIEQLWD 208 (215)
Q Consensus 191 ~~L~~L~L~~s~i~~L~~ 208 (215)
.+|..|+.++|+++.||+
T Consensus 2 ~~L~~L~vs~N~Lt~LPe 19 (26)
T smart00364 2 PSLKELNVSNNQLTSLPE 19 (26)
T ss_pred cccceeecCCCccccCcc
Confidence 578999999999999997
No 15
>KOG0617 consensus Ras suppressor protein (contains leucine-rich repeats) [Signal transduction mechanisms]
Probab=91.44 E-value=0.043 Score=42.81 Aligned_cols=32 Identities=31% Similarity=0.450 Sum_probs=19.3
Q ss_pred CCCCCC-CCCCceEEEcCCCCccccccccccCC
Q 041805 183 SLPSNI-SAKKLVFLEMPNSSIEQLWDGMKVCE 214 (215)
Q Consensus 183 ~lP~~~-~~~~L~~L~L~~s~i~~L~~~~~~l~ 214 (215)
.+|.++ ++++|.+|++++++|++||..+..|.
T Consensus 47 ~vppnia~l~nlevln~~nnqie~lp~~issl~ 79 (264)
T KOG0617|consen 47 VVPPNIAELKNLEVLNLSNNQIEELPTSISSLP 79 (264)
T ss_pred ecCCcHHHhhhhhhhhcccchhhhcChhhhhch
Confidence 555555 56666666666666666665555443
No 16
>PF13855 LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RFS_A 3G39_A 3VQ2_A 3VQ1_B 2Z64_A 2Z66_C 3FXI_A 2Z63_A ....
Probab=91.22 E-value=0.2 Score=31.38 Aligned_cols=32 Identities=13% Similarity=0.246 Sum_probs=24.0
Q ss_pred CCCC-CC-CCCCceEEEcCCCCcccccccc-ccCC
Q 041805 183 SLPS-NI-SAKKLVFLEMPNSSIEQLWDGM-KVCE 214 (215)
Q Consensus 183 ~lP~-~~-~~~~L~~L~L~~s~i~~L~~~~-~~l~ 214 (215)
.+|. .| .+++|++|+|++|+|+.++.+. +.|+
T Consensus 15 ~i~~~~f~~l~~L~~L~l~~N~l~~i~~~~f~~l~ 49 (61)
T PF13855_consen 15 EIPPDSFSNLPNLETLDLSNNNLTSIPPDAFSNLP 49 (61)
T ss_dssp EECTTTTTTGTTESEEEETSSSESEEETTTTTTST
T ss_pred ccCHHHHcCCCCCCEeEccCCccCccCHHHHcCCC
Confidence 5665 45 6799999999999999998643 4443
No 17
>PF12799 LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_A 1XEU_A 2OMX_A 2OMU_A 2UZY_A 2WQU_D 1D0B_A 2WQW_A 1OTO_A 2WQV_B ....
Probab=91.17 E-value=0.12 Score=30.51 Aligned_cols=25 Identities=24% Similarity=0.248 Sum_probs=20.1
Q ss_pred CCceEEEcCCCCccccccccccCCC
Q 041805 191 KKLVFLEMPNSSIEQLWDGMKVCET 215 (215)
Q Consensus 191 ~~L~~L~L~~s~i~~L~~~~~~l~~ 215 (215)
++|++|+|++|+|+.++..+++|++
T Consensus 1 ~~L~~L~l~~N~i~~l~~~l~~l~~ 25 (44)
T PF12799_consen 1 KNLEELDLSNNQITDLPPELSNLPN 25 (44)
T ss_dssp TT-SEEEETSSS-SSHGGHGTTCTT
T ss_pred CcceEEEccCCCCcccCchHhCCCC
Confidence 5799999999999999987887764
No 18
>smart00365 LRR_SD22 Leucine-rich repeat, SDS22-like subfamily.
Probab=89.81 E-value=0.26 Score=25.71 Aligned_cols=18 Identities=17% Similarity=0.274 Sum_probs=15.2
Q ss_pred CCCceEEEcCCCCccccc
Q 041805 190 AKKLVFLEMPNSSIEQLW 207 (215)
Q Consensus 190 ~~~L~~L~L~~s~i~~L~ 207 (215)
+++|.+|+|++|+|+++-
T Consensus 1 L~~L~~L~L~~NkI~~IE 18 (26)
T smart00365 1 LTNLEELDLSQNKIKKIE 18 (26)
T ss_pred CCccCEEECCCCccceec
Confidence 468999999999997753
No 19
>COG3899 Predicted ATPase [General function prediction only]
Probab=89.20 E-value=2.4 Score=41.09 Aligned_cols=151 Identities=15% Similarity=0.184 Sum_probs=97.9
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCCchHHHHHHHHHHHhcCCchhHHhhhcccCCC-------CHHHHHHHHHHHhcCC-c
Q 041805 1 MEALEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVLGCFLYER-------EKEVWESAINKLQRIL-H 72 (215)
Q Consensus 1 v~~L~~~ea~~Lf~~~af~~~~~~~~~~~~~~~iv~~c~GlPLal~~ig~~L~~k-------~~~~w~~~l~~l~~~~-~ 72 (215)
|.||+..|...|..... +.... ...+....|+++..|.|+-+.-+-..+... +...|..=...+...+ .
T Consensus 216 L~PL~~~d~~~lV~~~l-~~~~~--~~~p~~~~i~~kt~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i~~~~~~ 292 (849)
T COG3899 216 LAPLSRADTNQLVAATL-GCTKL--LPAPLLELIFEKTKGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIASLGILATT 292 (849)
T ss_pred cCcCchhhHHHHHHHHh-CCccc--ccchHHHHHHHHhcCCCccHHHHHHHHHhCCeeEecCCCcceeccHHhcCCchhh
Confidence 57999999999888876 54322 234567899999999999887666655442 2334433222322221 1
Q ss_pred hhHHHHHHHhhcCccHHHHHHHHHHhhccCCCCHHHHHHHHHHcCCchhhhHHHHHhccCceecc----CC----eE---
Q 041805 73 PSILEVLKISYDGLDNKEKNIFLDVACFFQGEDVNLVMKFLNASGFYPKLGRSVLVDKSLIVKSN----NN----KI--- 141 (215)
Q Consensus 73 ~~i~~~l~~Sy~~L~~~~k~~fl~~a~fp~~~~~~~l~~~w~~~g~~~~~~l~~L~~~~Ll~~~~----~~----~~--- 141 (215)
.++.+.+..-.+.||...|+....-||+-..++.+.|..++...+......+-.....+++.+.. .+ ..
T Consensus 293 ~~vv~~l~~rl~kL~~~t~~Vl~~AA~iG~~F~l~~La~l~~~~~~~~a~~l~~al~e~lI~~~~~~yr~~~~~~~~~Y~ 372 (849)
T COG3899 293 DAVVEFLAARLQKLPGTTREVLKAAACIGNRFDLDTLAALAEDSPALEAAALLDALQEGLILPLSETYRFGSNVDIATYK 372 (849)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHhCccCCHHHHHHHHhhchHHHHHHHHHHhHhhceeccccccccccccchhhHH
Confidence 33666788899999999999999999999999999998888864444433333333344444321 11 12
Q ss_pred EecHHHHHHHHHH
Q 041805 142 TMHDLLQELGRDI 154 (215)
Q Consensus 142 ~mHdlvr~~a~~i 154 (215)
-.||.+++.|-..
T Consensus 373 F~H~~vqqaaY~~ 385 (849)
T COG3899 373 FLHDRVQQAAYNL 385 (849)
T ss_pred hhHHHHHHHHhcc
Confidence 3577777766543
No 20
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=84.54 E-value=14 Score=35.61 Aligned_cols=143 Identities=12% Similarity=0.110 Sum_probs=87.9
Q ss_pred CCHHHHHHHHHHhhcCCCCCCchHHHHHHHHHHHhcCCchhHHhhhcccCC-CCHHHHHHHHHHHhcCCchhHHH-HHHH
Q 041805 4 LEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVLGCFLYE-REKEVWESAINKLQRILHPSILE-VLKI 81 (215)
Q Consensus 4 L~~~ea~~Lf~~~af~~~~~~~~~~~~~~~iv~~c~GlPLal~~ig~~L~~-k~~~~w~~~l~~l~~~~~~~i~~-~l~~ 81 (215)
++.+|+-.+|...- +.. -...-.+.+.+..+|.+-|+..++=.+++ .+...--..++ .. .+.|.. ...-
T Consensus 194 f~~eE~~~fl~~~~-~l~----Ld~~~~~~L~~~teGW~~al~L~aLa~~~~~~~~q~~~~Ls---G~-~~~l~dYL~ee 264 (894)
T COG2909 194 FDTEEAAAFLNDRG-SLP----LDAADLKALYDRTEGWAAALQLIALALRNNTSAEQSLRGLS---GA-ASHLSDYLVEE 264 (894)
T ss_pred CChHHHHHHHHHcC-CCC----CChHHHHHHHhhcccHHHHHHHHHHHccCCCcHHHHhhhcc---ch-HHHHHHHHHHH
Confidence 57888988888754 111 11234567888899999999888877773 23222111111 10 111111 1223
Q ss_pred hhcCccHHHHHHHHHHhhccCCCCHHHHHHHHHHcCCchhhhHHHHHhccCceec--c-CCeEEecHHHHHHHHHHHhhc
Q 041805 82 SYDGLDNKEKNIFLDVACFFQGEDVNLVMKFLNASGFYPKLGRSVLVDKSLIVKS--N-NNKITMHDLLQELGRDIVSKE 158 (215)
Q Consensus 82 Sy~~L~~~~k~~fl~~a~fp~~~~~~~l~~~w~~~g~~~~~~l~~L~~~~Ll~~~--~-~~~~~mHdlvr~~a~~i~~~e 158 (215)
-+|.||+++|..++-||+++.- . +.|..-... .-.....+++|.+++|+-.. + ++.|+.|.++.+|-+...+.+
T Consensus 265 Vld~Lp~~l~~FLl~~svl~~f-~-~eL~~~Ltg-~~ng~amLe~L~~~gLFl~~Ldd~~~WfryH~LFaeFL~~r~~~~ 341 (894)
T COG2909 265 VLDRLPPELRDFLLQTSVLSRF-N-DELCNALTG-EENGQAMLEELERRGLFLQRLDDEGQWFRYHHLFAEFLRQRLQRE 341 (894)
T ss_pred HHhcCCHHHHHHHHHHHhHHHh-h-HHHHHHHhc-CCcHHHHHHHHHhCCCceeeecCCCceeehhHHHHHHHHhhhccc
Confidence 4688999999999999998521 1 122221111 11234569999999998843 2 456999999999988776554
No 21
>PF13516 LRR_6: Leucine Rich repeat; PDB: 3RGZ_A 3RJ0_A 3RIZ_A 3RGX_A 1DFJ_I 2BNH_A 3VQ1_A 3VQ2_A 2Z64_A 2OMX_A ....
Probab=84.33 E-value=0.57 Score=23.46 Aligned_cols=16 Identities=25% Similarity=0.405 Sum_probs=11.0
Q ss_pred CCCceEEEcCCCCccc
Q 041805 190 AKKLVFLEMPNSSIEQ 205 (215)
Q Consensus 190 ~~~L~~L~L~~s~i~~ 205 (215)
+++|++|+|++|+|..
T Consensus 1 ~~~L~~L~l~~n~i~~ 16 (24)
T PF13516_consen 1 NPNLETLDLSNNQITD 16 (24)
T ss_dssp -TT-SEEE-TSSBEHH
T ss_pred CCCCCEEEccCCcCCH
Confidence 3689999999999853
No 22
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=82.44 E-value=7.2 Score=31.77 Aligned_cols=52 Identities=15% Similarity=0.187 Sum_probs=38.0
Q ss_pred CCCCCHHHHHHHHHHhhcCCC--CCCchHHHHHHHHHHHhcCCchhHHhhhccc
Q 041805 1 MEALEYHLALERFSRHAFKQN--HPDVGYEELSSKAMKYAQGVPLALKVLGCFL 52 (215)
Q Consensus 1 v~~L~~~ea~~Lf~~~af~~~--~~~~~~~~~~~~iv~~c~GlPLal~~ig~~L 52 (215)
++|++.+|..+++...+-... ....--.+..+.|++.|+|.|..|..++..+
T Consensus 189 l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~ 242 (269)
T TIGR03015 189 LGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRL 242 (269)
T ss_pred CCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHH
Confidence 478999999998887652211 1111224678899999999999998888765
No 23
>smart00368 LRR_RI Leucine rich repeat, ribonuclease inhibitor type.
Probab=81.14 E-value=1.2 Score=23.40 Aligned_cols=14 Identities=21% Similarity=0.342 Sum_probs=12.4
Q ss_pred CCceEEEcCCCCcc
Q 041805 191 KKLVFLEMPNSSIE 204 (215)
Q Consensus 191 ~~L~~L~L~~s~i~ 204 (215)
++|++|||++|.|.
T Consensus 2 ~~L~~LdL~~N~i~ 15 (28)
T smart00368 2 PSLRELDLSNNKLG 15 (28)
T ss_pred CccCEEECCCCCCC
Confidence 57999999999985
No 24
>PF13855 LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RFS_A 3G39_A 3VQ2_A 3VQ1_B 2Z64_A 2Z66_C 3FXI_A 2Z63_A ....
Probab=74.99 E-value=2.7 Score=26.03 Aligned_cols=21 Identities=24% Similarity=0.619 Sum_probs=17.1
Q ss_pred CCCC-CC-CCCCceEEEcCCCCc
Q 041805 183 SLPS-NI-SAKKLVFLEMPNSSI 203 (215)
Q Consensus 183 ~lP~-~~-~~~~L~~L~L~~s~i 203 (215)
.+|+ .| .+.+|++|+|++|+|
T Consensus 39 ~i~~~~f~~l~~L~~L~l~~N~l 61 (61)
T PF13855_consen 39 SIPPDAFSNLPNLRYLDLSNNNL 61 (61)
T ss_dssp EEETTTTTTSTTESEEEETSSSB
T ss_pred ccCHHHHcCCCCCCEEeCcCCcC
Confidence 5554 45 789999999999986
No 25
>PF13730 HTH_36: Helix-turn-helix domain
Probab=73.92 E-value=7 Score=23.62 Aligned_cols=49 Identities=22% Similarity=0.209 Sum_probs=32.3
Q ss_pred CccHHHHHHHHHHhhccCCC-----CHHHHHHHHHHcCCchhhhHHHHHhccCc
Q 041805 85 GLDNKEKNIFLDVACFFQGE-----DVNLVMKFLNASGFYPKLGRSVLVDKSLI 133 (215)
Q Consensus 85 ~L~~~~k~~fl~~a~fp~~~-----~~~~l~~~w~~~g~~~~~~l~~L~~~~Ll 133 (215)
.|++.++.++.++.-|..+. +.+.+........--...++++|+++++|
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 58888999999998887332 44555544322211225679999999875
No 26
>KOG0617 consensus Ras suppressor protein (contains leucine-rich repeats) [Signal transduction mechanisms]
Probab=71.59 E-value=1.7 Score=34.03 Aligned_cols=31 Identities=29% Similarity=0.367 Sum_probs=15.7
Q ss_pred CCCCCC-CCCCceEEEcCCCCccccccccccC
Q 041805 183 SLPSNI-SAKKLVFLEMPNSSIEQLWDGMKVC 213 (215)
Q Consensus 183 ~lP~~~-~~~~L~~L~L~~s~i~~L~~~~~~l 213 (215)
.||.++ ++.+|+.|++.-+++..||+|.+.+
T Consensus 70 ~lp~~issl~klr~lnvgmnrl~~lprgfgs~ 101 (264)
T KOG0617|consen 70 ELPTSISSLPKLRILNVGMNRLNILPRGFGSF 101 (264)
T ss_pred hcChhhhhchhhhheecchhhhhcCccccCCC
Confidence 444444 3455555555555555555555443
No 27
>KOG0472 consensus Leucine-rich repeat protein [Function unknown]
Probab=65.05 E-value=2.2 Score=37.73 Aligned_cols=26 Identities=15% Similarity=0.236 Sum_probs=14.3
Q ss_pred CCCCceEEEcCCCCccccccccccCC
Q 041805 189 SAKKLVFLEMPNSSIEQLWDGMKVCE 214 (215)
Q Consensus 189 ~~~~L~~L~L~~s~i~~L~~~~~~l~ 214 (215)
.+++|.+|||++|.|.+.|.+.+++.
T Consensus 503 nm~nL~tLDL~nNdlq~IPp~Lgnmt 528 (565)
T KOG0472|consen 503 NMRNLTTLDLQNNDLQQIPPILGNMT 528 (565)
T ss_pred hhhhcceeccCCCchhhCChhhcccc
Confidence 44555555555555555555555544
No 28
>PLN03150 hypothetical protein; Provisional
Probab=61.29 E-value=5.1 Score=37.42 Aligned_cols=31 Identities=16% Similarity=0.351 Sum_probs=15.5
Q ss_pred CCCCCC-CCCCceEEEcCCCCcc-ccccccccC
Q 041805 183 SLPSNI-SAKKLVFLEMPNSSIE-QLWDGMKVC 213 (215)
Q Consensus 183 ~lP~~~-~~~~L~~L~L~~s~i~-~L~~~~~~l 213 (215)
.+|..+ .+.+|++|||++|+|. .+|+.+++|
T Consensus 457 ~iP~~~~~l~~L~~LdLs~N~lsg~iP~~l~~L 489 (623)
T PLN03150 457 NIPPSLGSITSLEVLDLSYNSFNGSIPESLGQL 489 (623)
T ss_pred cCChHHhCCCCCCEEECCCCCCCCCCchHHhcC
Confidence 444444 4455555566555554 344444433
No 29
>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]
Probab=56.48 E-value=4.8 Score=37.82 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=22.6
Q ss_pred CCCCCC-CCCCceEEEcCCCCccccccc
Q 041805 183 SLPSNI-SAKKLVFLEMPNSSIEQLWDG 209 (215)
Q Consensus 183 ~lP~~~-~~~~L~~L~L~~s~i~~L~~~ 209 (215)
..|.+. ..+++.+||||||+|+++|+.
T Consensus 117 EvP~~LE~AKn~iVLNLS~N~IetIPn~ 144 (1255)
T KOG0444|consen 117 EVPTNLEYAKNSIVLNLSYNNIETIPNS 144 (1255)
T ss_pred hcchhhhhhcCcEEEEcccCccccCCch
Confidence 778877 668899999999999988864
No 30
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=55.54 E-value=1.4e+02 Score=25.81 Aligned_cols=129 Identities=12% Similarity=0.041 Sum_probs=75.4
Q ss_pred CCCCCHHHHHHHHHHhh---cCCCCC-CchHHHHHHHHHHHhcCCchhHHhhhccc-----CCC---CHHHHHHHHHHHh
Q 041805 1 MEALEYHLALERFSRHA---FKQNHP-DVGYEELSSKAMKYAQGVPLALKVLGCFL-----YER---EKEVWESAINKLQ 68 (215)
Q Consensus 1 v~~L~~~ea~~Lf~~~a---f~~~~~-~~~~~~~~~~iv~~c~GlPLal~~ig~~L-----~~k---~~~~w~~~l~~l~ 68 (215)
++|++.++..+++..++ |..... +..++.+++.+....|.++.|+.++-... .++ +...++.+.+.+.
T Consensus 204 f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~ 283 (394)
T PRK00411 204 FPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSE 283 (394)
T ss_pred cCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHH
Confidence 46888999999998776 222222 22334444444444566888877654321 111 4566666666542
Q ss_pred cCCchhHHHHHHHhhcCccHHHHHHHHHHhhcc----CCCCHHHHHHH----HHHcCCch------hhhHHHHHhccCce
Q 041805 69 RILHPSILEVLKISYDGLDNKEKNIFLDVACFF----QGEDVNLVMKF----LNASGFYP------KLGRSVLVDKSLIV 134 (215)
Q Consensus 69 ~~~~~~i~~~l~~Sy~~L~~~~k~~fl~~a~fp----~~~~~~~l~~~----w~~~g~~~------~~~l~~L~~~~Ll~ 134 (215)
...+.-.+..||.+.|..+..++..- ...+...+... ....|..+ ..+++.|.+.++|.
T Consensus 284 -------~~~~~~~~~~L~~~~k~~L~ai~~~~~~~~~~~~~~~i~~~y~~l~~~~~~~~~~~~~~~~~l~~L~~~glI~ 356 (394)
T PRK00411 284 -------IVHLSEVLRTLPLHEKLLLRAIVRLLKKGGDEVTTGEVYEEYKELCEELGYEPRTHTRFYEYINKLDMLGIIN 356 (394)
T ss_pred -------HHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHHHhcCCeE
Confidence 23345568899999888877766443 22234333322 22234432 35799999999998
Q ss_pred ec
Q 041805 135 KS 136 (215)
Q Consensus 135 ~~ 136 (215)
..
T Consensus 357 ~~ 358 (394)
T PRK00411 357 TR 358 (394)
T ss_pred EE
Confidence 64
No 31
>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=53.63 E-value=20 Score=21.91 Aligned_cols=53 Identities=15% Similarity=0.050 Sum_probs=38.9
Q ss_pred CccHHHHHHHHHHhhccCC-CCHHHHHHHHHHcCCchhhhHHHHHhccCceecc
Q 041805 85 GLDNKEKNIFLDVACFFQG-EDVNLVMKFLNASGFYPKLGRSVLVDKSLIVKSN 137 (215)
Q Consensus 85 ~L~~~~k~~fl~~a~fp~~-~~~~~l~~~w~~~g~~~~~~l~~L~~~~Ll~~~~ 137 (215)
+|++..-.++.++.-+|++ .+...+...+.-..-.....++.|..++|+....
T Consensus 2 glt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~ 55 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERER 55 (62)
T ss_dssp TSTHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred ccCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence 4667777888888888876 4777777776544444466799999999998653
No 32
>PF14580 LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQD_A.
Probab=52.65 E-value=10 Score=29.43 Aligned_cols=28 Identities=21% Similarity=0.361 Sum_probs=10.3
Q ss_pred CCCCCCCCCCceEEEcCCCCcccccccc
Q 041805 183 SLPSNISAKKLVFLEMPNSSIEQLWDGM 210 (215)
Q Consensus 183 ~lP~~~~~~~L~~L~L~~s~i~~L~~~~ 210 (215)
+++..-.+++|++|+|++|+|+.+.+++
T Consensus 56 ~l~~l~~L~~L~~L~L~~N~I~~i~~~l 83 (175)
T PF14580_consen 56 KLEGLPGLPRLKTLDLSNNRISSISEGL 83 (175)
T ss_dssp --TT----TT--EEE--SS---S-CHHH
T ss_pred cccCccChhhhhhcccCCCCCCccccch
Confidence 5544336788999999999998886554
No 33
>KOG3665 consensus ZYG-1-like serine/threonine protein kinases [General function prediction only]
Probab=52.39 E-value=7.5 Score=36.90 Aligned_cols=25 Identities=20% Similarity=0.352 Sum_probs=21.8
Q ss_pred CCCceEEEcCCCCccccccccccCCC
Q 041805 190 AKKLVFLEMPNSSIEQLWDGMKVCET 215 (215)
Q Consensus 190 ~~~L~~L~L~~s~i~~L~~~~~~l~~ 215 (215)
..+|..||+|+|+|+.| .|+.+|+|
T Consensus 172 FpNL~sLDIS~TnI~nl-~GIS~Lkn 196 (699)
T KOG3665|consen 172 FPNLRSLDISGTNISNL-SGISRLKN 196 (699)
T ss_pred cCccceeecCCCCccCc-HHHhcccc
Confidence 47899999999999999 78888775
No 34
>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]
Probab=52.32 E-value=7.4 Score=38.00 Aligned_cols=33 Identities=27% Similarity=0.492 Sum_probs=26.3
Q ss_pred CCCCCC-CCCCceEEEcCCCCccccccccccCCC
Q 041805 183 SLPSNI-SAKKLVFLEMPNSSIEQLWDGMKVCET 215 (215)
Q Consensus 183 ~lP~~~-~~~~L~~L~L~~s~i~~L~~~~~~l~~ 215 (215)
.||+.+ ++-+|++|||+++.|++||.|+++|++
T Consensus 586 ~LP~~I~~Li~LryL~L~~t~I~~LP~~l~~Lk~ 619 (889)
T KOG4658|consen 586 KLPSSIGELVHLRYLDLSDTGISHLPSGLGNLKK 619 (889)
T ss_pred cCChHHhhhhhhhcccccCCCccccchHHHHHHh
Confidence 588877 577888888888888888888887753
No 35
>PLN03150 hypothetical protein; Provisional
Probab=49.21 E-value=9.7 Score=35.59 Aligned_cols=32 Identities=16% Similarity=0.305 Sum_probs=25.8
Q ss_pred CCCCCC-CCCCceEEEcCCCCcc-ccccccccCC
Q 041805 183 SLPSNI-SAKKLVFLEMPNSSIE-QLWDGMKVCE 214 (215)
Q Consensus 183 ~lP~~~-~~~~L~~L~L~~s~i~-~L~~~~~~l~ 214 (215)
.+|..+ .+.+|+.|+|++|+|. .+|..+..|+
T Consensus 433 ~ip~~i~~L~~L~~L~Ls~N~l~g~iP~~~~~l~ 466 (623)
T PLN03150 433 FIPNDISKLRHLQSINLSGNSIRGNIPPSLGSIT 466 (623)
T ss_pred cCCHHHhCCCCCCEEECCCCcccCcCChHHhCCC
Confidence 677777 6799999999999997 7877666554
No 36
>KOG4237 consensus Extracellular matrix protein slit, contains leucine-rich and EGF-like repeats [Extracellular structures; Signal transduction mechanisms]
Probab=47.42 E-value=8.4 Score=34.04 Aligned_cols=24 Identities=21% Similarity=0.444 Sum_probs=20.5
Q ss_pred CCCCCC--CCCCceEEEcCCCCcccc
Q 041805 183 SLPSNI--SAKKLVFLEMPNSSIEQL 206 (215)
Q Consensus 183 ~lP~~~--~~~~L~~L~L~~s~i~~L 206 (215)
+||+.. .+++|+.||||+|+|+.+
T Consensus 81 ~iP~~aF~~l~~LRrLdLS~N~Is~I 106 (498)
T KOG4237|consen 81 SIPPGAFKTLHRLRRLDLSKNNISFI 106 (498)
T ss_pred cCChhhccchhhhceecccccchhhc
Confidence 888874 679999999999999765
No 37
>KOG0472 consensus Leucine-rich repeat protein [Function unknown]
Probab=46.96 E-value=6.4 Score=34.95 Aligned_cols=31 Identities=23% Similarity=0.321 Sum_probs=21.8
Q ss_pred CCCCCCCC-CCceEEEcCCCCccccccccccC
Q 041805 183 SLPSNISA-KKLVFLEMPNSSIEQLWDGMKVC 213 (215)
Q Consensus 183 ~lP~~~~~-~~L~~L~L~~s~i~~L~~~~~~l 213 (215)
++|..+++ ++|..||||+|.|..||-+.++|
T Consensus 266 e~Pde~clLrsL~rLDlSNN~is~Lp~sLgnl 297 (565)
T KOG0472|consen 266 EVPDEICLLRSLERLDLSNNDISSLPYSLGNL 297 (565)
T ss_pred cCchHHHHhhhhhhhcccCCccccCCcccccc
Confidence 67777643 66777777777777777666654
No 38
>PF14580 LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQD_A.
Probab=44.51 E-value=9.6 Score=29.58 Aligned_cols=24 Identities=25% Similarity=0.358 Sum_probs=10.2
Q ss_pred CCCCCC--CCCCceEEEcCCCCcccc
Q 041805 183 SLPSNI--SAKKLVFLEMPNSSIEQL 206 (215)
Q Consensus 183 ~lP~~~--~~~~L~~L~L~~s~i~~L 206 (215)
+++..+ .+++|++|+|++|+|..+
T Consensus 78 ~i~~~l~~~lp~L~~L~L~~N~I~~l 103 (175)
T PF14580_consen 78 SISEGLDKNLPNLQELYLSNNKISDL 103 (175)
T ss_dssp S-CHHHHHH-TT--EEE-TTS---SC
T ss_pred ccccchHHhCCcCCEEECcCCcCCCh
Confidence 554433 357788888888888774
No 39
>PLN00113 leucine-rich repeat receptor-like protein kinase; Provisional
Probab=40.31 E-value=16 Score=35.70 Aligned_cols=31 Identities=10% Similarity=0.217 Sum_probs=18.4
Q ss_pred CCCCCC-CCCCceEEEcCCCCcc-ccccccccC
Q 041805 183 SLPSNI-SAKKLVFLEMPNSSIE-QLWDGMKVC 213 (215)
Q Consensus 183 ~lP~~~-~~~~L~~L~L~~s~i~-~L~~~~~~l 213 (215)
.+|..+ ++++|++|+|++|++. .+|.+++.|
T Consensus 203 ~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l 235 (968)
T PLN00113 203 QIPRELGQMKSLKWIYLGYNNLSGEIPYEIGGL 235 (968)
T ss_pred cCChHHcCcCCccEEECcCCccCCcCChhHhcC
Confidence 455555 5566777777766665 455555444
No 40
>KOG0618 consensus Serine/threonine phosphatase 2C containing leucine-rich repeats, similar to SCN circadian oscillatory protein (SCOP) [Signal transduction mechanisms]
Probab=40.29 E-value=3.7 Score=39.88 Aligned_cols=25 Identities=16% Similarity=0.287 Sum_probs=14.3
Q ss_pred CCCCCCCCCCceEEEcCCCCccccc
Q 041805 183 SLPSNISAKKLVFLEMPNSSIEQLW 207 (215)
Q Consensus 183 ~lP~~~~~~~L~~L~L~~s~i~~L~ 207 (215)
++|-..+.+||++|+|+||+|..+|
T Consensus 375 c~p~l~~~~hLKVLhLsyNrL~~fp 399 (1081)
T KOG0618|consen 375 CFPVLVNFKHLKVLHLSYNRLNSFP 399 (1081)
T ss_pred chhhhccccceeeeeecccccccCC
Confidence 5555555566666666666555554
No 41
>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional
Probab=40.04 E-value=22 Score=34.28 Aligned_cols=25 Identities=8% Similarity=0.011 Sum_probs=16.8
Q ss_pred HHHHHHHHHhhccCCCCHHHHHHHH
Q 041805 89 KEKNIFLDVACFFQGEDVNLVMKFL 113 (215)
Q Consensus 89 ~~k~~fl~~a~fp~~~~~~~l~~~w 113 (215)
+++.|..++.=-|.+.+++.+....
T Consensus 48 ~a~~c~~~~~~~~~~~~~~~~~~~~ 72 (788)
T PRK15387 48 EALECIWTICHPPAGTTREDVINRF 72 (788)
T ss_pred HHHHHHHHHhCCCCCCCHHHHHHHH
Confidence 6778888876666666666665443
No 42
>smart00367 LRR_CC Leucine-rich repeat - CC (cysteine-containing) subfamily.
Probab=39.65 E-value=20 Score=18.01 Aligned_cols=13 Identities=15% Similarity=0.276 Sum_probs=10.7
Q ss_pred CCCceEEEcCCCC
Q 041805 190 AKKLVFLEMPNSS 202 (215)
Q Consensus 190 ~~~L~~L~L~~s~ 202 (215)
+++|+.|+|++|.
T Consensus 1 c~~L~~L~l~~C~ 13 (26)
T smart00367 1 CPNLRELDLSGCT 13 (26)
T ss_pred CCCCCEeCCCCCC
Confidence 3679999999984
No 43
>PF03861 ANTAR: ANTAR domain; InterPro: IPR005561 ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins []. This domain has been detected in various response regulators of two-component systems, which are structured around two proteins, a histidine kinase and a response regulator. This domain is also found in one-component sensory regulators from a variety of bacteria. Most response regulators interact with DNA, however ANTAR-containing regulators interact with RNA. The majority of the domain consists of a coiled-coil.; PDB: 4AKK_A 1SD5_A 1S8N_A 1QO0_E.
Probab=38.22 E-value=38 Score=20.67 Aligned_cols=30 Identities=13% Similarity=0.292 Sum_probs=19.1
Q ss_pred CCCHHHHHHHHHHhhcCCCCCCchHHHHHHHHH
Q 041805 3 ALEYHLALERFSRHAFKQNHPDVGYEELSSKAM 35 (215)
Q Consensus 3 ~L~~~ea~~Lf~~~af~~~~~~~~~~~~~~~iv 35 (215)
.+++++|+.++.+.|...+. .+.++|..|+
T Consensus 27 g~~e~~A~~~Lr~~Am~~~~---~l~~vA~~ii 56 (56)
T PF03861_consen 27 GLSEDEAYRLLRRQAMRRRR---SLADVAEEII 56 (56)
T ss_dssp T--HHHHHHHHHHHHHHCTS----HHHHHHHHH
T ss_pred CcCHHHHHHHHHHHHHHcCC---CHHHHHHHHC
Confidence 47899999999999854433 3456666654
No 44
>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]
Probab=37.78 E-value=21 Score=33.80 Aligned_cols=20 Identities=30% Similarity=0.193 Sum_probs=11.6
Q ss_pred hhhhHHHHHhccCceeccCCe
Q 041805 120 PKLGRSVLVDKSLIVKSNNNK 140 (215)
Q Consensus 120 ~~~~l~~L~~~~Ll~~~~~~~ 140 (215)
+...+-.|.|--++..+ +++
T Consensus 142 Pn~lfinLtDLLfLDLS-~Nr 161 (1255)
T KOG0444|consen 142 PNSLFINLTDLLFLDLS-NNR 161 (1255)
T ss_pred CchHHHhhHhHhhhccc-cch
Confidence 34455566666666666 444
No 45
>PLN00113 leucine-rich repeat receptor-like protein kinase; Provisional
Probab=36.60 E-value=19 Score=35.12 Aligned_cols=32 Identities=16% Similarity=0.354 Sum_probs=21.9
Q ss_pred CCCCCC-CCCCceEEEcCCCCcc-ccccccccCC
Q 041805 183 SLPSNI-SAKKLVFLEMPNSSIE-QLWDGMKVCE 214 (215)
Q Consensus 183 ~lP~~~-~~~~L~~L~L~~s~i~-~L~~~~~~l~ 214 (215)
.+|..+ ++++|++|+|++|++. .+|+++++++
T Consensus 179 ~~p~~~~~l~~L~~L~L~~n~l~~~~p~~l~~l~ 212 (968)
T PLN00113 179 KIPNSLTNLTSLEFLTLASNQLVGQIPRELGQMK 212 (968)
T ss_pred cCChhhhhCcCCCeeeccCCCCcCcCChHHcCcC
Confidence 566666 6778888888888775 4666655544
No 46
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=35.95 E-value=1.4e+02 Score=20.34 Aligned_cols=64 Identities=9% Similarity=0.146 Sum_probs=40.4
Q ss_pred HhhcCccHHHHHHHHHHhh--c--c---CCCCHHHHHHHHHHcCCchhhhHHHHHhccCceecc-CCeEEec
Q 041805 81 ISYDGLDNKEKNIFLDVAC--F--F---QGEDVNLVMKFLNASGFYPKLGRSVLVDKSLIVKSN-NNKITMH 144 (215)
Q Consensus 81 ~Sy~~L~~~~k~~fl~~a~--f--p---~~~~~~~l~~~w~~~g~~~~~~l~~L~~~~Ll~~~~-~~~~~mH 144 (215)
+.+..+++.+-+|++.++- + + ...+...+..+....---....++.|..+++|.... -|.+.|.
T Consensus 18 l~~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~~~~~~~~n 89 (95)
T TIGR01610 18 LPGADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQGMMGIVGVN 89 (95)
T ss_pred HHhCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeecCCceeecC
Confidence 4567788888888888873 1 1 122555565554433333456799999999998653 2445553
No 47
>PRK15386 type III secretion protein GogB; Provisional
Probab=34.53 E-value=17 Score=32.38 Aligned_cols=21 Identities=19% Similarity=0.199 Sum_probs=10.4
Q ss_pred CCceEEEcCCC-Cccccccccc
Q 041805 191 KKLVFLEMPNS-SIEQLWDGMK 211 (215)
Q Consensus 191 ~~L~~L~L~~s-~i~~L~~~~~ 211 (215)
.+|++|++++| +|..||.+.+
T Consensus 94 ~nLe~L~Ls~Cs~L~sLP~sLe 115 (426)
T PRK15386 94 EGLEKLTVCHCPEISGLPESVR 115 (426)
T ss_pred hhhhheEccCcccccccccccc
Confidence 44555555554 4444444443
No 48
>KOG4579 consensus Leucine-rich repeat (LRR) protein associated with apoptosis in muscle tissue [General function prediction only]
Probab=34.46 E-value=4.8 Score=30.47 Aligned_cols=29 Identities=10% Similarity=0.135 Sum_probs=15.8
Q ss_pred CCCCCC-CCCCceEEEcCCCCccccccccc
Q 041805 183 SLPSNI-SAKKLVFLEMPNSSIEQLWDGMK 211 (215)
Q Consensus 183 ~lP~~~-~~~~L~~L~L~~s~i~~L~~~~~ 211 (215)
.+|..+ .+..|+.||++.|.|...|+-+.
T Consensus 91 dvPeE~Aam~aLr~lNl~~N~l~~~p~vi~ 120 (177)
T KOG4579|consen 91 DVPEELAAMPALRSLNLRFNPLNAEPRVIA 120 (177)
T ss_pred hchHHHhhhHHhhhcccccCccccchHHHH
Confidence 455554 44556666666666655554433
No 49
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=34.42 E-value=1.3e+02 Score=19.63 Aligned_cols=63 Identities=16% Similarity=0.095 Sum_probs=38.8
Q ss_pred HHHHhhccCCCCHHHHHHHHHHcCCchhhhHHHHHhccCceecc-CCeEEecHHHHHHHHHHHh
Q 041805 94 FLDVACFFQGEDVNLVMKFLNASGFYPKLGRSVLVDKSLIVKSN-NNKITMHDLLQELGRDIVS 156 (215)
Q Consensus 94 fl~~a~fp~~~~~~~l~~~w~~~g~~~~~~l~~L~~~~Ll~~~~-~~~~~mHdlvr~~a~~i~~ 156 (215)
+.+++--+...+...+.....-.--....+++.|.+.+++...+ ++.|++-.-+.+++.....
T Consensus 11 l~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~~~~~~~~~~~~ 74 (91)
T smart00346 11 LRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNGRYRLGPKVLELGQSYLS 74 (91)
T ss_pred HHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCCCceeecHHHHHHHHHHHh
Confidence 33444433344555555544221122356799999999999764 6678887777777766543
No 50
>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=33.89 E-value=73 Score=21.00 Aligned_cols=53 Identities=21% Similarity=0.144 Sum_probs=33.2
Q ss_pred HHHHHHHhhccCCC--CHHHHHHHHHHcCCchhhhHHHHHhccCceecc--CCeEEe
Q 041805 91 KNIFLDVACFFQGE--DVNLVMKFLNASGFYPKLGRSVLVDKSLIVKSN--NNKITM 143 (215)
Q Consensus 91 k~~fl~~a~fp~~~--~~~~l~~~w~~~g~~~~~~l~~L~~~~Ll~~~~--~~~~~m 143 (215)
=++..|++..+.+. +.+.+.......--.....++.|...+++.... +|.|.+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L 67 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRL 67 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEE
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceee
Confidence 45677777777543 666666543332223366799999999998663 454443
No 51
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=33.35 E-value=1.5e+02 Score=21.72 Aligned_cols=61 Identities=21% Similarity=0.272 Sum_probs=40.7
Q ss_pred hHHHHHHHhhcCccHHHHHHHHHHhhc-cCCC-CHHHHHHHHHHcCCchhhhHHHHHhccCceecc
Q 041805 74 SILEVLKISYDGLDNKEKNIFLDVACF-FQGE-DVNLVMKFLNASGFYPKLGRSVLVDKSLIVKSN 137 (215)
Q Consensus 74 ~i~~~l~~Sy~~L~~~~k~~fl~~a~f-p~~~-~~~~l~~~w~~~g~~~~~~l~~L~~~~Ll~~~~ 137 (215)
.+..+++..|. |++..-.||. ++. .++. +.+.+.....-+--.+...++.|+++||++...
T Consensus 14 ~~~dvl~c~~G-Ls~~Dv~v~~--~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek 76 (126)
T COG3355 14 RCEDVLKCVYG-LSELDVEVYK--ALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREK 76 (126)
T ss_pred cHHHHHHHHhC-CcHHHHHHHH--HHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeee
Confidence 45566666664 5554444433 334 5665 888888776655555577899999999999654
No 52
>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.
Probab=33.15 E-value=2.8e+02 Score=22.91 Aligned_cols=98 Identities=15% Similarity=0.128 Sum_probs=63.1
Q ss_pred HHHHHHHHHHhhcCCCCCCchHHHHHHHHHHHhcCCch-hHHhhhcccCC--CCHHHHHHHHHHHhcC-CchhHHHHHHH
Q 041805 6 YHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPL-ALKVLGCFLYE--REKEVWESAINKLQRI-LHPSILEVLKI 81 (215)
Q Consensus 6 ~~ea~~Lf~~~af~~~~~~~~~~~~~~~iv~~c~GlPL-al~~ig~~L~~--k~~~~w~~~l~~l~~~-~~~~i~~~l~~ 81 (215)
.+.|..+|.+.. .......+.--....+--.|++-|- |.++.=..++. .+...|...++-+... ...+++.++.-
T Consensus 17 ~~~aR~vF~~a~-~~~~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f~~~~~~~~~Y~~~l~~~~d~~~aR~lfer 95 (280)
T PF05843_consen 17 IEAARKVFKRAR-KDKRCTYHVYVAYALMEYYCNKDPKRARKIFERGLKKFPSDPDFWLEYLDFLIKLNDINNARALFER 95 (280)
T ss_dssp HHHHHHHHHHHH-CCCCS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred hHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhCcHHHHHHHHHH
Confidence 367888888765 3333333333333344456688888 78777666653 5788999988875544 44789999999
Q ss_pred hhcCccHH--HHHHHHHHhhccCCC
Q 041805 82 SYDGLDNK--EKNIFLDVACFFQGE 104 (215)
Q Consensus 82 Sy~~L~~~--~k~~fl~~a~fp~~~ 104 (215)
+...|+.. .+..|-...-|-..+
T Consensus 96 ~i~~l~~~~~~~~iw~~~i~fE~~~ 120 (280)
T PF05843_consen 96 AISSLPKEKQSKKIWKKFIEFESKY 120 (280)
T ss_dssp HCCTSSCHHHCHHHHHHHHHHHHHH
T ss_pred HHHhcCchhHHHHHHHHHHHHHHHc
Confidence 99999874 477776666665333
No 53
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=31.48 E-value=36 Score=34.32 Aligned_cols=28 Identities=43% Similarity=0.635 Sum_probs=21.4
Q ss_pred CCCCCC-CCCCceEEEcCCC-Ccccccccc
Q 041805 183 SLPSNI-SAKKLVFLEMPNS-SIEQLWDGM 210 (215)
Q Consensus 183 ~lP~~~-~~~~L~~L~L~~s-~i~~L~~~~ 210 (215)
.+|+.+ ++.+|+.|+|++| +++.+|.++
T Consensus 793 ~lP~si~~L~~L~~L~Ls~C~~L~~LP~~~ 822 (1153)
T PLN03210 793 ELPSSIQNLHKLEHLEIENCINLETLPTGI 822 (1153)
T ss_pred ccChhhhCCCCCCEEECCCCCCcCeeCCCC
Confidence 577777 6788888888876 677777664
No 54
>KOG4194 consensus Membrane glycoprotein LIG-1 [Signal transduction mechanisms]
Probab=31.33 E-value=27 Score=32.78 Aligned_cols=21 Identities=29% Similarity=0.412 Sum_probs=15.4
Q ss_pred CCCCceEEEcCCCCccccccc
Q 041805 189 SAKKLVFLEMPNSSIEQLWDG 209 (215)
Q Consensus 189 ~~~~L~~L~L~~s~i~~L~~~ 209 (215)
...+|.+|||++|+|.+|++|
T Consensus 315 ftqkL~~LdLs~N~i~~l~~~ 335 (873)
T KOG4194|consen 315 FTQKLKELDLSSNRITRLDEG 335 (873)
T ss_pred hcccceeEeccccccccCChh
Confidence 356778888888888777765
No 55
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=31.05 E-value=1.2e+02 Score=20.95 Aligned_cols=66 Identities=26% Similarity=0.266 Sum_probs=43.2
Q ss_pred hHHHHHHHhhcCccHHHHHHHHHHhhccCCC-CHHHHHHHHHHcCC--chhhhHHHHHhccCceeccCCeE
Q 041805 74 SILEVLKISYDGLDNKEKNIFLDVACFFQGE-DVNLVMKFLNASGF--YPKLGRSVLVDKSLIVKSNNNKI 141 (215)
Q Consensus 74 ~i~~~l~~Sy~~L~~~~k~~fl~~a~fp~~~-~~~~l~~~w~~~g~--~~~~~l~~L~~~~Ll~~~~~~~~ 141 (215)
.+.-+.+.|-+.|++..-..|.+++- ++| +...+......+-- .....+..|+.++|++.++||.+
T Consensus 2 Ki~yI~K~s~nalsE~~~~ilI~v~K--k~Fit~~ev~e~l~~~~~~~~V~SNIGvLIKkglIEKSGDGlv 70 (96)
T PF09114_consen 2 KITYIIKASNNALSENAANILIQVAK--KNFITASEVREALATEMNKASVNSNIGVLIKKGLIEKSGDGLV 70 (96)
T ss_dssp THHHHHHHTTTSS-HHHHHHHHHHHH--STTB-HHHHHH-T-TTS-HHHHHHHHHHHHHTTSEEEETTEEE
T ss_pred cchhHHHHhhhhhhHHHHHHHHHHHH--HccCCHHHHHHHHHHHhhhhHHHHhHHHHHHcCcccccCCceE
Confidence 35567888888988887777777653 666 66666554422111 12456899999999999988853
No 56
>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=30.87 E-value=67 Score=20.35 Aligned_cols=35 Identities=9% Similarity=-0.106 Sum_probs=25.8
Q ss_pred ccHHHHHHHHHHhhccCCC-CHHHHH-HHHHHcCCch
Q 041805 86 LDNKEKNIFLDVACFFQGE-DVNLVM-KFLNASGFYP 120 (215)
Q Consensus 86 L~~~~k~~fl~~a~fp~~~-~~~~l~-~~w~~~g~~~ 120 (215)
|++....++.+++.-|... +++.++ .+|.......
T Consensus 6 Lt~~e~~lL~~L~~~~~~~vs~~~l~~~~w~~~~~~~ 42 (77)
T PF00486_consen 6 LTPKEFRLLELLLRNPGRVVSREELIEALWGDEEDVS 42 (77)
T ss_dssp SSHHHHHHHHHHHHTTTSEEEHHHHHHHHTSSSSTTC
T ss_pred cCHHHHHHHHHHHhCCCCCCCHHHhCChhhhcccccc
Confidence 6778888888888887665 888877 5787766343
No 57
>KOG0618 consensus Serine/threonine phosphatase 2C containing leucine-rich repeats, similar to SCN circadian oscillatory protein (SCOP) [Signal transduction mechanisms]
Probab=30.62 E-value=25 Score=34.50 Aligned_cols=32 Identities=19% Similarity=0.238 Sum_probs=28.3
Q ss_pred CCCCCC--CCCCceEEEcCCCCccccccccccCC
Q 041805 183 SLPSNI--SAKKLVFLEMPNSSIEQLWDGMKVCE 214 (215)
Q Consensus 183 ~lP~~~--~~~~L~~L~L~~s~i~~L~~~~~~l~ 214 (215)
++|.++ +++.|.+|+||+|++++||+.+.++.
T Consensus 397 ~fpas~~~kle~LeeL~LSGNkL~~Lp~tva~~~ 430 (1081)
T KOG0618|consen 397 SFPASKLRKLEELEELNLSGNKLTTLPDTVANLG 430 (1081)
T ss_pred cCCHHHHhchHHhHHHhcccchhhhhhHHHHhhh
Confidence 899997 78999999999999999998776653
No 58
>KOG3926 consensus F-box proteins [Amino acid transport and metabolism]
Probab=30.51 E-value=1.1e+02 Score=25.67 Aligned_cols=76 Identities=8% Similarity=0.018 Sum_probs=43.6
Q ss_pred HHHHHHhcCCchhHH--hhhcccCCCCHHHHHHHHHHHhcCCchhHHHHHHHhhcCccHHHHHHHHHHhhccCCCCHHHH
Q 041805 32 SKAMKYAQGVPLALK--VLGCFLYEREKEVWESAINKLQRILHPSILEVLKISYDGLDNKEKNIFLDVACFFQGEDVNLV 109 (215)
Q Consensus 32 ~~iv~~c~GlPLal~--~ig~~L~~k~~~~w~~~l~~l~~~~~~~i~~~l~~Sy~~L~~~~k~~fl~~a~fp~~~~~~~l 109 (215)
-.+.++||+-||.-. .-..+| .+.-.|++++..+.-..+.. -.+.+.+||.+...-.++ .+|.+.+...+
T Consensus 155 ~~~nq~cg~~~Lvsn~~~w~~~m--~til~~qqv~~~iqi~~~~~----~~ltl~dLP~e~vl~Il~--rlsDh~dL~s~ 226 (332)
T KOG3926|consen 155 CQLNQKCGKSVLVSNINLWKERM--ETILRWQQVLSQIQITEPDP----AGLTLHDLPLECVLNILL--RLSDHRDLESL 226 (332)
T ss_pred HHHHhhhCcccccchHHHHHHHH--HHHHHHHHHHHhhcccCCCc----CCCCcccchHHHHHHHHH--HccCcchHHHH
Confidence 345568888776321 111111 24556777776654322211 234567888776555444 36666688888
Q ss_pred HHHHHH
Q 041805 110 MKFLNA 115 (215)
Q Consensus 110 ~~~w~~ 115 (215)
.+.|.+
T Consensus 227 aqa~et 232 (332)
T KOG3926|consen 227 AQAWET 232 (332)
T ss_pred HHhhHH
Confidence 888876
No 59
>PF14050 Nudc_N: N-terminal conserved domain of Nudc.
Probab=30.06 E-value=56 Score=20.75 Aligned_cols=30 Identities=13% Similarity=0.243 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhcCCchhHHhhhcccCCCC
Q 041805 27 YEELSSKAMKYAQGVPLALKVLGCFLYERE 56 (215)
Q Consensus 27 ~~~~~~~iv~~c~GlPLal~~ig~~L~~k~ 56 (215)
+..+.-.|++.|+|++=-+.++-+.|+.||
T Consensus 3 ~D~~ll~iaq~~~~I~~~Ld~fF~FL~RkT 32 (62)
T PF14050_consen 3 FDNMLLSIAQQCGGIEDFLDTFFSFLRRKT 32 (62)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHhccC
Confidence 456777899999999999999999998775
No 60
>COG2033 Desulfoferrodoxin [Energy production and conversion]
Probab=28.90 E-value=17 Score=26.27 Aligned_cols=17 Identities=24% Similarity=0.567 Sum_probs=14.2
Q ss_pred EcCCCCccccccccccC
Q 041805 197 EMPNSSIEQLWDGMKVC 213 (215)
Q Consensus 197 ~L~~s~i~~L~~~~~~l 213 (215)
-++||||.-||++.+.+
T Consensus 109 A~~yCNiHGLWe~~~~i 125 (126)
T COG2033 109 ALSYCNIHGLWEGEVTI 125 (126)
T ss_pred eEeecceeeeeeccEEe
Confidence 46899999999997754
No 61
>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=28.79 E-value=96 Score=17.83 Aligned_cols=44 Identities=16% Similarity=-0.038 Sum_probs=21.1
Q ss_pred HHHHHHHHhhccCCCCHHHHHHHHHHcCCchhhhHHHHHhccCce
Q 041805 90 EKNIFLDVACFFQGEDVNLVMKFLNASGFYPKLGRSVLVDKSLIV 134 (215)
Q Consensus 90 ~k~~fl~~a~fp~~~~~~~l~~~w~~~g~~~~~~l~~L~~~~Ll~ 134 (215)
.++.+.++.--|. .+...+.....-..-....+++.|.+.++|+
T Consensus 5 ~~~Il~~l~~~~~-~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPR-ITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTT-S-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCC-CCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 3444444443222 3444444443322222355788888888764
No 62
>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=28.11 E-value=1.1e+02 Score=19.28 Aligned_cols=31 Identities=10% Similarity=-0.052 Sum_probs=22.6
Q ss_pred ccHHHHHHHHHHhhccCCC-CHHHHHH-HHHHc
Q 041805 86 LDNKEKNIFLDVACFFQGE-DVNLVMK-FLNAS 116 (215)
Q Consensus 86 L~~~~k~~fl~~a~fp~~~-~~~~l~~-~w~~~ 116 (215)
|++....+|.++..-+... +.+.++. +|...
T Consensus 6 Lt~~e~~lL~~L~~~~~~~vs~~~l~~~lw~~~ 38 (78)
T smart00862 6 LTPKEFRLLELLLRNPGRVVSREELLEAVWGDD 38 (78)
T ss_pred cCHHHHHHHHHHHhCCCCccCHHHHHHHHcCCC
Confidence 5666677888888888665 8887775 57643
No 63
>PRK13342 recombination factor protein RarA; Reviewed
Probab=27.41 E-value=4.3e+02 Score=23.22 Aligned_cols=47 Identities=11% Similarity=-0.062 Sum_probs=30.8
Q ss_pred CCCCCHHHHHHHHHHhhcCCCC-CCchHHHHHHHHHHHhcCCchhHHh
Q 041805 1 MEALEYHLALERFSRHAFKQNH-PDVGYEELSSKAMKYAQGVPLALKV 47 (215)
Q Consensus 1 v~~L~~~ea~~Lf~~~af~~~~-~~~~~~~~~~~iv~~c~GlPLal~~ 47 (215)
+.+|+.++...++.+.+-.... ...--.+....+++.|+|-|..+..
T Consensus 148 ~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd~R~aln 195 (413)
T PRK13342 148 LKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALN 195 (413)
T ss_pred eCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCCCHHHHHH
Confidence 4688999999999986522111 1012245667888999998865543
No 64
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=26.07 E-value=48 Score=21.11 Aligned_cols=41 Identities=20% Similarity=0.089 Sum_probs=30.1
Q ss_pred CHHHHHHHHHHcCCchhhhHHHHHhccCceeccCCeEEecHH
Q 041805 105 DVNLVMKFLNASGFYPKLGRSVLVDKSLIVKSNNNKITMHDL 146 (215)
Q Consensus 105 ~~~~l~~~w~~~g~~~~~~l~~L~~~~Ll~~~~~~~~~mHdl 146 (215)
+.+.+..+.....-.....++.|.+.++|... .+++.++|.
T Consensus 30 t~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~-~~~i~I~d~ 70 (76)
T PF13545_consen 30 TQEEIADMLGVSRETVSRILKRLKDEGIIEVK-RGKIIILDP 70 (76)
T ss_dssp SHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE-TTEEEESSH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEc-CCEEEECCH
Confidence 66777766554433446779999999999976 668888875
No 65
>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional
Probab=26.06 E-value=58 Score=31.52 Aligned_cols=29 Identities=24% Similarity=0.123 Sum_probs=19.9
Q ss_pred CCCCCCCCCCceEEEcCCCCccccccccccC
Q 041805 183 SLPSNISAKKLVFLEMPNSSIEQLWDGMKVC 213 (215)
Q Consensus 183 ~lP~~~~~~~L~~L~L~~s~i~~L~~~~~~l 213 (215)
+||.. +.+|++|+|++|+|+.+|...+.|
T Consensus 236 ~LP~l--p~~Lk~LdLs~N~LtsLP~lp~sL 264 (788)
T PRK15387 236 SLPAL--PPELRTLEVSGNQLTSLPVLPPGL 264 (788)
T ss_pred CCCCC--CCCCcEEEecCCccCcccCccccc
Confidence 45542 467888888888888887654444
No 66
>PF04089 BRICHOS: BRICHOS domain; InterPro: IPR007084 The BRICHOS family is defined by a 100 amino acid region found in a variety of proteins implicated in dementia, respiratory distress and cancer, including BRI-2, Chondromodulin-I (ChM-I), CA11, and surfactant protein C []. In several cases, the BRICHOS region is located in the propeptide region that is removed after proteolytic processing. This domain could be involved in the complex post-translational processing of these proteins.; PDB: 2YAD_F.
Probab=25.76 E-value=42 Score=22.78 Aligned_cols=18 Identities=22% Similarity=0.348 Sum_probs=10.0
Q ss_pred hHHHHHHHHHHHhcCCch
Q 041805 26 GYEELSSKAMKYAQGVPL 43 (215)
Q Consensus 26 ~~~~~~~~iv~~c~GlPL 43 (215)
+...++..|.+.|+|+|.
T Consensus 77 D~~~lg~~I~~lC~~~p~ 94 (97)
T PF04089_consen 77 DLSFLGSPIQELCEGLPT 94 (97)
T ss_dssp ------HHHHHHHTTS-E
T ss_pred CHHHHhhHHHHHhCCCCc
Confidence 456678899999999994
No 67
>PRK07471 DNA polymerase III subunit delta'; Validated
Probab=25.35 E-value=4.5e+02 Score=22.83 Aligned_cols=42 Identities=10% Similarity=0.067 Sum_probs=28.7
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCCchHHHHHHHHHHHhcCCchhHHhh
Q 041805 1 MEALEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVL 48 (215)
Q Consensus 1 v~~L~~~ea~~Lf~~~af~~~~~~~~~~~~~~~iv~~c~GlPLal~~i 48 (215)
+.||+.++..+.+.+.. +. .. ......+++.++|.|.....+
T Consensus 197 l~~l~~~~i~~~L~~~~-~~--~~---~~~~~~l~~~s~Gsp~~Al~l 238 (365)
T PRK07471 197 LRPLAPEDVIDALAAAG-PD--LP---DDPRAALAALAEGSVGRALRL 238 (365)
T ss_pred CCCCCHHHHHHHHHHhc-cc--CC---HHHHHHHHHHcCCCHHHHHHH
Confidence 46899999999998754 11 11 112267889999999865544
No 68
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=24.59 E-value=2.7e+02 Score=21.93 Aligned_cols=48 Identities=19% Similarity=0.302 Sum_probs=32.9
Q ss_pred HHhhccCCCCH-HHHHHHHHHcCCchhhhHHHHHhccCceeccCCeEEe
Q 041805 96 DVACFFQGEDV-NLVMKFLNASGFYPKLGRSVLVDKSLIVKSNNNKITM 143 (215)
Q Consensus 96 ~~a~fp~~~~~-~~l~~~w~~~g~~~~~~l~~L~~~~Ll~~~~~~~~~m 143 (215)
.++.+|.+... .-++.+-.+.|..+++.++++++.+++...++|+|.+
T Consensus 131 e~~~~~~~~~aK~vi~~~s~~~g~~p~evie~~~e~Gll~~~E~~k~~L 179 (190)
T PF09840_consen 131 ELRFQPLGTKAKRVIAAVSYATGLDPEEVIEELLEKGLLEEGEDGKIEL 179 (190)
T ss_pred HHhcCccCHHHHHHHHHHHHHhCCCHHHHHHHHHhCcccccCCCceEEE
Confidence 34444444433 3334445567888999999999999999877776654
No 69
>COG4886 Leucine-rich repeat (LRR) protein [Function unknown]
Probab=24.52 E-value=35 Score=29.44 Aligned_cols=20 Identities=15% Similarity=0.180 Sum_probs=9.9
Q ss_pred CCCCceEEEcCCCCcccccc
Q 041805 189 SAKKLVFLEMPNSSIEQLWD 208 (215)
Q Consensus 189 ~~~~L~~L~L~~s~i~~L~~ 208 (215)
.+++|..|++++|+|..++.
T Consensus 161 ~l~~L~~L~l~~N~l~~l~~ 180 (394)
T COG4886 161 NLPNLKNLDLSFNDLSDLPK 180 (394)
T ss_pred ccccccccccCCchhhhhhh
Confidence 44455555555555554444
No 70
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=23.65 E-value=1.3e+02 Score=22.59 Aligned_cols=48 Identities=10% Similarity=0.021 Sum_probs=29.0
Q ss_pred HHHHHHHHhhccCCC-CHHHHHHHHHHcCCchhhhHHHHHhccCceecc
Q 041805 90 EKNIFLDVACFFQGE-DVNLVMKFLNASGFYPKLGRSVLVDKSLIVKSN 137 (215)
Q Consensus 90 ~k~~fl~~a~fp~~~-~~~~l~~~w~~~g~~~~~~l~~L~~~~Ll~~~~ 137 (215)
.=++++|+|..+.+. +...+...-.-..-.-...+..|...+++....
T Consensus 10 Alr~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~r 58 (153)
T PRK11920 10 AIRMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVR 58 (153)
T ss_pred HHHHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec
Confidence 345677888766543 444444332211112255788999999999764
No 71
>KOG0531 consensus Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms]
Probab=23.20 E-value=35 Score=29.98 Aligned_cols=20 Identities=25% Similarity=0.264 Sum_probs=17.0
Q ss_pred CCCCceEEEcCCCCcccccc
Q 041805 189 SAKKLVFLEMPNSSIEQLWD 208 (215)
Q Consensus 189 ~~~~L~~L~L~~s~i~~L~~ 208 (215)
++.+|++|+|++|+|++++.
T Consensus 116 ~~~~L~~L~ls~N~I~~i~~ 135 (414)
T KOG0531|consen 116 SLVNLQVLDLSFNKITKLEG 135 (414)
T ss_pred hhhcchheeccccccccccc
Confidence 57899999999999988873
No 72
>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional
Probab=23.20 E-value=51 Score=31.72 Aligned_cols=20 Identities=5% Similarity=-0.110 Sum_probs=9.4
Q ss_pred HHHHHHHHHhhccCCCCHHH
Q 041805 89 KEKNIFLDVACFFQGEDVNL 108 (215)
Q Consensus 89 ~~k~~fl~~a~fp~~~~~~~ 108 (215)
+++.|..++.=-|.|.+++.
T Consensus 45 ~~~~~~~~~~~~~~~~~~~~ 64 (754)
T PRK15370 45 EAQNCIAYLCHPPETASPEE 64 (754)
T ss_pred HHHHHHHHHhCCCCCCCHHH
Confidence 45555555544344444433
No 73
>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional
Probab=23.18 E-value=56 Score=31.48 Aligned_cols=27 Identities=19% Similarity=0.288 Sum_probs=18.8
Q ss_pred CCCCCCCCCCceEEEcCCCCcccccccc
Q 041805 183 SLPSNISAKKLVFLEMPNSSIEQLWDGM 210 (215)
Q Consensus 183 ~lP~~~~~~~L~~L~L~~s~i~~L~~~~ 210 (215)
+||..+. .+|++|+|++|+|+.+|.++
T Consensus 213 sLP~~l~-~nL~~L~Ls~N~LtsLP~~l 239 (754)
T PRK15370 213 SLPENLQ-GNIKTLYANSNQLTSIPATL 239 (754)
T ss_pred cCChhhc-cCCCEEECCCCccccCChhh
Confidence 6666543 47888888888888777644
No 74
>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=22.55 E-value=70 Score=20.06 Aligned_cols=52 Identities=17% Similarity=0.178 Sum_probs=30.3
Q ss_pred CccHHHHHHHHHHhhccCCCCHHHHHHHHHHcCCchhhhHHHHHhccCceecc
Q 041805 85 GLDNKEKNIFLDVACFFQGEDVNLVMKFLNASGFYPKLGRSVLVDKSLIVKSN 137 (215)
Q Consensus 85 ~L~~~~k~~fl~~a~fp~~~~~~~l~~~w~~~g~~~~~~l~~L~~~~Ll~~~~ 137 (215)
+|++...+++.++.-. +..+...+.....-..-.....++.|.++++++...
T Consensus 5 gLs~~E~~vy~~Ll~~-~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 5 GLSENEAKVYLALLKN-GPATAEEIAEELGISRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp CHHHHHHHHHHHHHHH-CHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred CcCHHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 3556666666666411 222555555433222222356799999999999875
No 75
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=22.40 E-value=2.8e+02 Score=19.39 Aligned_cols=43 Identities=9% Similarity=0.114 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHhhcCCCCCCchHHHHHHHHHHHhcCCchhHHhh
Q 041805 4 LEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVPLALKVL 48 (215)
Q Consensus 4 L~~~ea~~Lf~~~af~~~~~~~~~~~~~~~iv~~c~GlPLal~~i 48 (215)
|+.+++...|...+|.... +++-..+..+|.+.+|+--..+-.
T Consensus 17 l~~ee~ia~yL~~~le~~d--~a~i~~alg~var~~GMsqvA~~a 59 (100)
T COG3636 17 LTDEEAIAAYLNAALEEGD--PALIAAALGVVARSRGMSQVARKA 59 (100)
T ss_pred hCCHHHHHHHHHHHHHcCC--HHHHHHHHHHHHHhcCHHHHHHHh
Confidence 5678888888888887665 677778888999998876544433
No 76
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=21.16 E-value=1.2e+02 Score=16.93 Aligned_cols=23 Identities=17% Similarity=0.218 Sum_probs=17.8
Q ss_pred hhhHHHHHhccCceeccCCeEEec
Q 041805 121 KLGRSVLVDKSLIVKSNNNKITMH 144 (215)
Q Consensus 121 ~~~l~~L~~~~Ll~~~~~~~~~mH 144 (215)
...++.|.+.+++... .+.|.+|
T Consensus 26 ~~~l~~L~~~g~l~~~-~~~~~i~ 48 (48)
T smart00419 26 SRTLKRLEKEGLISRE-GGRIVIL 48 (48)
T ss_pred HHHHHHHHHCCCEEEe-CCEEEEC
Confidence 4578899999999876 4677765
No 77
>KOG4194 consensus Membrane glycoprotein LIG-1 [Signal transduction mechanisms]
Probab=21.00 E-value=31 Score=32.39 Aligned_cols=27 Identities=15% Similarity=0.357 Sum_probs=20.5
Q ss_pred CCCCCceEEEcCCCCcccc----ccccccCC
Q 041805 188 ISAKKLVFLEMPNSSIEQL----WDGMKVCE 214 (215)
Q Consensus 188 ~~~~~L~~L~L~~s~i~~L----~~~~~~l~ 214 (215)
|.+..|+.|+||+|.|.+. |+-+|+|+
T Consensus 290 fgLt~L~~L~lS~NaI~rih~d~WsftqkL~ 320 (873)
T KOG4194|consen 290 FGLTSLEQLDLSYNAIQRIHIDSWSFTQKLK 320 (873)
T ss_pred cccchhhhhccchhhhheeecchhhhcccce
Confidence 5788899999999988764 66666654
No 78
>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=20.74 E-value=1.7e+02 Score=19.25 Aligned_cols=32 Identities=13% Similarity=-0.052 Sum_probs=22.1
Q ss_pred ccHHHHHHHHHHhhccCCC-CHHHHH-HHHHHcC
Q 041805 86 LDNKEKNIFLDVACFFQGE-DVNLVM-KFLNASG 117 (215)
Q Consensus 86 L~~~~k~~fl~~a~fp~~~-~~~~l~-~~w~~~g 117 (215)
|++.+..+|.+++.-|... +++.++ .+|...+
T Consensus 24 Lt~~e~~lL~~L~~~~~~~vs~~~l~~~lw~~~~ 57 (95)
T cd00383 24 LTPKEFELLELLARNPGRVLSREQLLEAVWGDDY 57 (95)
T ss_pred eCHHHHHHHHHHHhCCCCcCCHHHHHHHhcCCCC
Confidence 5567777788888777655 877776 4676543
No 79
>PF03849 Tfb2: Transcription factor Tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=20.42 E-value=3.6e+02 Score=23.50 Aligned_cols=69 Identities=10% Similarity=0.026 Sum_probs=49.6
Q ss_pred hcCccHHHHHHHHHHhhccCCCCHHHHHHHHHHcCCch--hhhHHHHHhccCceecc-C---CeEEecHHHHHHHH
Q 041805 83 YDGLDNKEKNIFLDVACFFQGEDVNLVMKFLNASGFYP--KLGRSVLVDKSLIVKSN-N---NKITMHDLLQELGR 152 (215)
Q Consensus 83 y~~L~~~~k~~fl~~a~fp~~~~~~~l~~~w~~~g~~~--~~~l~~L~~~~Ll~~~~-~---~~~~mHdlvr~~a~ 152 (215)
|..||+-+|++...+-..+...+. ..+..|+..+... +..++.|.+-.+++... . ..+.++...+.=-+
T Consensus 25 fR~LP~LAK~~VmrLL~~~~pv~~-~~l~~Wv~~~~~~~~~~al~~L~~L~Ii~~~~~~~~~~~~~Ln~~F~~~Lr 99 (366)
T PF03849_consen 25 FRSLPPLAKQYVMRLLFVEQPVPQ-ADLESWVKPESKKEHDEALKRLRSLHIIQESESPGGKQQYQLNPIFRKNLR 99 (366)
T ss_pred HHhccHHHHHHHHHHHhcCCCcCH-HHHHHHhCccchHHHHHHHHHHhhCeeEeeccCCCCceeEEeCHHHHHHHH
Confidence 447999999988887666554554 5566788865543 56799999999998664 2 24999998876433
No 80
>PRK06893 DNA replication initiation factor; Validated
Probab=20.19 E-value=2.4e+02 Score=22.50 Aligned_cols=40 Identities=13% Similarity=0.124 Sum_probs=24.7
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCCchHHHHHHHHHHHhcCCc
Q 041805 1 MEALEYHLALERFSRHAFKQNHPDVGYEELSSKAMKYAQGVP 42 (215)
Q Consensus 1 v~~L~~~ea~~Lf~~~af~~~~~~~~~~~~~~~iv~~c~GlP 42 (215)
++++++++.++++.+.++...-.. -+++..-|++.+.|-.
T Consensus 158 l~~pd~e~~~~iL~~~a~~~~l~l--~~~v~~~L~~~~~~d~ 197 (229)
T PRK06893 158 LNDLTDEQKIIVLQRNAYQRGIEL--SDEVANFLLKRLDRDM 197 (229)
T ss_pred CCCCCHHHHHHHHHHHHHHcCCCC--CHHHHHHHHHhccCCH
Confidence 467888888888888875433211 1345556666666543
Done!