Query psy2669
Match_columns 166
No_of_seqs 204 out of 1102
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 22:08:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2669.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2669hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5022 Myosin heavy chain [Cy 100.0 2.6E-39 5.7E-44 299.6 13.1 150 3-153 275-425 (1463)
2 cd01377 MYSc_type_II Myosin mo 100.0 3.1E-38 6.7E-43 284.7 16.8 150 1-150 219-368 (693)
3 PTZ00014 myosin-A; Provisional 100.0 4.5E-38 9.7E-43 286.8 16.0 150 1-151 303-457 (821)
4 cd01383 MYSc_type_VIII Myosin 100.0 9.6E-38 2.1E-42 280.6 15.5 149 1-150 209-358 (677)
5 KOG0164|consensus 100.0 3.1E-38 6.7E-43 276.9 11.4 149 1-152 217-365 (1001)
6 cd01381 MYSc_type_VII Myosin m 100.0 1.3E-37 2.9E-42 279.6 15.8 150 1-151 204-356 (671)
7 cd01380 MYSc_type_V Myosin mot 100.0 1.6E-37 3.4E-42 280.0 15.6 149 1-150 210-359 (691)
8 cd01384 MYSc_type_XI Myosin mo 100.0 2.9E-37 6.2E-42 277.5 16.0 149 1-150 209-361 (674)
9 cd01378 MYSc_type_I Myosin mot 100.0 1.3E-36 2.7E-41 273.6 16.1 148 1-150 207-359 (674)
10 cd01387 MYSc_type_XV Myosin mo 100.0 1.5E-36 3.2E-41 273.1 15.8 148 2-150 206-356 (677)
11 cd01385 MYSc_type_IX Myosin mo 100.0 3.7E-36 7.9E-41 271.1 16.4 148 2-150 216-367 (692)
12 cd00124 MYSc Myosin motor doma 100.0 5.6E-36 1.2E-40 270.0 16.5 149 1-150 205-356 (679)
13 PF00063 Myosin_head: Myosin h 100.0 5.2E-36 1.1E-40 270.8 15.2 148 2-150 209-357 (689)
14 cd01379 MYSc_type_III Myosin m 100.0 1.1E-35 2.3E-40 266.6 16.8 149 2-151 207-363 (653)
15 smart00242 MYSc Myosin. Large 100.0 1.1E-35 2.3E-40 268.0 16.2 149 1-150 213-363 (677)
16 KOG0162|consensus 100.0 1.2E-35 2.5E-40 261.2 12.3 148 2-152 226-378 (1106)
17 cd01382 MYSc_type_VI Myosin mo 100.0 4E-35 8.7E-40 265.2 15.4 147 1-148 209-390 (717)
18 cd01386 MYSc_type_XVIII Myosin 100.0 1.3E-31 2.8E-36 243.4 15.7 147 2-150 207-367 (767)
19 KOG0163|consensus 100.0 3.8E-32 8.3E-37 239.7 11.4 152 1-154 262-449 (1259)
20 KOG0161|consensus 100.0 6.8E-30 1.5E-34 245.2 12.0 149 2-150 294-442 (1930)
21 KOG0160|consensus 100.0 1.2E-28 2.7E-33 223.1 13.1 148 1-150 213-361 (862)
22 KOG4229|consensus 99.9 9.8E-24 2.1E-28 195.2 7.1 148 6-153 271-422 (1062)
23 PF07499 RuvA_C: RuvA, C-termi 77.7 6.4 0.00014 23.3 4.2 25 30-54 3-27 (47)
24 COG4056 McrC Methyl coenzyme M 61.0 1.3 2.9E-05 33.6 -1.7 29 36-64 87-115 (204)
25 PF12844 HTH_19: Helix-turn-he 60.1 31 0.00068 21.0 4.9 57 32-98 3-60 (64)
26 PF01978 TrmB: Sugar-specific 59.8 18 0.00039 22.7 3.7 43 37-100 1-43 (68)
27 COG2355 Zn-dependent dipeptida 57.6 21 0.00046 30.1 4.7 32 21-52 269-300 (313)
28 PHA02591 hypothetical protein; 57.1 8.8 0.00019 25.7 1.9 44 57-100 32-80 (83)
29 PF10440 WIYLD: Ubiquitin-bind 54.9 31 0.00067 22.2 4.1 39 28-67 9-47 (65)
30 PF12728 HTH_17: Helix-turn-he 54.4 13 0.00028 21.9 2.2 24 82-105 4-27 (51)
31 PF08671 SinI: Anti-repressor 54.4 34 0.00074 18.5 3.7 25 28-52 3-27 (30)
32 PF13833 EF-hand_8: EF-hand do 51.1 38 0.00083 19.8 4.0 25 26-53 6-33 (54)
33 PF02954 HTH_8: Bacterial regu 49.5 19 0.00042 20.5 2.4 19 82-100 21-39 (42)
34 PHA01976 helix-turn-helix prot 48.3 63 0.0014 19.8 5.2 57 32-97 6-62 (67)
35 PF08667 BetR: BetR domain; I 47.2 40 0.00087 25.2 4.3 67 26-97 3-69 (147)
36 PF03683 UPF0175: Uncharacteri 46.8 79 0.0017 20.5 6.0 53 36-105 6-60 (76)
37 cd07311 terB_like_1 tellurium 46.6 30 0.00065 25.8 3.6 80 20-100 35-131 (150)
38 TIGR01764 excise DNA binding d 46.4 24 0.00052 19.9 2.5 23 82-104 4-26 (49)
39 PF13309 HTH_22: HTH domain 45.7 23 0.0005 22.4 2.5 21 80-100 43-63 (64)
40 PF01465 GRIP: GRIP domain; I 44.6 25 0.00053 20.8 2.3 15 46-60 23-37 (46)
41 smart00027 EH Eps15 homology d 44.4 37 0.00081 22.7 3.6 25 29-53 28-52 (96)
42 PRK10856 cytoskeletal protein 44.0 48 0.001 28.0 4.8 64 31-101 17-84 (331)
43 cd00052 EH Eps15 homology doma 44.0 45 0.00097 20.0 3.6 23 31-53 19-41 (67)
44 PRK13379 protocatechuate 4,5-d 41.9 18 0.00039 26.1 1.6 60 25-100 39-101 (119)
45 cd04762 HTH_MerR-trunc Helix-T 41.3 29 0.00064 19.3 2.3 24 82-105 3-26 (49)
46 PF01876 RNase_P_p30: RNase P 40.0 1.1E+02 0.0024 22.3 5.8 59 43-102 88-149 (150)
47 TIGR03264 met_CoM_red_C methyl 40.0 4.4 9.6E-05 31.4 -1.8 26 39-64 88-113 (194)
48 PRK13377 protocatechuate 4,5-d 39.5 22 0.00047 26.0 1.8 74 25-102 38-114 (129)
49 PF10075 PCI_Csn8: COP9 signal 39.0 29 0.00064 25.1 2.5 39 81-119 99-137 (143)
50 cd07925 LigA_like_1 The A subu 38.8 28 0.00061 24.6 2.2 71 24-98 26-99 (106)
51 PF12244 DUF3606: Protein of u 38.8 40 0.00087 20.9 2.7 27 74-100 15-41 (57)
52 PF00126 HTH_1: Bacterial regu 38.5 56 0.0012 19.9 3.4 19 82-100 16-34 (60)
53 cd08315 Death_TRAILR_DR4_DR5 D 37.9 45 0.00097 22.9 3.1 23 28-50 17-39 (96)
54 cd01301 rDP_like renal dipepti 37.7 53 0.0012 27.4 4.1 31 21-51 272-302 (309)
55 cd08313 Death_TNFR1 Death doma 37.6 48 0.001 22.1 3.1 23 28-50 9-31 (80)
56 PF01152 Bac_globin: Bacterial 37.4 74 0.0016 22.0 4.3 27 31-57 87-113 (120)
57 TIGR02792 PCA_ligA protocatech 37.2 24 0.00053 25.4 1.7 74 24-101 31-107 (117)
58 COG1378 Predicted transcriptio 37.1 2.2E+02 0.0048 22.9 10.0 74 32-126 4-83 (247)
59 PRK13378 protocatechuate 4,5-d 37.1 26 0.00057 25.2 1.9 73 24-100 37-112 (117)
60 PRK13890 conjugal transfer pro 36.4 58 0.0013 23.2 3.6 60 30-98 7-66 (120)
61 cd04761 HTH_MerR-SF Helix-Turn 35.6 39 0.00085 19.2 2.2 23 82-104 3-25 (49)
62 PF01244 Peptidase_M19: Membra 34.8 43 0.00092 28.1 3.1 31 21-51 280-310 (320)
63 cd07924 PCA_45_Doxase_A The A 34.5 31 0.00066 25.0 1.9 74 24-101 34-110 (121)
64 smart00497 IENR1 Intron encode 34.4 44 0.00094 19.5 2.4 30 79-108 17-46 (53)
65 cd08784 Death_DRs Death Domain 33.8 61 0.0013 21.2 3.2 23 28-50 9-31 (79)
66 COG4103 Uncharacterized protei 33.8 39 0.00085 25.3 2.4 20 79-98 123-142 (148)
67 PF09048 Cro: Cro; InterPro: 33.7 42 0.0009 21.2 2.2 23 82-104 15-37 (59)
68 COG2522 Predicted transcriptio 33.4 39 0.00084 24.4 2.3 23 82-104 25-47 (119)
69 PF12802 MarR_2: MarR family; 32.4 1.1E+02 0.0024 18.1 5.0 41 41-100 2-42 (62)
70 PF00376 MerR: MerR family reg 31.8 54 0.0012 18.4 2.3 19 82-100 2-20 (38)
71 cd07923 Gallate_dioxygenase_C 30.8 1.5E+02 0.0033 20.4 4.8 60 27-101 21-82 (94)
72 PF13443 HTH_26: Cro/C1-type H 29.4 24 0.00053 21.4 0.6 21 78-98 39-59 (63)
73 PRK09430 djlA Dna-J like membr 28.5 1.3E+02 0.0028 24.5 4.9 78 20-101 67-173 (267)
74 PF01476 LysM: LysM domain; I 28.3 73 0.0016 17.6 2.5 24 76-99 3-26 (44)
75 PRK13372 pcmA protocatechuate 28.2 43 0.00094 29.6 2.1 79 21-103 34-115 (444)
76 PF07126 DUF1379: Protein of u 28.0 88 0.0019 23.5 3.5 35 23-57 30-65 (153)
77 PF09278 MerR-DNA-bind: MerR, 27.8 95 0.0021 18.9 3.2 22 32-53 5-26 (65)
78 PF05225 HTH_psq: helix-turn-h 27.2 68 0.0015 18.7 2.3 22 80-101 17-38 (45)
79 PF02376 CUT: CUT domain; Int 26.7 52 0.0011 22.2 1.9 42 84-141 32-73 (87)
80 COG0599 Uncharacterized homolo 26.5 1.1E+02 0.0023 21.7 3.6 26 30-56 74-99 (124)
81 cd08815 Death_TNFRSF25_DR3 Dea 26.4 65 0.0014 21.5 2.3 25 26-50 7-31 (77)
82 PF09288 UBA_3: Fungal ubiquit 25.9 1.1E+02 0.0023 19.1 3.0 21 32-52 11-31 (55)
83 PRK09706 transcriptional repre 25.9 2.2E+02 0.0047 20.3 5.3 58 31-97 8-65 (135)
84 PF01381 HTH_3: Helix-turn-hel 25.8 52 0.0011 19.2 1.6 21 76-96 35-55 (55)
85 TIGR03060 PS_II_psb29 photosys 25.8 1.1E+02 0.0024 24.4 3.9 82 41-144 66-149 (214)
86 PF13411 MerR_1: MerR HTH fami 25.8 75 0.0016 19.5 2.5 22 82-103 3-24 (69)
87 cd08316 Death_FAS_TNFRSF6 Deat 25.8 40 0.00087 23.3 1.2 28 23-50 13-40 (97)
88 TIGR02675 tape_meas_nterm tape 25.6 1.6E+02 0.0035 19.1 4.1 68 35-105 3-70 (75)
89 PF02796 HTH_7: Helix-turn-hel 25.3 82 0.0018 18.1 2.4 22 80-101 22-43 (45)
90 PRK13266 Thf1-like protein; Re 25.0 1.3E+02 0.0029 24.1 4.2 84 41-144 66-151 (225)
91 smart00422 HTH_MERR helix_turn 24.4 1.4E+02 0.003 18.2 3.6 24 82-105 3-26 (70)
92 PF00356 LacI: Bacterial regul 24.2 1E+02 0.0023 18.1 2.7 22 82-103 2-23 (46)
93 PF11758 Bacteriocin_IIi: Aure 24.1 51 0.0011 20.1 1.3 12 135-146 36-47 (51)
94 cd04764 HTH_MlrA-like_sg1 Heli 23.8 78 0.0017 19.5 2.3 19 82-100 3-21 (67)
95 PF07804 HipA_C: HipA-like C-t 23.3 1.4E+02 0.0031 19.1 3.5 41 28-68 20-68 (79)
96 PF10260 SAYSvFN: Uncharacteri 23.3 82 0.0018 20.6 2.3 27 6-32 42-68 (71)
97 smart00389 HOX Homeodomain. DN 23.3 75 0.0016 18.5 2.0 29 76-104 24-52 (56)
98 cd00086 homeodomain Homeodomai 23.0 71 0.0015 18.7 1.9 30 76-105 24-53 (59)
99 COG1924 Activator of 2-hydroxy 22.8 3.3E+02 0.0071 23.8 6.4 70 78-148 264-344 (396)
100 PF03165 MH1: MH1 domain; Int 22.7 36 0.00078 23.8 0.5 46 93-139 19-66 (103)
101 PF08809 DUF1799: Phage relate 22.5 1.5E+02 0.0033 19.8 3.5 27 28-54 46-72 (83)
102 PF04609 MCR_C: Methyl-coenzym 22.5 12 0.00026 30.7 -2.2 27 38-64 115-141 (268)
103 PF04458 DUF505: Protein of un 22.3 67 0.0015 29.4 2.3 58 40-102 510-567 (591)
104 PF00392 GntR: Bacterial regul 22.3 1.2E+02 0.0026 18.5 2.9 22 132-153 1-22 (64)
105 PRK09943 DNA-binding transcrip 21.7 1.2E+02 0.0025 22.9 3.3 59 31-98 10-68 (185)
106 PF05099 TerB: Tellurite resis 21.2 1.2E+02 0.0025 21.4 3.0 20 79-98 118-137 (140)
107 cd04763 HTH_MlrA-like Helix-Tu 21.2 98 0.0021 19.1 2.3 19 82-100 3-21 (68)
108 cd00194 UBA Ubiquitin Associat 20.9 1.6E+02 0.0034 15.9 2.9 19 32-50 3-21 (38)
109 PF13384 HTH_23: Homeodomain-l 20.7 1.1E+02 0.0024 17.5 2.4 22 80-101 18-39 (50)
110 PF00046 Homeobox: Homeobox do 20.2 60 0.0013 19.2 1.1 28 77-104 25-52 (57)
111 PF13105 DUF3959: Protein of u 20.2 1E+02 0.0022 24.2 2.6 18 127-144 36-53 (239)
No 1
>COG5022 Myosin heavy chain [Cytoskeleton]
Probab=100.00 E-value=2.6e-39 Score=299.64 Aligned_cols=150 Identities=28% Similarity=0.419 Sum_probs=142.8
Q ss_pred CCCCCCCccccccCC-CCCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCchh
Q psy2669 3 MLTNDIYDYYNVSQG-KITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTEE 81 (166)
Q Consensus 3 ~L~~~~~~y~yL~~~-~~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~~ 81 (166)
++.+.|++|.||++| |..++|+||+++|+.|++||+++||+++||..||++||||||||||+|... +++.+.+++.+.
T Consensus 275 ~~~~~~~dY~Yl~~~~~~~I~gIdD~kefk~t~~AlktiGi~~eeq~~IF~iLAaILhiGNIef~~~-r~g~a~~~~~~~ 353 (1463)
T COG5022 275 LLLQNPKDYIYLSQGGCDKIDGIDDAKEFKITLDALKTIGIDEEEQDQIFKILAAILHIGNIEFKED-RNGAAIFSDNSV 353 (1463)
T ss_pred hhccChHhhHhHhhcCCCcCCCcccHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhcceeeeec-ccchhhcCCchH
Confidence 445899999999998 789999999999999999999999999999999999999999999999986 467889999999
Q ss_pred HHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCccccc
Q psy2669 82 GDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMKFKQ 153 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~~~~ 153 (166)
++.+|+|||||++.|.++|+.|.+++|||.+.+|+|..||...||||||+||++||+|||.|||.+...+..
T Consensus 354 ~~~~c~LLgId~~~f~k~lvk~~ikt~~E~i~~~~n~~QA~~irdslAK~lY~~lFdwiV~rIN~sL~~~~~ 425 (1463)
T COG5022 354 LDKACYLLGIDPSLFVKWLVKRQIKTGGEWIVVPLNLEQALAIRDSLAKALYSNLFDWIVDRINKSLDHSAA 425 (1463)
T ss_pred HHHHHHHhCCCHHHHHHHHHHhHhhcCceEEEecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCccc
Confidence 999999999999999999999999999999999999999999999999999999999999999998877654
No 2
>cd01377 MYSc_type_II Myosin motor domain, type II myosins. Myosin II mediates cortical contraction in cell motility, and is the motor in smooth and skeletal muscle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydro
Probab=100.00 E-value=3.1e-38 Score=284.67 Aligned_cols=150 Identities=50% Similarity=0.803 Sum_probs=141.8
Q ss_pred CCCCCCCCCccccccCCCCCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCch
Q psy2669 1 MCMLTNDIYDYYNVSQGKITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTE 80 (166)
Q Consensus 1 ~l~L~~~~~~y~yL~~~~~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~ 80 (166)
+|+|...+++|+||++++..++++||+++|++++.||+.|||+++|+..||+|||||||||||+|.+.+.++.+.+.+.+
T Consensus 219 ~l~L~~~~~~y~yL~~~~~~~~~~~d~~~f~~~~~al~~lG~~~~e~~~i~~iLaaILhLGni~F~~~~~~~~~~~~~~~ 298 (693)
T cd01377 219 MLLLTGNPNDYRYLSQGELTIPGVDDAEEFKLTDEAFDILGFSDEEKNSIFKIVAAILHLGNIKFKQRQREEQAELDGTE 298 (693)
T ss_pred HcCCCCchhcCeeeCCCCccCCCCcHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcceEEEecCCCCccccCChH
Confidence 47787777999999999877899999999999999999999999999999999999999999999987666788899999
Q ss_pred hHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCcc
Q psy2669 81 EGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMK 150 (166)
Q Consensus 81 ~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~ 150 (166)
.+..+|+||||++++|.++|+++++.++++.+.+|+++++|..+||+|||+||++||+|||.+||.++..
T Consensus 299 ~l~~~a~LLgv~~~~L~~~l~~~~~~~~~e~i~~~~~~~~A~~~rDalak~lY~~LF~wiV~~IN~~l~~ 368 (693)
T cd01377 299 EADKAAHLLGVNSADLLKALLHPRIKVGREWVTKGQNVEQVSFSVGALAKALYERLFLWLVKRINKTLDT 368 (693)
T ss_pred HHHHHHHHhCCCHHHHHHHhcceEEEECCeeEeeCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999997643
No 3
>PTZ00014 myosin-A; Provisional
Probab=100.00 E-value=4.5e-38 Score=286.78 Aligned_cols=150 Identities=17% Similarity=0.274 Sum_probs=138.1
Q ss_pred CCCCCCCCCccccccCCCCCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCC---CCccccC
Q psy2669 1 MCMLTNDIYDYYNVSQGKITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGR---EEQAEPD 77 (166)
Q Consensus 1 ~l~L~~~~~~y~yL~~~~~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~---~~~~~v~ 77 (166)
+|+| .++++|+||+++|..++++||+++|++|++||++|||+++|+..||+|||||||||||+|.+.+. ++.+.+.
T Consensus 303 ~l~L-~~~~~y~yL~~~~~~~~~~dD~~~f~~~~~A~~~lg~s~~e~~~If~ilaaILhLGNi~F~~~~~~~~~~~~~i~ 381 (821)
T PTZ00014 303 KYKL-KSLEEYKYINPKCLDVPGIDDVKDFEEVMESFDSMGLSESQIEDIFSILSGVLLLGNVEIEGKEEGGLTDAAAIS 381 (821)
T ss_pred HcCC-CChHhccccCCCCccCCCCchHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcceeEeccccCCCCCceecc
Confidence 4678 58999999999999999999999999999999999999999999999999999999999987532 3566776
Q ss_pred Cc--hhHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCccc
Q psy2669 78 GT--EEGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMKF 151 (166)
Q Consensus 78 ~~--~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~~ 151 (166)
+. +.+..+|+||||++++|.++|+++++.+||+.+.+|++++||..+||||||+||+|||+|||.+||.++...
T Consensus 382 ~~~~~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~i~~~~~~~qA~~~rdalaK~lY~rLF~wiV~~IN~~l~~~ 457 (821)
T PTZ00014 382 DESLEVFNEACELLFLDYESLKKELTVKVTYAGNQKIEGPWSKDESEMLKDSLSKAVYEKLFLWIIRNLNATIEPP 457 (821)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHhhceEEEeCCeeEecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 54 499999999999999999999999999999999999999999999999999999999999999999986543
No 4
>cd01383 MYSc_type_VIII Myosin motor domain, plant-specific type VIII myosins, a subgroup which has been associated with endocytosis, cytokinesis, cell-to-cell coupling and gating at plasmodesmata. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates f
Probab=100.00 E-value=9.6e-38 Score=280.63 Aligned_cols=149 Identities=23% Similarity=0.340 Sum_probs=138.6
Q ss_pred CCCCCCCCCccccccCC-CCCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCc
Q psy2669 1 MCMLTNDIYDYYNVSQG-KITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGT 79 (166)
Q Consensus 1 ~l~L~~~~~~y~yL~~~-~~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~ 79 (166)
+|+| .++++|+||+++ +..++++||+++|+++++||+.|||+++|+..||+|||||||||||+|.+.++++.+.+.+.
T Consensus 209 ~l~L-~~~~~y~yL~~~~~~~~~~~dd~~~f~~~~~al~~lG~~~~e~~~I~~iLaaILhLGNi~F~~~~~~~~~~~~~~ 287 (677)
T cd01383 209 KLNL-KSASEYKYLKQSCCYSINGVDDAQRFHTLVEALDIVHISKEDQENVFAMLAAVLWLGNVSFTVIDNENHVEPVAD 287 (677)
T ss_pred HhCC-CCHHHCceecCCCcccCCCccHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcceEEEecCCCcccccCCh
Confidence 3677 578999999987 57889999999999999999999999999999999999999999999998655556677788
Q ss_pred hhHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCcc
Q psy2669 80 EEGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMK 150 (166)
Q Consensus 80 ~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~ 150 (166)
+.++.+|+||||++++|.++|+++++.++|+.+.+|++++||..+||+|||+||+|||+|||.+||.++..
T Consensus 288 ~~l~~~a~LLgv~~~~L~~~l~~~~~~~~~e~~~~~~~~~qa~~~rdalak~lY~~lF~wiV~~IN~~l~~ 358 (677)
T cd01383 288 EALSTAAKLIGCNIEDLMLALSTRKMHVNNDNIVQKLTLQQAIDARDALAKSIYASLFDWLVEQINKSLEV 358 (677)
T ss_pred HHHHHHHHHhCCCHHHHHHHhhhcEEEeCCceEeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 89999999999999999999999999999999999999999999999999999999999999999997543
No 5
>KOG0164|consensus
Probab=100.00 E-value=3.1e-38 Score=276.87 Aligned_cols=149 Identities=22% Similarity=0.392 Sum_probs=140.4
Q ss_pred CCCCCCCCCccccccCCCCCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCch
Q psy2669 1 MCMLTNDIYDYYNVSQGKITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTE 80 (166)
Q Consensus 1 ~l~L~~~~~~y~yL~~~~~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~ 80 (166)
+|+|+++|..|+||++|+..+.+++|+.+|+.+++||+++||+++|+..+|+|+|||||||||+|.+. ++...+.+..
T Consensus 217 ~l~Ler~~~~Y~ylnqg~~~v~sinD~~dfk~V~~Am~vIgFs~eEVe~v~~iiAavLhLGNv~f~~~--ed~~~~~~~~ 294 (1001)
T KOG0164|consen 217 QLGLERNPQSYNYLNQGSAKVSSINDASDFKAVQKAMRVIGFSEEEVESVLSIIAAVLHLGNVEFADN--EDSSGIVNGA 294 (1001)
T ss_pred HhccccCcchhhhhhhhhhhhcccccHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccceEEeec--CcccccchhH
Confidence 47999999999999999989999999999999999999999999999999999999999999999986 3555666669
Q ss_pred hHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCcccc
Q psy2669 81 EGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMKFK 152 (166)
Q Consensus 81 ~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~~~ 152 (166)
.+..+|+||+++++++.++|++|++.++||.+.++++++||.++||||||++|+|||+|||.|||.++ .++
T Consensus 295 ~l~~~aell~v~~del~~aL~~Rtvaa~~e~v~k~hn~~qA~YaRDAlAKaiY~RlF~Wiv~rIn~~i-~~~ 365 (1001)
T KOG0164|consen 295 QLKYIAELLSVTGDELERALTSRTVAAGGEIVLKQHNVEQASYARDALAKAIYSRLFTWIVNRINRSI-EVK 365 (1001)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHhccchhhccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhe-ecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999975 443
No 6
>cd01381 MYSc_type_VII Myosin motor domain, type VII myosins. Myosins in this group have been associated with functions in sensory systems such as vision and hearing. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydr
Probab=100.00 E-value=1.3e-37 Score=279.58 Aligned_cols=150 Identities=27% Similarity=0.320 Sum_probs=139.4
Q ss_pred CCCCCCCCCccccccCC-CCCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCC--CCccccC
Q psy2669 1 MCMLTNDIYDYYNVSQG-KITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGR--EEQAEPD 77 (166)
Q Consensus 1 ~l~L~~~~~~y~yL~~~-~~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~--~~~~~v~ 77 (166)
+|+| .++++|+||+++ +..++++||+++|++++.||+.|||+++|+..||+|||||||||||+|.+.+. .+.+.+.
T Consensus 204 ~l~L-~~~~~y~yL~~~~~~~~~~~dD~~~f~~~~~al~~lG~~~~e~~~i~~ilaaILhLGni~F~~~~~~~~~~~~i~ 282 (671)
T cd01381 204 RLKL-GEASDYHYLAQGGCITCEGRDDAKDFADIRSAMKVLMFTDQEIWEIFKLLAAILHIGNLRFEATEVDNLAACEVD 282 (671)
T ss_pred HcCC-CChhhceeecCCCCccCCCccHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcceEEeeccCCCCCceeeC
Confidence 3677 558999999987 57889999999999999999999999999999999999999999999997642 3578899
Q ss_pred CchhHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCccc
Q psy2669 78 GTEEGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMKF 151 (166)
Q Consensus 78 ~~~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~~ 151 (166)
+.+.++.+|+||||++++|.++|+++++.++||.+.+|++++||..+||||||+||+|||+|||.+||.++..+
T Consensus 283 ~~~~l~~~a~LLgv~~~~L~~~lt~~~~~~~~e~i~~~~~~~qA~~~rdalak~lY~~lF~wiV~~IN~~l~~~ 356 (671)
T cd01381 283 DTPNLQRVAQLLGVPIQDLMDALTSRTIFTRGETVVTPLSREQAVDVRDAFVKGIYGRLFVWIVRKINAAIYKP 356 (671)
T ss_pred ChHHHHHHHHHhCCCHHHHhhhhceEEEEeCCceEEecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999986544
No 7
>cd01380 MYSc_type_V Myosin motor domain, type V myosins. Myosins V transport a variety of intracellular cargo processively along actin filaments, such as membraneous organelles and mRNA. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an act
Probab=100.00 E-value=1.6e-37 Score=280.02 Aligned_cols=149 Identities=23% Similarity=0.356 Sum_probs=136.3
Q ss_pred CCCCCCCCCccccccCC-CCCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCc
Q psy2669 1 MCMLTNDIYDYYNVSQG-KITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGT 79 (166)
Q Consensus 1 ~l~L~~~~~~y~yL~~~-~~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~ 79 (166)
+|+| .++++|+||++| +..++++||+++|+++++||+.|||+++|+..||+|||||||||||+|.+.+.+..+...+.
T Consensus 210 ~l~L-~~~~~y~yl~~~~~~~~~~~~d~~~f~~~~~al~~lg~s~~e~~~I~~iLaaILhLGni~F~~~~~~~~~~~~~~ 288 (691)
T cd01380 210 ELHL-GHADKFNYLNQGGAPTIEGVDDAEDFNATVQALTLLGISEEQQMDIFKLLAALLHLGNIEIEATRNDSSSISPKD 288 (691)
T ss_pred HhCC-CCHHHCccccCCCCccCCCCChHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccceeeeccCCccceecCCh
Confidence 3677 567899999997 47889999999999999999999999999999999999999999999998754433444567
Q ss_pred hhHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCcc
Q psy2669 80 EEGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMK 150 (166)
Q Consensus 80 ~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~ 150 (166)
+.++.+|+||||++++|.++|+++++.++||.+.+|++++||..+||+|||+||++||+|||.+||.++..
T Consensus 289 ~~l~~~a~LLgv~~~~L~~~l~~~~~~~~~e~i~~~~~~~qA~~~rdalak~lY~~LF~wiV~~iN~~l~~ 359 (691)
T cd01380 289 ENLQIACELLGVDASDLRKWLVKRQIVTRSEKIVKPLTKEQAIVARDALAKHIYSKLFDWIVDVINKSLNT 359 (691)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHhCEEEECCeeEEecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence 89999999999999999999999999999999999999999999999999999999999999999997654
No 8
>cd01384 MYSc_type_XI Myosin motor domain, plant-specific type XI myosin, involved in organelle transport. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new act
Probab=100.00 E-value=2.9e-37 Score=277.45 Aligned_cols=149 Identities=18% Similarity=0.322 Sum_probs=137.1
Q ss_pred CCCCCCCCCccccccCC-CCCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCC-
Q psy2669 1 MCMLTNDIYDYYNVSQG-KITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDG- 78 (166)
Q Consensus 1 ~l~L~~~~~~y~yL~~~-~~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~- 78 (166)
+|+| .++++|+||+++ +..++++||+++|+++++||+.|||+++|+..||+|||||||||||+|.+.+..+.+.+.+
T Consensus 209 ~l~L-~~~~~y~yL~~~~~~~~~~~~D~~~f~~~~~al~~lG~~~~e~~~I~~iLaaILhLGni~F~~~~~~~~~~~~~~ 287 (674)
T cd01384 209 KYKL-GDPKEFHYLNQSNCFELDGVDDAEEYLATRRAMDVVGISEEEQDAIFRVVAAILHLGNIEFAKGEEIDSSVLKDE 287 (674)
T ss_pred HcCC-CChHhCccccCCCCccccccchHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccceeeeccCCCCcccccCc
Confidence 4678 689999999997 5788999999999999999999999999999999999999999999999875445555544
Q ss_pred --chhHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCcc
Q psy2669 79 --TEEGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMK 150 (166)
Q Consensus 79 --~~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~ 150 (166)
.+.++.+|+||||++++|.++|+++++.+++|.+.+|+++++|..+||+|||+||++||+|||.+||.++..
T Consensus 288 ~~~~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~i~~~~~~~~a~~~rdalak~lY~~LF~wiV~~iN~~l~~ 361 (674)
T cd01384 288 KSEFHLKTAAELLMCDEKALEDALCKRVMVTPEEVITKPLDPDSAELSRDALAKTIYSRLFDWLVNKINSSIGQ 361 (674)
T ss_pred ccHHHHHHHHHHhCCCHHHHHHHhcccEEEeCCceEEecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 589999999999999999999999999999999999999999999999999999999999999999997643
No 9
>cd01378 MYSc_type_I Myosin motor domain, type I myosins. Myosin I generates movement at the leading edge in cell motility, and class I myosins have been implicated in phagocytosis and vesicle transport. Myosin I, an unconventional myosin, does not form dimers. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 picon
Probab=100.00 E-value=1.3e-36 Score=273.57 Aligned_cols=148 Identities=26% Similarity=0.430 Sum_probs=137.2
Q ss_pred CCCCCCCCCccccccCCC-CCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCc
Q psy2669 1 MCMLTNDIYDYYNVSQGK-ITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGT 79 (166)
Q Consensus 1 ~l~L~~~~~~y~yL~~~~-~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~ 79 (166)
+|+| .++++|+||++++ ..++++||+++|+++++||+.|||+++|+..||+|||||||||||+|...++ +.+.+.+.
T Consensus 207 ~l~L-~~~~~y~yL~~~~~~~~~~~~d~~~f~~~~~al~~lG~s~~e~~~i~~ilaaILhLGni~f~~~~~-~~~~~~~~ 284 (674)
T cd01378 207 ELGL-QKPEYYYYLNQSQCYTVDGIDDKKDFKETQNAMKVIGFSEDEQDEIFRIVAAILHLGNVQFAENGD-GAAVISDK 284 (674)
T ss_pred HhCC-CChhhCeeecCCCccCCCCccHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcceEEeccCC-CccccCCh
Confidence 3677 4569999999984 6899999999999999999999999999999999999999999999998643 44788899
Q ss_pred hhHHHHHhhhCCCHHHHHhhhccceeeeCC----eeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCcc
Q psy2669 80 EEGDRVSKLLGVDSQQLYTNLVKPRIKVGN----EFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMK 150 (166)
Q Consensus 80 ~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~----e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~ 150 (166)
+.++.+|+||||++++|.++|+++++.+++ |.+.+|++++||..+||+|||+||++||+|||.+||.++..
T Consensus 285 ~~l~~~a~LLgv~~~~L~~~l~~~~~~~~~~~~~e~i~~~~~~~~a~~~rdalak~lY~~lF~wiV~~IN~~l~~ 359 (674)
T cd01378 285 DVLDFAAYLLGVDPSELEKALTSRTIETGGGGRGEVYDVPLNVEQAAYTRDALAKAIYSRLFDWLVSRINKALQV 359 (674)
T ss_pred HHHHHHHHHcCCCHHHHHHHhcccEEEeCCCCCceeEEecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 999999999999999999999999999998 99999999999999999999999999999999999997644
No 10
>cd01387 MYSc_type_XV Myosin motor domain, type XV myosins. In vertebrates, myosin XV appears to be expressed in sensory tissue and play a role in hearing. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis caus
Probab=100.00 E-value=1.5e-36 Score=273.12 Aligned_cols=148 Identities=21% Similarity=0.320 Sum_probs=137.0
Q ss_pred CCCCCCCCccccccCCC-CCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCC--CCccccCC
Q psy2669 2 CMLTNDIYDYYNVSQGK-ITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGR--EEQAEPDG 78 (166)
Q Consensus 2 l~L~~~~~~y~yL~~~~-~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~--~~~~~v~~ 78 (166)
|+| .++++|+||++++ ..+++.+|+++|++++.||+.|||+++|+..||+|||||||||||+|...+. .+.+.+.+
T Consensus 206 ~~L-~~~~~y~yL~~~~~~~~~~~~d~~~f~~~~~al~~lg~~~~e~~~i~~iLaaILhLGni~F~~~~~~~~~~~~~~~ 284 (677)
T cd01387 206 FSL-QEAETYYYLNQGGNCEIAGKSDADDFRRLLAAMEVLGFSSEDQDSIFRILASILHLGNVYFEKRETDAQEVASVVS 284 (677)
T ss_pred hcC-CCHHhCchhcCCCcccCCCcCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCeEEeeccCCCCcccccCC
Confidence 667 5689999999984 6688999999999999999999999999999999999999999999987642 24578888
Q ss_pred chhHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCcc
Q psy2669 79 TEEGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMK 150 (166)
Q Consensus 79 ~~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~ 150 (166)
++.+..+|+||||++++|.++|+++++.+++|.+.+|+++++|..+||+|||+||+|||+|||.+||.++..
T Consensus 285 ~~~l~~~a~LLgv~~~~L~~~lt~~~~~~~~e~i~~~~~~~~a~~~rdalak~lY~~lF~wiV~~iN~~l~~ 356 (677)
T cd01387 285 AREIQAVAELLQISPEGLQKAITFKVTETRREKIFTPLTVESAVDARDAIAKVLYALLFNWLITRVNALVSP 356 (677)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhccCeEEeCCceEeccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 999999999999999999999999999999999999999999999999999999999999999999997643
No 11
>cd01385 MYSc_type_IX Myosin motor domain, type IX myosins. Myosin IX is a processive single-headed motor, which might play a role in signalling. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the hea
Probab=100.00 E-value=3.7e-36 Score=271.08 Aligned_cols=148 Identities=22% Similarity=0.332 Sum_probs=135.6
Q ss_pred CCCCCCCCccccccCCCC-CCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecC---CCCccccC
Q psy2669 2 CMLTNDIYDYYNVSQGKI-TIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRG---REEQAEPD 77 (166)
Q Consensus 2 l~L~~~~~~y~yL~~~~~-~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~---~~~~~~v~ 77 (166)
++|. ++.+|+||++++. ..+++||+++|+++++||+.+||+++++..||+|||||||||||+|.+.. .++.+.+.
T Consensus 216 ~~l~-~~~~y~yL~~~~~~~~~~~dd~~~f~~~~~al~~lG~~~~~~~~i~~iLaaILhLGni~F~~~~~~~~~~~~~~~ 294 (692)
T cd01385 216 EFLL-KQPDYFYLNQHNLKIEDGEDEKHEFERLKQAMEMVGFLAATQKQIFAVLSAVLLLGNVTYKKRATYHRDESLEVG 294 (692)
T ss_pred hcCC-ChhcCCeeCCCCCccCCCCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccCceeeecccCCCCCceecC
Confidence 4563 4569999999864 45799999999999999999999999999999999999999999998753 24667889
Q ss_pred CchhHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCcc
Q psy2669 78 GTEEGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMK 150 (166)
Q Consensus 78 ~~~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~ 150 (166)
+++.+..+|+||||++++|.++|+++++.++||.+++|++++||..+||+|||+||++||+|||.+||.++..
T Consensus 295 ~~~~l~~~a~LLgv~~~~L~~~l~~~~~~~~~e~i~~~~~~~qa~~~rdalak~lY~~LF~wiV~~IN~~l~~ 367 (692)
T cd01385 295 NPEVVDLLSQLLKVKRETLMEALTKKRTVTVNETLILPYSLSEAITARDAMAKCLYSALFDWIVLRINHALLN 367 (692)
T ss_pred CHHHHHHHHHHhCCCHHHHHHHhccCeEEeCCCeEEecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999998654
No 12
>cd00124 MYSc Myosin motor domain. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the fila
Probab=100.00 E-value=5.6e-36 Score=270.00 Aligned_cols=149 Identities=28% Similarity=0.404 Sum_probs=137.9
Q ss_pred CCCCCCCCCccccccCCC-CCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCC--ccccC
Q psy2669 1 MCMLTNDIYDYYNVSQGK-ITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREE--QAEPD 77 (166)
Q Consensus 1 ~l~L~~~~~~y~yL~~~~-~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~--~~~v~ 77 (166)
+|+| .++++|+||++++ ..+++++|+++|++++.||+.|||+++|+..||+|||||||||||+|.+.+.++ .+.+.
T Consensus 205 ~l~L-~~~~~y~yL~~~~~~~~~~~~d~~~f~~~~~al~~lg~~~~e~~~i~~iLaaILhLGni~f~~~~~~~~~~~~~~ 283 (679)
T cd00124 205 KLGL-KRPESYRYLNQGGCNDVDGIDDAEEFEELKEALKSLGFSEEEIESIFRILAAILHLGNIEFKSVGGEGQEAAEVK 283 (679)
T ss_pred hcCC-CCcccCeeeCCCCcccCCCCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCeeEEecCCCCcceeecC
Confidence 4678 5679999999985 556999999999999999999999999999999999999999999999875443 37788
Q ss_pred CchhHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCcc
Q psy2669 78 GTEEGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMK 150 (166)
Q Consensus 78 ~~~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~ 150 (166)
+.+.++.+|+||||+.++|.++|+++++.++|+.+.+|+++++|...||+|||+||++||+|||.+||.++..
T Consensus 284 ~~~~l~~~a~LLgv~~~~L~~~l~~~~~~~~~~~~~~~~~~~~a~~~rdalak~lY~~lF~wiV~~iN~~l~~ 356 (679)
T cd00124 284 NTEVLSKAAELLGLDPEELEEALTYKVTKVGGEVITIPLTKEEAVDSRDSLAKALYSRLFDWIVSRINSSLKP 356 (679)
T ss_pred CHHHHHHHHHHhCCCHHHHHHHhhccEEEeCCceEEecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999997643
No 13
>PF00063 Myosin_head: Myosin head (motor domain); InterPro: IPR001609 Muscle contraction is caused by sliding between the thick and thin filaments of the myofibril. Myosin is a major component of thick filaments and exists as a hexamer of 2 heavy chains [], 2 alkali light chains, and 2 regulatory light chains. The heavy chain can be subdivided into the N-terminal globular head and the C-terminal coiled-coil rod-like tail, although some forms have a globular region in their C-terminal. There are many cell-specific isoforms of myosin heavy chains, coded for by a multi-gene family []. Myosin interacts with actin to convert chemical energy, in the form of ATP, to mechanical energy []. The 3-D structure of the head portion of myosin has been determined [] and a model for actin-myosin complex has been constructed []. The globular head is well conserved, some highly-conserved regions possibly relating to functional and structural domains []. The rod-like tail starts with an invariant proline residue, and contains many repeats of a 28 residue region, interrupted at 4 regularly-spaced points known as skip residues. Although the sequence of the tail is not well conserved, the chemical character is, hydrophobic, charged and skip residues occuring in a highly ordered and repeated fashion [].; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 1LKX_A 2V26_A 2BKI_A 3L9I_A 2BKH_A 2X51_A 2VB6_A 2VAS_A 1OE9_A 1W8J_A ....
Probab=100.00 E-value=5.2e-36 Score=270.76 Aligned_cols=148 Identities=34% Similarity=0.507 Sum_probs=133.8
Q ss_pred CCCCCCCCccccccCC-CCCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCch
Q psy2669 2 CMLTNDIYDYYNVSQG-KITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTE 80 (166)
Q Consensus 2 l~L~~~~~~y~yL~~~-~~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~ 80 (166)
|+| .++++|+||+++ +..+++.+|.++|+++++||+.|||+++|+..||+|||||||||||+|.+...++.+.+.+.+
T Consensus 209 l~L-~~~~~~~yL~~~~~~~~~~~~d~~~f~~l~~al~~lg~~~~e~~~I~~iLaaILhLGni~F~~~~~~~~~~~~~~~ 287 (689)
T PF00063_consen 209 LRL-NDASDYRYLNQSGCSTIPGIDDAEEFQELKDALKTLGFSDEEIDDIFRILAAILHLGNIEFVEDESDESAEVENSE 287 (689)
T ss_dssp TT--S-GGGSTTCCTTSSSSBTTCTHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTTSSEEEETTSSSEEESTSH
T ss_pred ccc-cccccccceecccccccCCccCHHHhhhhhhhhccccCchhHHHHHHHHHHHHhhhccccccccccccceeechHH
Confidence 677 489999999996 578899999999999999999999999999999999999999999999998766788999999
Q ss_pred hHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCcc
Q psy2669 81 EGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMK 150 (166)
Q Consensus 81 ~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~ 150 (166)
.++.+|+||||++++|.++|+++++.+++|.+.+++++++|..+||+|||+||++||+|||.+||.++..
T Consensus 288 ~l~~~a~LLgv~~~~L~~~l~~~~~~~~~e~~~~~~~~~~a~~~rdalak~LY~~LF~wIV~~iN~~L~~ 357 (689)
T PF00063_consen 288 ELQKAAELLGVDSEELEKALTTRTIKVGGETVTKPLSVEQASDARDALAKALYSRLFDWIVERINSALSP 357 (689)
T ss_dssp HHHHHHHHTTS-HHHHHHHHHSEEEESTTSEEEEE-BHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--
T ss_pred HHHHhhhhcCCCHHHHHHHHhhccccccccccccccchhhhhhhhhhhhhhhhhHHHHHHHHhhhhcccc
Confidence 9999999999999999999999999999999999999999999999999999999999999999997533
No 14
>cd01379 MYSc_type_III Myosin motor domain, type III myosins. Myosin III has been shown to play a role in the vision process in insects and in hearing in mammals. Myosin III, an unconventional myosin, does not form dimers. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the
Probab=100.00 E-value=1.1e-35 Score=266.55 Aligned_cols=149 Identities=15% Similarity=0.237 Sum_probs=134.4
Q ss_pred CCCCCCCCccccccCCC-CCCCCCC----cHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCC---CCc
Q psy2669 2 CMLTNDIYDYYNVSQGK-ITIPGMD----DGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGR---EEQ 73 (166)
Q Consensus 2 l~L~~~~~~y~yL~~~~-~~~~~~d----D~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~---~~~ 73 (166)
|+| .+++.|+||++++ ..+++++ |+++|+++++||+.|||+++|+..||+|||||||||||+|.+.+. .+.
T Consensus 207 ~~L-~~~~~~~yL~~~~~~~~~~~~~~~~~~~~f~~~~~al~~lg~~~~e~~~I~~iLaaILhLGNi~F~~~~~~~~~~~ 285 (653)
T cd01379 207 YKL-PESKTPRYLQNEATRVVQDITSNKFYKDQFEQIEQCFRVIGFTDEEVGSVYRILAAILNLGDIEFGSVASEHQTDK 285 (653)
T ss_pred cCC-CCccccCccCCCCccccCCCccchhHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcceEEEeccccCCCcc
Confidence 567 4678999999885 4566664 478999999999999999999999999999999999999987642 246
Q ss_pred cccCCchhHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCccc
Q psy2669 74 AEPDGTEEGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMKF 151 (166)
Q Consensus 74 ~~v~~~~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~~ 151 (166)
+.+.+.+.++.+|+||||+.++|.++|+++++.++|+.+.+|++++||..+||+|||+||+|||+|||.+||.++...
T Consensus 286 ~~i~~~~~l~~~A~LLgv~~~~L~~~L~~~~~~~~ge~i~~~~~~~qA~~~rdalak~lY~~LF~wiV~~IN~~l~~~ 363 (653)
T cd01379 286 SRVSNVAALENAASLLCIRSDELQEALTSHCVVTRGETIVRHNTVEKATDARDAMAKALYGRLFSWIVNRINSLLKHD 363 (653)
T ss_pred cccCCHHHHHHHHHHhCCCHHHHHHHhcccEEEeCCceeeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 788899999999999999999999999999999999999999999999999999999999999999999999976543
No 15
>smart00242 MYSc Myosin. Large ATPases. ATPase; molecular motor. Muscle contraction consists of a cyclical interaction between myosin and actin. The core of the myosin structure is similar in fold to that of kinesin.
Probab=100.00 E-value=1.1e-35 Score=267.96 Aligned_cols=149 Identities=30% Similarity=0.463 Sum_probs=137.3
Q ss_pred CCCCCCCCCccccccCC-CCCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCc-cccCC
Q psy2669 1 MCMLTNDIYDYYNVSQG-KITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQ-AEPDG 78 (166)
Q Consensus 1 ~l~L~~~~~~y~yL~~~-~~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~-~~v~~ 78 (166)
+|+| .++++|+||+++ +..+++++|+++|++++.||+.|||+++|+..||+|||||||||||+|.+.+.++. +.+.+
T Consensus 213 ~l~L-~~~~~y~yL~~~~~~~~~~~~d~~~f~~~~~al~~lG~~~~e~~~I~~iLaaILhLGni~F~~~~~~~~~~~~~~ 291 (677)
T smart00242 213 ELGL-KSPEDYRYLNQGGCLSVDGIDDAEEFKETLNAMRVLGFSEEEQESIFKILAAILHLGNIEFEEGRNDNAASTVKD 291 (677)
T ss_pred hcCC-CChhhCceeCCCCCccCCCCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcceeEEecCCCCcccccCC
Confidence 3678 458999999998 67889999999999999999999999999999999999999999999998754332 34788
Q ss_pred chhHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCcc
Q psy2669 79 TEEGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMK 150 (166)
Q Consensus 79 ~~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~ 150 (166)
.+.++.+|+||||+.++|.++|+++++.++||.+.+++++++|...||+|||+||++||+|||.+||.++..
T Consensus 292 ~~~l~~~a~LLgv~~~~L~~~l~~~~~~~~~e~~~~~~~~~~a~~~rd~lak~lY~~lF~wiV~~iN~~l~~ 363 (677)
T smart00242 292 KEELENAAELLGVDPEELEKALTKRKIKTGGEVITKPLNVEQALDARDALAKALYSRLFDWLVKRINKSLSF 363 (677)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhcccEEEeCCceEEecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 999999999999999999999999999999999999999999999999999999999999999999997643
No 16
>KOG0162|consensus
Probab=100.00 E-value=1.2e-35 Score=261.18 Aligned_cols=148 Identities=20% Similarity=0.324 Sum_probs=138.0
Q ss_pred CCCCCCCCccccccCC-CCCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCch
Q psy2669 2 CMLTNDIYDYYNVSQG-KITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTE 80 (166)
Q Consensus 2 l~L~~~~~~y~yL~~~-~~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~ 80 (166)
||+ ..|+.|.||+.+ |+.++++||.++|++|+.||+++|+.++||+.||++||+|||||||.|.+. +..+.|.+.+
T Consensus 226 ~Gi-~~pe~Y~Y~~~sg~~s~D~idd~kdfq~Tl~AM~vIGi~~~eQ~~v~rmva~IL~lGNIsF~Ee--~~~a~V~~~~ 302 (1106)
T KOG0162|consen 226 FGI-QEPEYYVYLNASGCYSVDDIDDRKDFQETLHAMKVIGINQEEQDEVLRMVAGILHLGNISFIEE--GNYAAVSDKS 302 (1106)
T ss_pred hCc-CCchheeeeccccceeccccchHHHHHHHHHHheeccCChHHHHHHHHHHHHHHhccceeEEee--CCcceeccch
Confidence 566 789999999985 789999999999999999999999999999999999999999999999984 5678999999
Q ss_pred hHHHHHhhhCCCHHHHHhhhccceeee----CCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCcccc
Q psy2669 81 EGDRVSKLLGVDSQQLYTNLVKPRIKV----GNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMKFK 152 (166)
Q Consensus 81 ~l~~~a~LLgv~~~~L~~~L~~~~~~~----~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~~~ 152 (166)
.++..|.||||+...|.+.|+.|.+.+ +.|++..|++++||...||||||+||.|||+|||+|||.+.-.|+
T Consensus 303 ~~~f~ayLlgi~s~~l~~~Lt~R~M~s~~G~kr~~~~v~LNv~QA~~~RDAlakaiy~~lFD~lV~rvNkam~~~~ 378 (1106)
T KOG0162|consen 303 VLEFPAYLLGIDSARLEEKLTSRIMESKWGGKREVIHVPLNVEQASYTRDALAKAIYARLFDWLVERVNKAMQAFK 378 (1106)
T ss_pred HHHhHHHHhcCCHHHHHHHHHHHHHhhcccccceeEEecccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 999999999999999999999998875 358999999999999999999999999999999999999866554
No 17
>cd01382 MYSc_type_VI Myosin motor domain, type VI myosins. Myosin VI is a monomeric myosin, which moves towards the minus-end of actin filaments, in contrast to most other myosins. It has been implicated in endocytosis, secretion, and cell migration. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the minus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of
Probab=100.00 E-value=4e-35 Score=265.19 Aligned_cols=147 Identities=19% Similarity=0.284 Sum_probs=131.7
Q ss_pred CCCCCCCCCccccccCCCC---------------------------CCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHH
Q psy2669 1 MCMLTNDIYDYYNVSQGKI---------------------------TIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKI 53 (166)
Q Consensus 1 ~l~L~~~~~~y~yL~~~~~---------------------------~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~i 53 (166)
+|+| .++++|+||++|+. .++++||+++|++++.||+.|||+++|+..||+|
T Consensus 209 ~l~L-~~~~~y~yL~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~dD~~~f~~~~~Al~~lg~s~~e~~~i~~i 287 (717)
T cd01382 209 KLHL-SSPDDFRYLNRGCTRYFANKETDKQILQNRKSPEHLKKGALKDPLLDDYGDFQRMCVALKKIGLDDTEKLDLFRV 287 (717)
T ss_pred HhcC-CChhhCeeecCCcccccccccccccccccccccccccccccCCCCCcHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3677 57899999997642 3568999999999999999999999999999999
Q ss_pred HHHHHhhcCceEeecCCC-Ccccc--CCchhHHHHHhhhCCCHHHHHhhhccceee-----eCCeeEEecCChhHHHHhh
Q psy2669 54 TASVMHMGGMKFKQRGRE-EQAEP--DGTEEGDRVSKLLGVDSQQLYTNLVKPRIK-----VGNEFVTQGRNVNQQAFDI 125 (166)
Q Consensus 54 laaILhLGNi~F~~~~~~-~~~~v--~~~~~l~~~a~LLgv~~~~L~~~L~~~~~~-----~~~e~~~~~~~~~~A~~~r 125 (166)
||||||||||+|.+.+.. +.|.+ .+.+.++.+|+||||++++|.++|++|++. ++|+.+.+|++++||..+|
T Consensus 288 LaaILhLGni~F~~~~~~~~~~~~~~~~~~~l~~~a~LLgv~~~~L~~~l~~r~~~~~~g~~~~~~i~~~l~~~qA~~~r 367 (717)
T cd01382 288 VAGVLHLGNIDFEEAGSTSGGCNVKNQSEQSLEYCAELLGLDQDDLRVSLTTRVMLTTAGGAKGTVIKVPLKVEQANNAR 367 (717)
T ss_pred HHHHHhcCceeEeccCCCCCcceecCCCHHHHHHHHHHcCCCHHHHHHHHhheEEecccccCCCceEEecCCHHHHHHHH
Confidence 999999999999975432 34444 457899999999999999999999999988 7889999999999999999
Q ss_pred hhhhHHHHHHHHHHHHHHHhccC
Q psy2669 126 LGFTKEEKENVYKITASVMHMGG 148 (166)
Q Consensus 126 dalaK~lY~~LF~wiV~~IN~~~ 148 (166)
|+|||+||++||+|||.+||.++
T Consensus 368 dalak~lY~~LF~wiV~~IN~~l 390 (717)
T cd01382 368 DALAKAVYSHLFDHVVSRVNQCF 390 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999975
No 18
>cd01386 MYSc_type_XVIII Myosin motor domain, type XVIII myosins. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the
Probab=99.97 E-value=1.3e-31 Score=243.44 Aligned_cols=147 Identities=14% Similarity=0.164 Sum_probs=122.8
Q ss_pred CCCCCCCCccccccCC-CCCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCch
Q psy2669 2 CMLTNDIYDYYNVSQG-KITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTE 80 (166)
Q Consensus 2 l~L~~~~~~y~yL~~~-~~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~ 80 (166)
|+|...++.|.|...+ +...++++|+++|++|++||++|||+++|+..||+|||||||||||+|... .+.+.+.+.+
T Consensus 207 l~L~~~~~~~~~~~~~~~~~~d~~~D~~~f~~~~~Al~~lGfs~~e~~~If~iLaaILhLGNi~f~~~--~~~~~~~~~~ 284 (767)
T cd01386 207 LHLEQMAESSSFGMGGLSKPEDKQKAAIDFSRLQQAMEVLGISEGEQRAIWRVLAAIYHLGAAGATKV--AGRKQFARPE 284 (767)
T ss_pred hcCCCccccchhhcCCCCCCcCcccHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccCceeeec--CCccccCCHH
Confidence 5675545444443222 345678999999999999999999999999999999999999999999873 2456788889
Q ss_pred hHHHHHhhhCCCHHHHHhhhccceeeeCCee-------------EEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhcc
Q psy2669 81 EGDRVSKLLGVDSQQLYTNLVKPRIKVGNEF-------------VTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMG 147 (166)
Q Consensus 81 ~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~-------------~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~ 147 (166)
.++.+|+||||+.++|.++|+++++..+++. +..+.++.+|.++||||||+||+|||+|||.+||.+
T Consensus 285 ~~~~vA~LLgv~~~~L~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~rdalaK~lY~rLF~wiV~~IN~~ 364 (767)
T cd01386 285 WAQKAAELLGCPLEELSSATFKHTLRGGINQMTTGPQRPGLSDTETSSGLKMTAVECLEGMASGLYSELFAAVVSLINRS 364 (767)
T ss_pred HHHHHHHHhCCCHHHHHHHhcccEEeecceeeeccccccccccccccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999887766432 234567889999999999999999999999999997
Q ss_pred Ccc
Q psy2669 148 GMK 150 (166)
Q Consensus 148 ~~~ 150 (166)
+..
T Consensus 365 l~~ 367 (767)
T cd01386 365 ISS 367 (767)
T ss_pred hCC
Confidence 643
No 19
>KOG0163|consensus
Probab=99.97 E-value=3.8e-32 Score=239.72 Aligned_cols=152 Identities=18% Similarity=0.327 Sum_probs=133.8
Q ss_pred CCCCCCCCCccccccCCCC----------CC-----------------CCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHH
Q psy2669 1 MCMLTNDIYDYYNVSQGKI----------TI-----------------PGMDDGEEFQLTDQAFDILGFTKEEKENVYKI 53 (166)
Q Consensus 1 ~l~L~~~~~~y~yL~~~~~----------~~-----------------~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~i 53 (166)
+|.| ..|++|+||+.||. .+ +-+||..+|+.+..||..+|++++|...||++
T Consensus 262 kL~L-~~pd~f~YL~rG~t~yFan~~t~~ki~~nr~S~~~~~~~~~kD~iidD~~dF~rl~~Al~~~Glsd~Ekl~i~s~ 340 (1259)
T KOG0163|consen 262 KLSL-GKPDDFRYLKRGCTQYFANAKTEQKIPGNRKSKNHQQKGSLKDPIIDDYQDFHRLEKALKLLGLSDTEKLFIWST 340 (1259)
T ss_pred Hhcc-CCchhhhHHhcchhhhccCcchhhcCcccccCccccccCcccCcccccHHHHHHHHHHHHhcCCChHHHHHHHHH
Confidence 4667 77999999998762 11 23789999999999999999999999999999
Q ss_pred HHHHHhhcCceEeecCCC--CccccCC--chhHHHHHhhhCCCHHHHHhhhccceeee-----CCeeEEecCChhHHHHh
Q psy2669 54 TASVMHMGGMKFKQRGRE--EQAEPDG--TEEGDRVSKLLGVDSQQLYTNLVKPRIKV-----GNEFVTQGRNVNQQAFD 124 (166)
Q Consensus 54 laaILhLGNi~F~~~~~~--~~~~v~~--~~~l~~~a~LLgv~~~~L~~~L~~~~~~~-----~~e~~~~~~~~~~A~~~ 124 (166)
+|||||||||+|.+...+ .+|.|.+ .++|..+|+|||+++.+|.-.||.|.+.+ .|..|.+|+.+.+|...
T Consensus 341 vA~vLHLGNieFEE~~ddsrGGC~v~n~seqsL~~~a~LLGld~~elr~~L~aRvMqtt~GG~kGTvIrVPLK~~eA~n~ 420 (1259)
T KOG0163|consen 341 VAAVLHLGNIEFEEIPDDSRGGCQVSNGSEQSLTIAAELLGLDQTELRTGLCARVMQTTKGGFKGTVIRVPLKIHEASNA 420 (1259)
T ss_pred HHHHHHccccchhcccCcCCCceecccCchhhHHHHHHHhCCCHHHHHHHHHHHHHHhccCCccceEEEeeccHHhhcch
Confidence 999999999999987543 5788765 68899999999999999999999998764 36789999999999999
Q ss_pred hhhhhHHHHHHHHHHHHHHHhccCcccccC
Q psy2669 125 ILGFTKEEKENVYKITASVMHMGGMKFKQR 154 (166)
Q Consensus 125 rdalaK~lY~~LF~wiV~~IN~~~~~~~~~ 154 (166)
||||||++|++||+|||.+||.+ ++|..+
T Consensus 421 RDALaKaiYSkLFD~lV~~iNqs-iPFe~S 449 (1259)
T KOG0163|consen 421 RDALAKAIYSKLFDWLVGRINQS-IPFEKS 449 (1259)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcc-cccccc
Confidence 99999999999999999999997 577554
No 20
>KOG0161|consensus
Probab=99.96 E-value=6.8e-30 Score=245.15 Aligned_cols=149 Identities=41% Similarity=0.700 Sum_probs=143.3
Q ss_pred CCCCCCCCccccccCCCCCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCchh
Q psy2669 2 CMLTNDIYDYYNVSQGKITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTEE 81 (166)
Q Consensus 2 l~L~~~~~~y~yL~~~~~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~~ 81 (166)
|.|...+.+|.|+.++...++|+||+++|+.+..||++|||+++|+.+||+|+|||||||||.|....+.+.+.+.+...
T Consensus 294 l~L~~~~~~Y~f~~~~~~~i~g~dd~eef~~t~~a~~ilgfs~~E~~~~~~i~sailhlGn~~f~~~~~~~qa~~~~~~~ 373 (1930)
T KOG0161|consen 294 LLLSDNVKDYKFLSNGESTIPGVDDAEEFQETDEAMDILGFSEEEKISIFRIVSAILHLGNIKFKQEPREEQAEFDNTEV 373 (1930)
T ss_pred HhhcccchhhhhhccccCCCCCcchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhhhccccccccCCCCchH
Confidence 66878899999999987899999999999999999999999999999999999999999999999987778999999999
Q ss_pred HHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCcc
Q psy2669 82 GDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMK 150 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~ 150 (166)
...+|+|||++..+|.++++++++++|++.+.+..+.+|+..+..+|||++|+|+|.|+|.|||.+...
T Consensus 374 a~ka~~llg~~~~~~~~al~~priKvg~e~v~k~q~~~q~~~~v~alAk~lYerlF~wlV~riN~sld~ 442 (1930)
T KOG0161|consen 374 ADKACHLLGINVEEFLKALLRPRIKVGREWVSKAQNVEQVLFAVEALAKALYERLFGWLVKRINKSLDS 442 (1930)
T ss_pred HHHHHHHcCCCHHHHHHHhcccceeccchhhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 999999999999999999999999999999999999999999999999999999999999999997644
No 21
>KOG0160|consensus
Probab=99.96 E-value=1.2e-28 Score=223.12 Aligned_cols=148 Identities=19% Similarity=0.275 Sum_probs=134.7
Q ss_pred CCCCCCCCCccccccCC-CCCCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCc
Q psy2669 1 MCMLTNDIYDYYNVSQG-KITIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGT 79 (166)
Q Consensus 1 ~l~L~~~~~~y~yL~~~-~~~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~ 79 (166)
+|.| .++..|.|++|+ |..+++++|+.+|..++.||..+|++.++|..||++|+||||||||+|.....+ .+..+..
T Consensus 213 ~l~L-~~~~~f~yl~q~~~~~i~~v~d~~e~~~t~~A~~~vgi~~~~q~~if~lla~ilhlGni~f~~~~~~-~~~~~~~ 290 (862)
T KOG0160|consen 213 KLKL-GTLRRFSYLNQSACVLISGVSDAEEFLSTTEAMLFVGISESHQELIFRLLAAILHLGNIQFSSGVEE-TSSSPVD 290 (862)
T ss_pred ccCc-CccccceecccccchhhcccccHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHhccCceEeeccccc-ccccccc
Confidence 3556 478999999998 588999999999999999999999999999999999999999999999987544 3333333
Q ss_pred hhHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCcc
Q psy2669 80 EEGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMK 150 (166)
Q Consensus 80 ~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~ 150 (166)
+.+..+|.|+|++.+.|.++|+.|.+.++++.+.++++..+|...||++||.||++||+|+|.+||.++..
T Consensus 291 ~~~~~~a~Llg~~~~~l~~~L~~r~i~~~~e~i~k~l~~~qa~~~rD~lak~iys~LFdwlV~~in~sL~~ 361 (862)
T KOG0160|consen 291 DHLWTAAELLGCDEEALEQWLSKRKILTARESIVKPLTLSQAVKRRDALAKQLYSLLFDWLVAKINGSLGA 361 (862)
T ss_pred hHHHHHHHHhCCCHHHHHHHHHHHHhhcccceeecccCHHHHHHhhhhhHHHHHHHHHHHHHHHhhccccc
Confidence 48999999999999999999999999999999999999999999999999999999999999999998654
No 22
>KOG4229|consensus
Probab=99.89 E-value=9.8e-24 Score=195.22 Aligned_cols=148 Identities=20% Similarity=0.252 Sum_probs=136.9
Q ss_pred CCCCccccccCCC-CCC-CCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCC--CCccccCCchh
Q psy2669 6 NDIYDYYNVSQGK-ITI-PGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGR--EEQAEPDGTEE 81 (166)
Q Consensus 6 ~~~~~y~yL~~~~-~~~-~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~--~~~~~v~~~~~ 81 (166)
..+++|.||+++. ..+ ++.++.++|..+..+|..+||+.+++..||++++||||+|||+|..... .+.+.+.+...
T Consensus 271 ~~~e~y~yL~~~~~~~~~d~~~~~~~~~~l~~~m~v~~f~~~~~~si~~~la~il~~gni~~~~~~~~~~d~~~v~~~~~ 350 (1062)
T KOG4229|consen 271 GEAENYEYLEQGALFTISDGEDDVAQFIRLEAAMSVVGFTDKVLGSIFKSLAAILHIGNISYIKFALDQQDSAEVENEEA 350 (1062)
T ss_pred cCCCCHHHhhccccccccchHHHHHhHHHHHHHHHHhccchhHHHHHHHhcccceeecceeHHhhhcccccchhcccchH
Confidence 4588999999984 667 8999999999999999999999999999999999999999999976543 36788999999
Q ss_pred HHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHHHHHhccCccccc
Q psy2669 82 GDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITASVMHMGGMKFKQ 153 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV~~IN~~~~~~~~ 153 (166)
+..+|.||.+++..|.++++.++..++||.+..+++.++|.+.||++||.+|++||.|||.|||..+.+...
T Consensus 351 v~~vA~lL~~~~~~l~~alt~~~~~~~ge~~~~~l~~~~A~d~rda~ak~ly~~lf~~iv~rIn~~~~~~~~ 422 (1062)
T KOG4229|consen 351 VERVACLLLIKEKLLQEALTARVNVTRGELLLAPLLVERAVDVRDAMAKTLYGRLFDWIVLRINAALSPESD 422 (1062)
T ss_pred HHHHHHHhhcCHHHhhhhhcccceeeehhhhhhhhhHHHhccCchHHHHHHHHHHHHHHHhhHHhccCcccc
Confidence 999999999999999999999999999999999999999999999999999999999999999997655443
No 23
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=77.65 E-value=6.4 Score=23.34 Aligned_cols=25 Identities=20% Similarity=0.250 Sum_probs=18.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2669 30 FQLTDQAFDILGFTKEEKENVYKIT 54 (166)
Q Consensus 30 f~~~~~al~~lg~~~~e~~~i~~il 54 (166)
..++..||..|||++.|...+.+-+
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~ 27 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKL 27 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 5788999999999997776554443
No 24
>COG4056 McrC Methyl coenzyme M reductase, subunit C [Coenzyme metabolism]
Probab=61.04 E-value=1.3 Score=33.63 Aligned_cols=29 Identities=28% Similarity=0.508 Sum_probs=25.3
Q ss_pred HHHHcCCCHHHHHHHHHHHHHHHhhcCce
Q psy2669 36 AFDILGFTKEEKENVYKITASVMHMGGMK 64 (166)
Q Consensus 36 al~~lg~~~~e~~~i~~ilaaILhLGNi~ 64 (166)
.=.++|++++|...|-+==.++.||||+.
T Consensus 87 ~g~tfgl~P~Eveqi~rHkl~ViHlGnvk 115 (204)
T COG4056 87 RGSTFGLSPEEVEQINRHKLAVIHLGNVK 115 (204)
T ss_pred cCCccccCHHHHHHhhhceEEEEEecchH
Confidence 34577999999999999888999999986
No 25
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=60.14 E-value=31 Score=20.99 Aligned_cols=57 Identities=12% Similarity=0.255 Sum_probs=31.8
Q ss_pred HHHHHHHHcCCCHHHHHHHHHH-HHHHHhhcCceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHh
Q psy2669 32 LTDQAFDILGFTKEEKENVYKI-TASVMHMGGMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYT 98 (166)
Q Consensus 32 ~~~~al~~lg~~~~e~~~i~~i-laaILhLGNi~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~ 98 (166)
.+++..+..|++..+......+ -+.|-++ + ..-..++...+..+|..|||+.+.|..
T Consensus 3 ~lk~~r~~~~lt~~~~a~~~~i~~~~i~~~---e-------~g~~~~~~~~l~~i~~~~~v~~~~l~~ 60 (64)
T PF12844_consen 3 RLKELREEKGLTQKDLAEKLGISRSTISKI---E-------NGKRKPSVSTLKKIAEALGVSLDELFD 60 (64)
T ss_dssp HHHHHHHHCT--HHHHHHHHTS-HHHHHHH---H-------TTSS--BHHHHHHHHHHHTS-HHHHCC
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHH---H-------CCCcCCCHHHHHHHHHHhCCCHHHHhc
Confidence 4567777778887666654444 2222222 0 111134467889999999999987753
No 26
>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=59.75 E-value=18 Score=22.67 Aligned_cols=43 Identities=19% Similarity=0.546 Sum_probs=30.1
Q ss_pred HHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHhhh
Q psy2669 37 FDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYTNL 100 (166)
Q Consensus 37 l~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~~L 100 (166)
|+.+|+++.|.. |+.++|.-|... ...+|+-+|++.....+.|
T Consensus 1 L~~~gLs~~E~~----vy~~Ll~~~~~t-----------------~~eIa~~l~i~~~~v~~~L 43 (68)
T PF01978_consen 1 LEVLGLSENEAK----VYLALLKNGPAT-----------------AEEIAEELGISRSTVYRAL 43 (68)
T ss_dssp HHHHCHHHHHHH----HHHHHHHHCHEE-----------------HHHHHHHHTSSHHHHHHHH
T ss_pred CCcCCcCHHHHH----HHHHHHHcCCCC-----------------HHHHHHHHCcCHHHHHHHH
Confidence 457899988755 555555555433 5689999999988776665
No 27
>COG2355 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]
Probab=57.62 E-value=21 Score=30.05 Aligned_cols=32 Identities=22% Similarity=0.286 Sum_probs=28.8
Q ss_pred CCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHH
Q psy2669 21 IPGMDDGEEFQLTDQAFDILGFTKEEKENVYK 52 (166)
Q Consensus 21 ~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ 52 (166)
.+|..|...|+.+..+|..-|++++++..|+.
T Consensus 269 p~gled~~~l~~l~~~L~~~G~~e~~i~~i~~ 300 (313)
T COG2355 269 PDGLEDVGKLPNLTAALIERGYSEEEIEKIAG 300 (313)
T ss_pred chhhcChhHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 46889999999999999999999999988753
No 28
>PHA02591 hypothetical protein; Provisional
Probab=57.08 E-value=8.8 Score=25.72 Aligned_cols=44 Identities=16% Similarity=0.314 Sum_probs=28.7
Q ss_pred HHhhcCceEeecCCCCcccc-----CCchhHHHHHhhhCCCHHHHHhhh
Q psy2669 57 VMHMGGMKFKQRGREEQAEP-----DGTEEGDRVSKLLGVDSQQLYTNL 100 (166)
Q Consensus 57 ILhLGNi~F~~~~~~~~~~v-----~~~~~l~~~a~LLgv~~~~L~~~L 100 (166)
+...|+..+--.+.++...+ .-.-..+.+|.+||++.+...+.+
T Consensus 32 ~vqv~~~ryfi~~~dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL 80 (83)
T PHA02591 32 VVQVGQTRYFVESEDDLISVTHELARKGFTVEKIASLLGVSVRKVRRYL 80 (83)
T ss_pred hheeCCEEEEEeccchHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 34679988443333333222 223567899999999999887765
No 29
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=54.90 E-value=31 Score=22.22 Aligned_cols=39 Identities=23% Similarity=0.308 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEee
Q psy2669 28 EEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQ 67 (166)
Q Consensus 28 ~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~ 67 (166)
..+..-.++|+.+||++..+..+.+=|--+. =||-.|-+
T Consensus 9 ~R~daA~dam~~lG~~~~~v~~vl~~LL~lY-~~nW~lIE 47 (65)
T PF10440_consen 9 ERIDAALDAMRQLGFSKKQVRPVLKNLLKLY-DGNWELIE 47 (65)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH-cCCchhhh
Confidence 5677888999999999987776655443322 26655554
No 30
>PF12728 HTH_17: Helix-turn-helix domain
Probab=54.41 E-value=13 Score=21.89 Aligned_cols=24 Identities=21% Similarity=0.437 Sum_probs=20.7
Q ss_pred HHHHHhhhCCCHHHHHhhhcccee
Q psy2669 82 GDRVSKLLGVDSQQLYTNLVKPRI 105 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L~~~~~ 105 (166)
.+.+|++|||+...+.+.+....+
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 578999999999999998877655
No 31
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=54.37 E-value=34 Score=18.54 Aligned_cols=25 Identities=24% Similarity=0.232 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHH
Q psy2669 28 EEFQLTDQAFDILGFTKEEKENVYK 52 (166)
Q Consensus 28 ~~f~~~~~al~~lg~~~~e~~~i~~ 52 (166)
++|..+..--..+|++.+|+...+.
T Consensus 3 ~EW~~Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 3 EEWVELIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4677777777788999999987764
No 32
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=51.08 E-value=38 Score=19.80 Aligned_cols=25 Identities=32% Similarity=0.663 Sum_probs=16.2
Q ss_pred cHHHHHHHHHHHHHcC---CCHHHHHHHHHH
Q psy2669 26 DGEEFQLTDQAFDILG---FTKEEKENVYKI 53 (166)
Q Consensus 26 D~~~f~~~~~al~~lg---~~~~e~~~i~~i 53 (166)
+.++|. .+|..+| +++++...+|+.
T Consensus 6 ~~~~~~---~~l~~~g~~~~s~~e~~~l~~~ 33 (54)
T PF13833_consen 6 TREEFR---RALSKLGIKDLSEEEVDRLFRE 33 (54)
T ss_dssp EHHHHH---HHHHHTTSSSSCHHHHHHHHHH
T ss_pred CHHHHH---HHHHHhCCCCCCHHHHHHHHHh
Confidence 445555 5555554 778888888775
No 33
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=49.47 E-value=19 Score=20.54 Aligned_cols=19 Identities=32% Similarity=0.697 Sum_probs=15.0
Q ss_pred HHHHHhhhCCCHHHHHhhh
Q psy2669 82 GDRVSKLLGVDSQQLYTNL 100 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L 100 (166)
...+|+.|||+...|.+-|
T Consensus 21 ~~~aA~~Lgisr~tL~~kl 39 (42)
T PF02954_consen 21 VSKAARLLGISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 5689999999999887654
No 34
>PHA01976 helix-turn-helix protein
Probab=48.32 E-value=63 Score=19.80 Aligned_cols=57 Identities=14% Similarity=0.053 Sum_probs=35.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCchhHHHHHhhhCCCHHHHH
Q psy2669 32 LTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLY 97 (166)
Q Consensus 32 ~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~ 97 (166)
.++.+....|++..+......+--. ++++++ .....++.+.+..+|+.|||+.+.|.
T Consensus 6 rl~~~R~~~glt~~~lA~~~gvs~~--~v~~~e-------~g~~~p~~~~l~~ia~~l~v~~~~l~ 62 (67)
T PHA01976 6 QLIKARNARAWSAPELSRRAGVRHS--LIYDFE-------ADKRLPNLKTLLRLADALGVTLDWLC 62 (67)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHH--HHHHHH-------cCCCCCCHHHHHHHHHHHCcCHHHHh
Confidence 4566677788887766555432211 122221 12234567889999999999998774
No 35
>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].
Probab=47.19 E-value=40 Score=25.24 Aligned_cols=67 Identities=18% Similarity=0.242 Sum_probs=44.7
Q ss_pred cHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCchhHHHHHhhhCCCHHHHH
Q psy2669 26 DGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLY 97 (166)
Q Consensus 26 D~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~ 97 (166)
|..-...+++.|..-|+++.+.. .-||-||.+.-=.+... -.+...=+-..+..+|+.+|++.+.|.
T Consensus 3 ~~~~~erV~~Ll~~~Gi~kr~~~---s~LA~iL~Is~ssa~RK--L~G~~~ftl~EI~~Ia~~fgvS~d~l~ 69 (147)
T PF08667_consen 3 DQAIAERVRELLDRKGIPKRKHA---SELADILGISYSSAYRK--LNGKSPFTLEEIKKIAKHFGVSPDELF 69 (147)
T ss_pred hHHHHHHHHHHHHHcCCcchhhH---HHHHHHHCCCHHHHHHH--hcCCCCCCHHHHHHHHHHhCcCHHHHH
Confidence 44556788999999999986664 47777876633222111 011112234678999999999999988
No 36
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=46.81 E-value=79 Score=20.54 Aligned_cols=53 Identities=17% Similarity=0.233 Sum_probs=38.7
Q ss_pred HHHHcCCCHHHHHHHHHHHHHHHhh--cCceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHhhhcccee
Q psy2669 36 AFDILGFTKEEKENVYKITASVMHM--GGMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYTNLVKPRI 105 (166)
Q Consensus 36 al~~lg~~~~e~~~i~~ilaaILhL--GNi~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~~L~~~~~ 105 (166)
.+..+..++++...-+++..||-.. |-| ++..+|++.|++.-++...|-.+-+
T Consensus 6 i~~~l~~~~~e~~~~~r~~~Ai~lY~~g~i-----------------S~gkAAelag~s~~eF~~~L~~~gI 60 (76)
T PF03683_consen 6 ILQALRLTPDEFEQELREELAIKLYEEGKI-----------------SLGKAAELAGMSRWEFLELLKERGI 60 (76)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHcCCC-----------------CHHHHHHHhCCCHHHHHHHHHHCCC
Confidence 3455667888777777766665332 444 3679999999999999999988764
No 37
>cd07311 terB_like_1 tellurium resistance terB-like protein, subgroup 1. This family includes several uncharacterized bacterial proteins. The prototype of this CD is tellurite resistance protein from Nostoc punctiforme that belongs to COG3793. Its precise biological function and its mechanism responsible for tellurium resistance still remains rather poorly understood.
Probab=46.61 E-value=30 Score=25.84 Aligned_cols=80 Identities=13% Similarity=0.120 Sum_probs=48.7
Q ss_pred CCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeec--C---------------CCCccccCCchhH
Q psy2669 20 TIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQR--G---------------REEQAEPDGTEEG 82 (166)
Q Consensus 20 ~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~--~---------------~~~~~~v~~~~~l 82 (166)
..+|.-+..+-+.+...|..+|+++++...+.+. .+--.+....|+.. . .++.......+.+
T Consensus 35 kADG~Vse~Ei~~~~~~m~~~~L~~e~~~~aie~-~~~~~L~~~~~~~~~~~~~~~~ll~~~l~vA~ADG~l~~~E~~lL 113 (150)
T cd07311 35 KGDGVISPEERDWAIGYAAARGGDADMVEELKEY-TADEDLEEVDFRSPNIKSSRRALLYDAIQVCAADGELSPGEVAAV 113 (150)
T ss_pred HcCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHh-CccccHHHHHHHHHhcchhHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence 4577778888888889999999999988877766 10000000000000 0 0001111224679
Q ss_pred HHHHhhhCCCHHHHHhhh
Q psy2669 83 DRVSKLLGVDSQQLYTNL 100 (166)
Q Consensus 83 ~~~a~LLgv~~~~L~~~L 100 (166)
..+|.+||++..++...+
T Consensus 114 ~~iA~~LGis~~~~~~l~ 131 (150)
T cd07311 114 RKAASLLGISEDEVQKLE 131 (150)
T ss_pred HHHHHHcCCCHHHHHHHH
Confidence 999999999998887644
No 38
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=46.39 E-value=24 Score=19.87 Aligned_cols=23 Identities=17% Similarity=0.362 Sum_probs=19.2
Q ss_pred HHHHHhhhCCCHHHHHhhhccce
Q psy2669 82 GDRVSKLLGVDSQQLYTNLVKPR 104 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L~~~~ 104 (166)
+..+|++||++...+.+.+-...
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 57899999999999998875554
No 39
>PF13309 HTH_22: HTH domain
Probab=45.73 E-value=23 Score=22.39 Aligned_cols=21 Identities=24% Similarity=0.417 Sum_probs=18.3
Q ss_pred hhHHHHHhhhCCCHHHHHhhh
Q psy2669 80 EEGDRVSKLLGVDSQQLYTNL 100 (166)
Q Consensus 80 ~~l~~~a~LLgv~~~~L~~~L 100 (166)
.+++.+|+.|||+...+.+.|
T Consensus 43 gav~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 43 GAVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred cHHHHHHHHHCCCHHHHHHHc
Confidence 468999999999999988765
No 40
>PF01465 GRIP: GRIP domain; InterPro: IPR000237 The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain [, , ] is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi []. The GRIP domain contains a completely conserved tyrosine residue.; GO: 0005515 protein binding, 0000042 protein targeting to Golgi; PDB: 1R4A_H 1UPT_B.
Probab=44.61 E-value=25 Score=20.85 Aligned_cols=15 Identities=20% Similarity=0.556 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHHHhh
Q psy2669 46 EKENVYKITASVMHM 60 (166)
Q Consensus 46 e~~~i~~ilaaILhL 60 (166)
++..+..++++||++
T Consensus 23 ~~~~llpvi~tlL~f 37 (46)
T PF01465_consen 23 EREQLLPVIATLLKF 37 (46)
T ss_dssp -HHHHHHHHHHHTT-
T ss_pred hHHHHHHHHHHHHCC
Confidence 455555666666654
No 41
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=44.36 E-value=37 Score=22.70 Aligned_cols=25 Identities=4% Similarity=0.050 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHH
Q psy2669 29 EFQLTDQAFDILGFTKEEKENVYKI 53 (166)
Q Consensus 29 ~f~~~~~al~~lg~~~~e~~~i~~i 53 (166)
.+.++..+|..+|++.+++..+++.
T Consensus 28 s~~el~~~l~~~~~~~~ev~~i~~~ 52 (96)
T smart00027 28 TGAQAKPILLKSGLPQTLLAKIWNL 52 (96)
T ss_pred eHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4566677778889999888888764
No 42
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=44.00 E-value=48 Score=28.03 Aligned_cols=64 Identities=14% Similarity=0.204 Sum_probs=38.6
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCcc-ccCC---chhHHHHHhhhCCCHHHHHhhhc
Q psy2669 31 QLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQA-EPDG---TEEGDRVSKLLGVDSQQLYTNLV 101 (166)
Q Consensus 31 ~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~-~v~~---~~~l~~~a~LLgv~~~~L~~~L~ 101 (166)
+.++++.+.+|++.++...-+.+=-.. +++++ .++.. .... ...+...|++|||+++.|...+-
T Consensus 17 ~~Lr~aRe~~GlSq~~vA~~l~l~~~~--I~~iE-----~g~~~~~~~~tf~RGyir~yA~~lgv~~~~L~~~~~ 84 (331)
T PRK10856 17 ERLRQAREQLGLTQQAVAERLCLKVST--VRDIE-----EDKAPADLASTFLRGYIRSYARLVHIPEEELLPGLE 84 (331)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHH--HHHHH-----CCCCCCChhHHHHHHHHHHHHHHHCcCHHHHHHhhh
Confidence 568888999999987766555432111 12221 11110 1111 13478899999999999987664
No 43
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=43.96 E-value=45 Score=20.02 Aligned_cols=23 Identities=4% Similarity=0.185 Sum_probs=16.7
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Q psy2669 31 QLTDQAFDILGFTKEEKENVYKI 53 (166)
Q Consensus 31 ~~~~~al~~lg~~~~e~~~i~~i 53 (166)
.++..+|..+|++.++...+|+.
T Consensus 19 ~el~~~l~~~g~~~~~~~~i~~~ 41 (67)
T cd00052 19 DEARPFLGKSGLPRSVLAQIWDL 41 (67)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Confidence 44556666779998888888764
No 44
>PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=41.95 E-value=18 Score=26.12 Aligned_cols=60 Identities=15% Similarity=0.250 Sum_probs=39.0
Q ss_pred CcHHHHH-HHHHHHHHcCCCHHHHHHHHHH-HHHHHhhc-CceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHhhh
Q psy2669 25 DDGEEFQ-LTDQAFDILGFTKEEKENVYKI-TASVMHMG-GMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYTNL 100 (166)
Q Consensus 25 dD~~~f~-~~~~al~~lg~~~~e~~~i~~i-laaILhLG-Ni~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~~L 100 (166)
...+.|. +-...|+.-|++++|...|..- ..+.||+| ||-| +++.+...|++...+.-++
T Consensus 39 ~~RerF~aDe~ay~~~~~Lt~eqk~aV~~RDw~~mi~~Ggn~y~----------------L~Kl~av~G~s~q~i~a~m 101 (119)
T PRK13379 39 PWRDRFLQDAEALMQEAGLTEQEKELIRARDWLGLVQYGANFFV----------------IEKFARVVRMTNLQVYAIM 101 (119)
T ss_pred HHHHHHHhCHHHHHHHcCCCHHHHHHHHhccHHHHHHcCccHHH----------------HHHHHHHcCCcHHHHHHHh
Confidence 3466776 4556688999999999888653 56778885 4443 3455555565555554444
No 45
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=41.28 E-value=29 Score=19.31 Aligned_cols=24 Identities=21% Similarity=0.347 Sum_probs=19.4
Q ss_pred HHHHHhhhCCCHHHHHhhhcccee
Q psy2669 82 GDRVSKLLGVDSQQLYTNLVKPRI 105 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L~~~~~ 105 (166)
+..+|++|||+...+.++.-...+
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 467999999999999988765543
No 46
>PF01876 RNase_P_p30: RNase P subunit p30; InterPro: IPR002738 Members of this protein family are part of the ribonuclease P complex () that takes part in endonucleolytic cleavage of RNA, removing 5'-extra-nucleotide from tRNA precursor. This process is essential for tRNA processing.; GO: 0004540 ribonuclease activity, 0008033 tRNA processing; PDB: 1V77_A 2CZV_A.
Probab=40.04 E-value=1.1e+02 Score=22.30 Aligned_cols=59 Identities=8% Similarity=0.141 Sum_probs=34.6
Q ss_pred CHHHHHHHHHHHHHHHhh---cCceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHhhhcc
Q psy2669 43 TKEEKENVYKITASVMHM---GGMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYTNLVK 102 (166)
Q Consensus 43 ~~~e~~~i~~ilaaILhL---GNi~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~~L~~ 102 (166)
.......+++-+.-++.+ -||-+... ......+-++..+...+.+||++.++-.+++++
T Consensus 88 ~~~~r~~~~~~~~~l~~~~~~~~iiiSSg-A~~~~elr~P~dv~~l~~~lGl~~~~a~~avs~ 149 (150)
T PF01876_consen 88 DGSNRRNFISNARRLIRLTKKKNIIISSG-ASSPLELRSPRDVINLLALLGLSEEEAKKAVST 149 (150)
T ss_dssp -HHHHHHHHHHHHHHHHHHHH--EEEE----SSGGG---HHHHHHHHHHTT--HHHHHHTTTH
T ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEcC-CCChhhCcCHHHHHHHHHHhCCCHHHHHHHHhc
Confidence 344455555555555555 36666654 345678888999999999999999998888764
No 47
>TIGR03264 met_CoM_red_C methyl-coenzyme M reductase I operon protein C. has several modified sites, so accessory proteins are expected. Several methanogens have encode two such enzymes, designated I and II; this protein occurs only operons of type I. The precise function is unknown.
Probab=40.02 E-value=4.4 Score=31.38 Aligned_cols=26 Identities=35% Similarity=0.641 Sum_probs=23.6
Q ss_pred HcCCCHHHHHHHHHHHHHHHhhcCce
Q psy2669 39 ILGFTKEEKENVYKITASVMHMGGMK 64 (166)
Q Consensus 39 ~lg~~~~e~~~i~~ilaaILhLGNi~ 64 (166)
+.|++++|++.|-+==.||+|+||+.
T Consensus 88 ~fgl~~~E~~qI~~HklAV~h~GNvk 113 (194)
T TIGR03264 88 TFGLTPEEIEQINRHKLAVIHLGNVK 113 (194)
T ss_pred ccCCCHHHHHHHhhcCEEEEEeCCHH
Confidence 56999999999999889999999984
No 48
>PRK13377 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=39.51 E-value=22 Score=26.05 Aligned_cols=74 Identities=16% Similarity=0.290 Sum_probs=48.8
Q ss_pred CcHHHHHH-HHHHHHHcCCCHHHHHHHHH-HHHHHHhhc-CceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHhhhc
Q psy2669 25 DDGEEFQL-TDQAFDILGFTKEEKENVYK-ITASVMHMG-GMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYTNLV 101 (166)
Q Consensus 25 dD~~~f~~-~~~al~~lg~~~~e~~~i~~-ilaaILhLG-Ni~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~~L~ 101 (166)
..++.|.+ -...++.-|++++|...|.. =+-+.||+| ||-|-.. -+.+....-....|..-|.+.+++...+.
T Consensus 38 ~nRerF~ade~Ay~de~~Lteeqr~aV~~RD~~~li~~Ggniy~L~K----l~av~G~s~q~i~a~mtG~t~eef~~mm~ 113 (129)
T PRK13377 38 ENRERFKADERAYLDEWPMTEEQKQAVLARDLNRCIALGGNIYFLAK----IGATDGKSFQQMAGSMTGMTEEEYRQMML 113 (129)
T ss_pred HHHHHHHhCHHHHHHHcCCCHHHHHHHHhhhHHHHHHccccHHHHHH----HHHHhCCcHHHHHHHhcCCCHHHHHHHHH
Confidence 34666763 44567889999999988865 356778884 5554432 23344455566677777777777776665
Q ss_pred c
Q psy2669 102 K 102 (166)
Q Consensus 102 ~ 102 (166)
.
T Consensus 114 ~ 114 (129)
T PRK13377 114 G 114 (129)
T ss_pred h
Confidence 4
No 49
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=39.05 E-value=29 Score=25.13 Aligned_cols=39 Identities=15% Similarity=0.144 Sum_probs=22.2
Q ss_pred hHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChh
Q psy2669 81 EGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVN 119 (166)
Q Consensus 81 ~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~ 119 (166)
.+..++++||++.+++.+.+..+-=...+..+..+.+++
T Consensus 99 s~~~la~~Lg~~~~el~~~~~~~gW~~d~~~~~~~~~~~ 137 (143)
T PF10075_consen 99 SLSDLAEMLGLSEEELEKFIKSRGWTVDGDGVLFPPNPE 137 (143)
T ss_dssp -HHHHHHHTTS-HHHHHHHHHHHT-EE-----EE---HH
T ss_pred CHHHHHHHhCCCHHHHHHHHHHcCCEECCCccEEecCCc
Confidence 578999999999999999888775444444444444443
No 50
>cd07925 LigA_like_1 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB). The proteins of unknown function in this subfamily are similar to the A subunit of the Protocatechuate (PCA) 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds.
Probab=38.81 E-value=28 Score=24.65 Aligned_cols=71 Identities=17% Similarity=0.242 Sum_probs=40.0
Q ss_pred CCcHHHHHH-HHHHHHHcCCCHHHHHHHHHH-HHHHHhhc-CceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHh
Q psy2669 24 MDDGEEFQL-TDQAFDILGFTKEEKENVYKI-TASVMHMG-GMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYT 98 (166)
Q Consensus 24 ~dD~~~f~~-~~~al~~lg~~~~e~~~i~~i-laaILhLG-Ni~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~ 98 (166)
.+..+.|.+ -...++.-|++++|...|..- +.+.+++| ||-|-.. -+.+....-....|..-|.+.+++.+
T Consensus 26 ~~nRe~F~aD~~Ay~~~~~Lteeqr~av~~RD~~~li~~Ggn~y~L~K----l~~~~G~s~q~i~a~mtG~t~eef~~ 99 (106)
T cd07925 26 AANREAFLADEEAYCEKFGLTPEQKQAVRNRDVLRMLEAGGNIYYLAK----LAGILGLNMQDIGGLQTGMSTEEFKA 99 (106)
T ss_pred HHHHHHHHhCHHHHHHHcCCCHHHHHHHHHhhHHHHHHccCcHHHHHH----HHHHhCCcHHHHHHHhcCCCHHHHHH
Confidence 345667764 445578899999999988653 56777884 4543321 12222233334444444444444443
No 51
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=38.77 E-value=40 Score=20.87 Aligned_cols=27 Identities=22% Similarity=0.182 Sum_probs=23.1
Q ss_pred cccCCchhHHHHHhhhCCCHHHHHhhh
Q psy2669 74 AEPDGTEEGDRVSKLLGVDSQQLYTNL 100 (166)
Q Consensus 74 ~~v~~~~~l~~~a~LLgv~~~~L~~~L 100 (166)
..+.++..+...|+-|||++++|..+.
T Consensus 15 I~~~e~~ev~ywa~~~gvt~~~L~~AV 41 (57)
T PF12244_consen 15 IDLSEPYEVRYWAKRFGVTEEQLREAV 41 (57)
T ss_pred cCCCCHHHHHHHHHHHCcCHHHHHHHH
Confidence 345667889999999999999999886
No 52
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=38.49 E-value=56 Score=19.89 Aligned_cols=19 Identities=11% Similarity=0.223 Sum_probs=14.7
Q ss_pred HHHHHhhhCCCHHHHHhhh
Q psy2669 82 GDRVSKLLGVDSQQLYTNL 100 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L 100 (166)
+..+|+.||+++..+.+.+
T Consensus 16 ~~~AA~~l~is~~~vs~~i 34 (60)
T PF00126_consen 16 ISAAAEELGISQSAVSRQI 34 (60)
T ss_dssp HHHHHHHCTSSHHHHHHHH
T ss_pred HHHHHHHhhccchHHHHHH
Confidence 3589999999988776655
No 53
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=37.94 E-value=45 Score=22.91 Aligned_cols=23 Identities=17% Similarity=0.293 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHH
Q psy2669 28 EEFQLTDQAFDILGFTKEEKENV 50 (166)
Q Consensus 28 ~~f~~~~~al~~lg~~~~e~~~i 50 (166)
-.|..+...++.||+++.+++.|
T Consensus 17 V~~~~Wk~laR~LGLse~~I~~i 39 (96)
T cd08315 17 VPFDSWNRLMRQLGLSENEIDVA 39 (96)
T ss_pred CCHHHHHHHHHHcCCCHHHHHHH
Confidence 34677888999999999998877
No 54
>cd01301 rDP_like renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics. Although the biological function of the enzyme is still unknown, it has been suggested to play a role in the renal glutathione metabolism.
Probab=37.71 E-value=53 Score=27.38 Aligned_cols=31 Identities=19% Similarity=0.296 Sum_probs=27.8
Q ss_pred CCCCCcHHHHHHHHHHHHHcCCCHHHHHHHH
Q psy2669 21 IPGMDDGEEFQLTDQAFDILGFTKEEKENVY 51 (166)
Q Consensus 21 ~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~ 51 (166)
.+|..|..+|..+.++|..-|++++++..|+
T Consensus 272 ~~gl~~~~~~~~l~~~L~~rG~s~~~i~~i~ 302 (309)
T cd01301 272 PGGLEDVSDLPNLTAELLERGYSEEEIEKIA 302 (309)
T ss_pred ccccCCHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 4678899999999999999999999988775
No 55
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=37.59 E-value=48 Score=22.10 Aligned_cols=23 Identities=22% Similarity=0.164 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHH
Q psy2669 28 EEFQLTDQAFDILGFTKEEKENV 50 (166)
Q Consensus 28 ~~f~~~~~al~~lg~~~~e~~~i 50 (166)
-.+..++..++.+|+|+.+++.|
T Consensus 9 v~~~~wk~~~R~LGlse~~Id~i 31 (80)
T cd08313 9 VPPRRWKEFVRRLGLSDNEIERV 31 (80)
T ss_pred CCHHHHHHHHHHcCCCHHHHHHH
Confidence 34677788899999999999877
No 56
>PF01152 Bac_globin: Bacterial-like globin; InterPro: IPR001486 Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms []. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors []. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): trimer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates []. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors []. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle []. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia []. Neuroglobin belongs to a branch of the globin family that diverged early in evolution. Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin []. Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers []. Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation. Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants []. Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin []. Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [, ]. Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors []. Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features []. This entry represents a group of haemoglobin-like proteins found in eubacteria, cyanobacteria, protozoa, algae and plants, but not in animals or yeast. These proteins have a truncated 2-over-2 rather than the canonical 3-over-3 alpha-helical sandwich fold []. This entry includes: HbN (or GlbN): a truncated haemoglobin-like protein that binds oxygen cooperatively with a very high affinity and a slow dissociation rate, which may exclude it from oxygen transport. It appears to be involved in bacterial nitric oxide detoxification and in nitrosative stress []. Cyanoglobin (or GlbN): a truncated haemoprotein found in cyanobacteria that has high oxygen affinity, and which appears to serve as part of a terminal oxidase, rather than as a respiratory pigment []. HbO (or GlbO): a truncated haemoglobin-like protein with a lower oxygen affinity than HbN. HbO associates with the bacterial cell membrane, where it significantly increases oxygen uptake over membranes lacking this protein. HbO appears to interact with a terminal oxidase, and could participate in an oxygen/electron-transfer process that facilitates oxygen transfer during aerobic metabolism []. Glb3: a nuclear-encoded truncated haemoglobin from plants that appears more closely related to HbO than HbN. Glb3 from Arabidopsis thaliana (Mouse-ear cress) exhibits an unusual concentration-independent binding of oxygen and carbon dioxide []. ; GO: 0019825 oxygen binding, 0015671 oxygen transport; PDB: 2BKM_B 1UVY_A 1DLW_A 2XYK_B 2IG3_A 2GKM_B 1S61_A 1S56_B 1RTE_B 2GLN_A ....
Probab=37.37 E-value=74 Score=22.03 Aligned_cols=27 Identities=30% Similarity=0.372 Sum_probs=22.1
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2669 31 QLTDQAFDILGFTKEEKENVYKITASV 57 (166)
Q Consensus 31 ~~~~~al~~lg~~~~e~~~i~~ilaaI 57 (166)
..+.+||+.+|++++.+..+++.+..+
T Consensus 87 ~~~~~al~~~~v~~~~~~~~~~~~~~~ 113 (120)
T PF01152_consen 87 ELLKQALDELGVPEELIDELLARLESL 113 (120)
T ss_dssp HHHHHHHHHTTCTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 356788999999999999998887654
No 57
>TIGR02792 PCA_ligA protocatechuate 4,5-dioxygenase, alpha subunit. Protocatechuate (PCA) 4,5-dioxygenase is the first enzyme in the PCA 4,5-cleavage pathway that is an alternative to PCA 3,4-cleavage and PCA 2,3 cleavage pathways. PCA is an intermediate in the breakdown of lignin (hence the gene symbol ligA) and other compounds. Members of this family are the alpha chain of PCA 4,5-dioxygenase, or the equivalent domain of a fusion protein.
Probab=37.16 E-value=24 Score=25.36 Aligned_cols=74 Identities=15% Similarity=0.277 Sum_probs=46.5
Q ss_pred CCcHHHHHH-HHHHHHHcCCCHHHHHHHHH-HHHHHHhhc-CceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHhhh
Q psy2669 24 MDDGEEFQL-TDQAFDILGFTKEEKENVYK-ITASVMHMG-GMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYTNL 100 (166)
Q Consensus 24 ~dD~~~f~~-~~~al~~lg~~~~e~~~i~~-ilaaILhLG-Ni~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~~L 100 (166)
....+.|.+ -...++.-|++++|...|.. =+-+.||+| ||-|-.. -+.+....-....|..-|.+.+++...+
T Consensus 31 ~~nRerF~ade~Ay~d~~~Lt~eqk~av~~RD~~~li~~Ggniy~L~K----l~a~~G~s~q~i~a~mtG~t~eef~~mm 106 (117)
T TIGR02792 31 AENRERFKADESAYLDEWNLTPAQKQAVLARDLNACIDEGGNIYFLAK----IGATDGKSFQQMAGSMTGMTEEEYRQMM 106 (117)
T ss_pred HHHHHHHHhCHHHHHHHcCCCHHHHHHHHhhhHHHHHHccchHHHHHH----HHHHhCCcHHHHHHHhcCCCHHHHHHHH
Confidence 345667763 44567889999999988865 356778884 5554432 2333344445566666677776666555
Q ss_pred c
Q psy2669 101 V 101 (166)
Q Consensus 101 ~ 101 (166)
.
T Consensus 107 ~ 107 (117)
T TIGR02792 107 I 107 (117)
T ss_pred H
Confidence 4
No 58
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=37.12 E-value=2.2e+02 Score=22.92 Aligned_cols=74 Identities=18% Similarity=0.231 Sum_probs=52.0
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHhhhc---cce-e--
Q psy2669 32 LTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYTNLV---KPR-I-- 105 (166)
Q Consensus 32 ~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~~L~---~~~-~-- 105 (166)
.+..-|+.+||++-|.. +..++|.+|... ...+++..|||...+.+.|- .|- +
T Consensus 4 ~~~~~L~~lGlt~yEa~----vY~aLl~~g~~t-----------------A~eis~~sgvP~~kvY~vl~sLe~kG~v~~ 62 (247)
T COG1378 4 ELEENLQKLGLTEYEAK----VYLALLCLGEAT-----------------AKEISEASGVPRPKVYDVLRSLEKKGLVEV 62 (247)
T ss_pred HHHHHHHHcCCCHHHHH----HHHHHHHhCCcc-----------------HHHHHHHcCCCchhHHHHHHHHHHCCCEEe
Confidence 56788999999998864 677888888664 46789999999987776653 221 1
Q ss_pred eeCCeeEEecCChhHHHHhhh
Q psy2669 106 KVGNEFVTQGRNVNQQAFDIL 126 (166)
Q Consensus 106 ~~~~e~~~~~~~~~~A~~~rd 126 (166)
..|.-..-++.++++....+.
T Consensus 63 ~~g~P~~y~av~p~~~i~~~~ 83 (247)
T COG1378 63 IEGRPKKYRAVPPEELIERIK 83 (247)
T ss_pred eCCCCceEEeCCHHHHHHHHH
Confidence 224455667888887654433
No 59
>PRK13378 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=37.07 E-value=26 Score=25.19 Aligned_cols=73 Identities=15% Similarity=0.186 Sum_probs=42.2
Q ss_pred CCcHHHHH-HHHHHHHHcCCCHHHHHHHHH-HHHHHHhhc-CceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHhhh
Q psy2669 24 MDDGEEFQ-LTDQAFDILGFTKEEKENVYK-ITASVMHMG-GMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYTNL 100 (166)
Q Consensus 24 ~dD~~~f~-~~~~al~~lg~~~~e~~~i~~-ilaaILhLG-Ni~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~~L 100 (166)
.+..+.|. +-...++.-|++++|...|.. =+.+.||+| ||-|-.. -+.+....-....|..-|.+.+++...+
T Consensus 37 ~~nRe~F~ade~Ay~~~~~Lteeqk~aV~~RD~~~mi~~Ggn~y~L~K----~~av~G~s~q~i~a~mtG~t~eef~~mm 112 (117)
T PRK13378 37 AANRAAFLADEAAYCRKYGLNEEQKEAIRNRDVLQLLAAGGNAYYLAK----FAGIFGLDMQDIGAQQTGMTKEEFKAKL 112 (117)
T ss_pred HHHHHHHHhCHHHHHHHcCCCHHHHHHHHhhhHHHHHHcCchHHHHHH----HHHHcCCcHHHHHHHhcCCCHHHHHHHH
Confidence 34566776 345567899999999998875 356777884 5544321 2222333334444555555555554433
No 60
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=36.36 E-value=58 Score=23.18 Aligned_cols=60 Identities=12% Similarity=0.087 Sum_probs=38.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHh
Q psy2669 30 FQLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYT 98 (166)
Q Consensus 30 f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~ 98 (166)
|..+...++..|++.+|......|=- =++.+++ ....-++.+.+..+|..||++.+.|..
T Consensus 7 ~~~l~~ll~~~Glsq~eLA~~~Gis~--~~is~iE-------~g~~~ps~~~l~kIa~aL~v~~~~L~~ 66 (120)
T PRK13890 7 FTNVLRLLDERHMTKKELSERSGVSI--SFLSDLT-------TGKANPSLKVMEAIADALETPLPLLLE 66 (120)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCH--HHHHHHH-------cCCCCCCHHHHHHHHHHHCCCHHHHhc
Confidence 56788889999999877555433210 0111111 111235678899999999999887753
No 61
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=35.55 E-value=39 Score=19.20 Aligned_cols=23 Identities=22% Similarity=0.062 Sum_probs=18.3
Q ss_pred HHHHHhhhCCCHHHHHhhhccce
Q psy2669 82 GDRVSKLLGVDSQQLYTNLVKPR 104 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L~~~~ 104 (166)
+..+|+++||++..+..+.-...
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 56799999999999988754443
No 62
>PF01244 Peptidase_M19: Membrane dipeptidase (Peptidase family M19); InterPro: IPR008257 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of peptidases belong to the MEROPS peptidase family M19 (membrane dipeptidase family, clan MJ). The protein fold of the peptidase domain for members of this family resembles that of Klebsiella urease, the type example for clan MJ. Renal dipeptidase (rDP) (3.4.13.19 from EC), also known as microsomal dipeptidase, is a zinc-dependent metalloenzyme that hydrolyzes a wide range of dipeptides. It is involved in renal metabolism of glutathione and its conjugates. It is a homodimeric disulphide-linked glycoprotein attached to the renal brush border microvilli membrane by a GPI-anchor. A glutamate residue has recently been shown [,] to be important for the catalytic activity of rDP. rDP seems to be evolutionary related to hypothetical proteins in the PQQ biosynthesis operons of Acinetobacter calcoaceticus and Klebsiella pneumoniae.; GO: 0008235 metalloexopeptidase activity, 0008239 dipeptidyl-peptidase activity, 0016805 dipeptidase activity, 0006508 proteolysis; PDB: 3NEH_B 2RAG_D 3LU2_A 3B40_A 3LY0_A 3FDG_B 2I5G_B 3S2J_A 3S2N_A 3S2L_A ....
Probab=34.84 E-value=43 Score=28.07 Aligned_cols=31 Identities=16% Similarity=0.367 Sum_probs=27.4
Q ss_pred CCCCCcHHHHHHHHHHHHHcCCCHHHHHHHH
Q psy2669 21 IPGMDDGEEFQLTDQAFDILGFTKEEKENVY 51 (166)
Q Consensus 21 ~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~ 51 (166)
.+|..|..+|..+.++|..-|++++++..|+
T Consensus 280 ~~gl~~~~~~~~l~~~L~~rG~s~~~i~kI~ 310 (320)
T PF01244_consen 280 PEGLEDPSDLPNLTEELLKRGYSEEDIEKIL 310 (320)
T ss_dssp BBTBSSGGGHHHHHHHHHHTTS-HHHHHHHH
T ss_pred CCccCCHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence 5788899999999999999999999998875
No 63
>cd07924 PCA_45_Doxase_A The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit. The A subunit is the non-catalytic subunit of Protocatechuate (PCA) 4,5-dioxygenase (LigAB), which is composed of A and B subunits that form a tetramer. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As a member of the Class III extradiol dioxygenase family, LigAB uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon.
Probab=34.54 E-value=31 Score=25.01 Aligned_cols=74 Identities=16% Similarity=0.293 Sum_probs=45.7
Q ss_pred CCcHHHHHH-HHHHHHHcCCCHHHHHHHHH-HHHHHHhhc-CceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHhhh
Q psy2669 24 MDDGEEFQL-TDQAFDILGFTKEEKENVYK-ITASVMHMG-GMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYTNL 100 (166)
Q Consensus 24 ~dD~~~f~~-~~~al~~lg~~~~e~~~i~~-ilaaILhLG-Ni~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~~L 100 (166)
....+.|.+ -..-++.-|++++|...|.. =.-+.||+| ||-|... -+.+....-....|..-|.+.+++...+
T Consensus 34 ~~nRerF~ade~Ay~~~~~Lteeqr~aV~~RD~~~li~~Ggniy~L~K----l~a~~G~s~q~i~a~mtG~s~eef~~mm 109 (121)
T cd07924 34 AENRERFKADERAYLDKWPMTEEQKQAVLARDYNRMLALGGNIYYLAK----IGATDGLSFQQAAGSMTGMSMEEYRQMM 109 (121)
T ss_pred HHHHHHHHhCHHHHHHHcCCCHHHHHHHHHhhHHHHHHhcCcHHHHHH----HHHHhCCcHHHHHHHhcCCCHHHHHHHH
Confidence 344667763 44567899999999988865 356778884 5544332 2333344445556666666666666544
Q ss_pred c
Q psy2669 101 V 101 (166)
Q Consensus 101 ~ 101 (166)
.
T Consensus 110 ~ 110 (121)
T cd07924 110 V 110 (121)
T ss_pred H
Confidence 3
No 64
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=34.38 E-value=44 Score=19.49 Aligned_cols=30 Identities=17% Similarity=0.165 Sum_probs=24.3
Q ss_pred chhHHHHHhhhCCCHHHHHhhhccceeeeC
Q psy2669 79 TEEGDRVSKLLGVDSQQLYTNLVKPRIKVG 108 (166)
Q Consensus 79 ~~~l~~~a~LLgv~~~~L~~~L~~~~~~~~ 108 (166)
-..+..+|+.||++...+.+++-.+....+
T Consensus 17 f~S~~eAa~~lg~~~~~I~~~~~~~~~~~g 46 (53)
T smart00497 17 FSSIREAAKYLGISHSSISKYLNTGKKFKG 46 (53)
T ss_pred ecCHHHHHHHhCCCHHHHHHHHhCCCccCC
Confidence 356789999999999999999887665444
No 65
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=33.77 E-value=61 Score=21.25 Aligned_cols=23 Identities=22% Similarity=0.349 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHH
Q psy2669 28 EEFQLTDQAFDILGFTKEEKENV 50 (166)
Q Consensus 28 ~~f~~~~~al~~lg~~~~e~~~i 50 (166)
-.|......++.|||++.+++.|
T Consensus 9 v~~~~Wk~laR~LGls~~~I~~i 31 (79)
T cd08784 9 VPFDQHKRFFRKLGLSDNEIKVA 31 (79)
T ss_pred CCHHHHHHHHHHcCCCHHHHHHH
Confidence 34667778889999999998877
No 66
>COG4103 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.75 E-value=39 Score=25.26 Aligned_cols=20 Identities=30% Similarity=0.288 Sum_probs=16.7
Q ss_pred chhHHHHHhhhCCCHHHHHh
Q psy2669 79 TEEGDRVSKLLGVDSQQLYT 98 (166)
Q Consensus 79 ~~~l~~~a~LLgv~~~~L~~ 98 (166)
...+.++|.||||++.++.+
T Consensus 123 d~vi~RvAeLLgV~~~d~V~ 142 (148)
T COG4103 123 DHVIWRVAELLGVSPEDRVR 142 (148)
T ss_pred HHHHHHHHHHhCCCHHHHHH
Confidence 35789999999999998743
No 67
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=33.70 E-value=42 Score=21.22 Aligned_cols=23 Identities=22% Similarity=0.345 Sum_probs=17.9
Q ss_pred HHHHHhhhCCCHHHHHhhhccce
Q psy2669 82 GDRVSKLLGVDSQQLYTNLVKPR 104 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L~~~~ 104 (166)
-.++|++|||....+.++|...+
T Consensus 15 Q~kaA~~lGV~Q~AIsKAlr~gR 37 (59)
T PF09048_consen 15 QAKAARALGVTQSAISKALRAGR 37 (59)
T ss_dssp HHHHHHHHTS-HHHHHHHHHCT-
T ss_pred hHHHHHHcCCcHHHHHHHHHcCC
Confidence 35789999999999999997543
No 68
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=33.37 E-value=39 Score=24.42 Aligned_cols=23 Identities=30% Similarity=0.421 Sum_probs=20.1
Q ss_pred HHHHHhhhCCCHHHHHhhhccce
Q psy2669 82 GDRVSKLLGVDSQQLYTNLVKPR 104 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L~~~~ 104 (166)
-..+|+|||+++....+.|..++
T Consensus 25 q~~iA~LLGltqaAVS~Yls~kr 47 (119)
T COG2522 25 QYRIAKLLGLTQAAVSQYLSGKR 47 (119)
T ss_pred HHHHHHHhCCCHHHHHHHHccCC
Confidence 35899999999999999998765
No 69
>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=32.40 E-value=1.1e+02 Score=18.12 Aligned_cols=41 Identities=12% Similarity=0.319 Sum_probs=25.9
Q ss_pred CCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHhhh
Q psy2669 41 GFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYTNL 100 (166)
Q Consensus 41 g~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~~L 100 (166)
||+..+ |.+|..|.+-+.=. -....+|+.+|++...+...+
T Consensus 2 glt~~q----~~vL~~l~~~~~~~---------------~t~~~la~~l~~~~~~vs~~v 42 (62)
T PF12802_consen 2 GLTPSQ----FRVLMALARHPGEE---------------LTQSELAERLGISKSTVSRIV 42 (62)
T ss_dssp TSTHHH----HHHHHHHHHSTTSG---------------EEHHHHHHHHTS-HHHHHHHH
T ss_pred ccCHHH----HHHHHHHHHCCCCC---------------cCHHHHHHHHCcCHHHHHHHH
Confidence 666555 66777777765411 125678999999987665544
No 70
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=31.82 E-value=54 Score=18.44 Aligned_cols=19 Identities=37% Similarity=0.356 Sum_probs=14.3
Q ss_pred HHHHHhhhCCCHHHHHhhh
Q psy2669 82 GDRVSKLLGVDSQQLYTNL 100 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L 100 (166)
...+|+++||+...|..+-
T Consensus 2 i~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 3578999999999987653
No 71
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=30.75 E-value=1.5e+02 Score=20.44 Aligned_cols=60 Identities=22% Similarity=0.387 Sum_probs=39.9
Q ss_pred HHHHH-HHHHHHHHcCCCHHHHHHHHHH-HHHHHhhcCceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHhhhc
Q psy2669 27 GEEFQ-LTDQAFDILGFTKEEKENVYKI-TASVMHMGGMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYTNLV 101 (166)
Q Consensus 27 ~~~f~-~~~~al~~lg~~~~e~~~i~~i-laaILhLGNi~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~~L~ 101 (166)
.+.|. +-...|+.-|++++|+..|..- +.+.+++|-.-| -|.+.+..+|++..+...+++
T Consensus 21 RerF~~D~ea~~~e~gLt~Ee~~av~~rD~~~li~~G~n~y---------------~L~K~a~~~G~~~~~~~a~m~ 82 (94)
T cd07923 21 RERFLEDPEALFDEAGLTEEERTLIRNRDWIGMIRYGVIFF---------------VLEKLAAVVGVSNLHVYAAMR 82 (94)
T ss_pred HHHHHhCHHHHHHHcCCCHHHHHHHHcchHHHHHHccCcHH---------------HHHHHHHHcCCCHHHHHHHhh
Confidence 45665 3456688899999999988753 466777753322 255677777777766665554
No 72
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=29.38 E-value=24 Score=21.44 Aligned_cols=21 Identities=14% Similarity=0.423 Sum_probs=15.3
Q ss_pred CchhHHHHHhhhCCCHHHHHh
Q psy2669 78 GTEEGDRVSKLLGVDSQQLYT 98 (166)
Q Consensus 78 ~~~~l~~~a~LLgv~~~~L~~ 98 (166)
+.+.+..+|..||+++++|..
T Consensus 39 ~~~~l~~ia~~l~~~~~el~~ 59 (63)
T PF13443_consen 39 SLDTLEKIAKALNCSPEELFE 59 (63)
T ss_dssp -HHHHHHHHHHHT--HHHCTE
T ss_pred cHHHHHHHHHHcCCCHHHHhh
Confidence 357899999999999988754
No 73
>PRK09430 djlA Dna-J like membrane chaperone protein; Provisional
Probab=28.49 E-value=1.3e+02 Score=24.55 Aligned_cols=78 Identities=14% Similarity=0.149 Sum_probs=45.9
Q ss_pred CCCCCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCce---E-----------eecC---------------C
Q psy2669 20 TIPGMDDGEEFQLTDQAFDILGFTKEEKENVYKITASVMHMGGMK---F-----------KQRG---------------R 70 (166)
Q Consensus 20 ~~~~~dD~~~f~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~---F-----------~~~~---------------~ 70 (166)
+.+|.-+..+-+.+..-|+.+++++++......+. ..|.-. + .... .
T Consensus 67 kADG~Vse~Ei~~~~~l~~~~~l~~~~r~~a~~lf----~~~k~~~~~l~~~~~~~~~~~~~r~~l~~~lL~~l~~vA~A 142 (267)
T PRK09430 67 KAKGRVTEADIRIASQLMDRMNLHGEARRAAQQAF----REGKEPDFPLREKLRQFRSVCGGRFDLLRMFLEIQIQAAFA 142 (267)
T ss_pred hcCCCcCHHHHHHHHHHHHHcCCCHHHHHHHHHHH----HHhcccCCCHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHh
Confidence 45777777778878888889999988744433222 222111 0 0000 0
Q ss_pred CCccccCCchhHHHHHhhhCCCHHHHHhhhc
Q psy2669 71 EEQAEPDGTEEGDRVSKLLGVDSQQLYTNLV 101 (166)
Q Consensus 71 ~~~~~v~~~~~l~~~a~LLgv~~~~L~~~L~ 101 (166)
+........+.+..+|.+||++..++...+-
T Consensus 143 DG~l~~~E~~~L~~Ia~~Lgis~~df~~~~~ 173 (267)
T PRK09430 143 DGSLHPNERQVLYVIAEELGFSRFQFDQLLR 173 (267)
T ss_pred cCCCCHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 0001111246799999999999988876654
No 74
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=28.27 E-value=73 Score=17.63 Aligned_cols=24 Identities=13% Similarity=0.098 Sum_probs=16.7
Q ss_pred cCCchhHHHHHhhhCCCHHHHHhh
Q psy2669 76 PDGTEEGDRVSKLLGVDSQQLYTN 99 (166)
Q Consensus 76 v~~~~~l~~~a~LLgv~~~~L~~~ 99 (166)
|...+.+..+|.-+|++.++|.++
T Consensus 3 V~~gDtl~~IA~~~~~~~~~l~~~ 26 (44)
T PF01476_consen 3 VQPGDTLWSIAKRYGISVDELMEL 26 (44)
T ss_dssp E-TT--HHHHHHHTTS-HHHHHHH
T ss_pred ECcCCcHHHHHhhhhhhHhHHHHh
Confidence 445677899999999999998765
No 75
>PRK13372 pcmA protocatechuate 4,5-dioxygenase; Provisional
Probab=28.23 E-value=43 Score=29.59 Aligned_cols=79 Identities=14% Similarity=0.248 Sum_probs=54.3
Q ss_pred CCCCCcHHHHHH-HHHHHHHcCCCHHHHHHHHHH-HHHHHhh-cCceEeecCCCCccccCCchhHHHHHhhhCCCHHHHH
Q psy2669 21 IPGMDDGEEFQL-TDQAFDILGFTKEEKENVYKI-TASVMHM-GGMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLY 97 (166)
Q Consensus 21 ~~~~dD~~~f~~-~~~al~~lg~~~~e~~~i~~i-laaILhL-GNi~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~ 97 (166)
......++.|.. -..-|+.-|++++|...|..- .-+.|++ |||-|... -..+....-....|..-|.+.+++.
T Consensus 34 l~~~~~R~~f~~d~~ay~~~~~lt~eq~~~v~~rd~~~~i~~G~n~y~l~K----~~~~~g~~~~~~~a~m~g~t~e~f~ 109 (444)
T PRK13372 34 LMKADNRARFKADEGAYLDEWALNEAQKQAVLAIDLNQCIAEGGNIYFLAK----IGATDGKSFQQMAGSMTGLSEAAYR 109 (444)
T ss_pred hcCHHHHHHHhhCHHHHHHHcCCCHHHHHHHHhhhHHHHHHcCchHHHHHH----HHHHcCCcHHHHHHhhcCCCHHHHH
Confidence 333445677764 445678999999999888653 5677888 56655442 3344455567778888899999998
Q ss_pred hhhccc
Q psy2669 98 TNLVKP 103 (166)
Q Consensus 98 ~~L~~~ 103 (166)
..+...
T Consensus 110 ~~~~~~ 115 (444)
T PRK13372 110 DMMIGG 115 (444)
T ss_pred HHHHhC
Confidence 877654
No 76
>PF07126 DUF1379: Protein of unknown function (DUF1379); InterPro: IPR009809 This family consists of several hypothetical bacterial proteins of around 180 residues in length. The function of this family is unknown.
Probab=27.97 E-value=88 Score=23.54 Aligned_cols=35 Identities=14% Similarity=0.308 Sum_probs=28.1
Q ss_pred CCCcHHHHHHHHHHHHHcCCCHHHHHHH-HHHHHHH
Q psy2669 23 GMDDGEEFQLTDQAFDILGFTKEEKENV-YKITASV 57 (166)
Q Consensus 23 ~~dD~~~f~~~~~al~~lg~~~~e~~~i-~~ilaaI 57 (166)
.+||++-|....+.+..+.++++++..| +..+||.
T Consensus 30 svdDA~~y~~f~E~l~~l~ls~~~~~elaLnA~Aa~ 65 (153)
T PF07126_consen 30 SVDDAALYQTFKEQLRQLDLSDAQRAELALNAVAAK 65 (153)
T ss_pred cHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence 4789999999999999999999988776 3344444
No 77
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=27.79 E-value=95 Score=18.93 Aligned_cols=22 Identities=23% Similarity=0.327 Sum_probs=15.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHHH
Q psy2669 32 LTDQAFDILGFTKEEKENVYKI 53 (166)
Q Consensus 32 ~~~~al~~lg~~~~e~~~i~~i 53 (166)
.....++.+|||=+|+..++.+
T Consensus 5 ~~I~~~r~lGfsL~eI~~~l~l 26 (65)
T PF09278_consen 5 QFIRRLRELGFSLEEIRELLEL 26 (65)
T ss_dssp HHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHhc
Confidence 4567889999999998888643
No 78
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=27.15 E-value=68 Score=18.69 Aligned_cols=22 Identities=23% Similarity=0.184 Sum_probs=16.0
Q ss_pred hhHHHHHhhhCCCHHHHHhhhc
Q psy2669 80 EEGDRVSKLLGVDSQQLYTNLV 101 (166)
Q Consensus 80 ~~l~~~a~LLgv~~~~L~~~L~ 101 (166)
-.+..+|..+||+...|.+.+.
T Consensus 17 ~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 17 MSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp S-HHHHHHHHT--HHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHc
Confidence 5688999999999999987653
No 79
>PF02376 CUT: CUT domain; InterPro: IPR003350 A class, also called ONECUT, of homeodomain proteins. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain (IPR001356 from INTERPRO), often found downstream of the CUT domain. Proteins display two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the cut domain, and two modes of transcriptional stimulation, which hinge on the homeodomain [].; GO: 0003677 DNA binding; PDB: 1WH6_A 2D5V_A 2CSF_A 1X2L_A 2O49_A 2O4A_A 1YSE_A 1S7E_A 1WIZ_A 1WH8_A.
Probab=26.74 E-value=52 Score=22.24 Aligned_cols=42 Identities=21% Similarity=0.192 Sum_probs=26.1
Q ss_pred HHHhhhCCCHHHHHhhhccceeeeCCeeEEecCChhHHHHhhhhhhHHHHHHHHHHHH
Q psy2669 84 RVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNVNQQAFDILGFTKEEKENVYKITA 141 (166)
Q Consensus 84 ~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~~~A~~~rdalaK~lY~~LF~wiV 141 (166)
.+...||.+...|.+.|..++ |.+ ..-.-.|.+|-|+++|+-
T Consensus 32 Fa~~vL~rsqgtlsdlL~~PK----------pW~------~L~~~gre~y~RM~nWL~ 73 (87)
T PF02376_consen 32 FAKKVLNRSQGTLSDLLRKPK----------PWN------KLKPKGREPYIRMYNWLS 73 (87)
T ss_dssp HHHHTTSS-HHHHHHHHHSCC----------TTC------HHHHHHHHHHHHHHHHHC
T ss_pred HHHHHhccChhHHHHHhCCCC----------CHH------HcCccccHHHHHHHHHhc
Confidence 344567777777777666542 222 222246889999999984
No 80
>COG0599 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]
Probab=26.52 E-value=1.1e+02 Score=21.71 Aligned_cols=26 Identities=27% Similarity=0.212 Sum_probs=20.1
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy2669 30 FQLTDQAFDILGFTKEEKENVYKITAS 56 (166)
Q Consensus 30 f~~~~~al~~lg~~~~e~~~i~~ilaa 56 (166)
--.++.|++. |.+++|+.+++.+++.
T Consensus 74 ~~H~~~Al~~-GaT~eEI~e~i~~~a~ 99 (124)
T COG0599 74 KVHVRAALEN-GATKEEIAEAIAVAAI 99 (124)
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHHHH
Confidence 3468899988 9999998888666543
No 81
>cd08815 Death_TNFRSF25_DR3 Death domain of Tumor Necrosis Factor Receptor superfamily 25. Death Domain (DD) found in Tumor Necrosis Factor (TNF) receptor superfamily 25 (TNFRSF25), also known as TRAMP (TNF receptor-related apoptosis-mediating protein), LARD, APO-3, WSL-1, or DR3 (Death Receptor-3). TNFRSF25 is primarily expressed in T cells, is activated by binding to its ligand TL1A, and plays an important role in T-cell function. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=26.42 E-value=65 Score=21.47 Aligned_cols=25 Identities=24% Similarity=0.231 Sum_probs=19.1
Q ss_pred cHHHHHHHHHHHHHcCCCHHHHHHH
Q psy2669 26 DGEEFQLTDQAFDILGFTKEEKENV 50 (166)
Q Consensus 26 D~~~f~~~~~al~~lg~~~~e~~~i 50 (166)
|.-.|....+-|+.||+++.++...
T Consensus 7 D~VP~~~wk~F~R~LGLsdn~Ie~~ 31 (77)
T cd08815 7 DAVPARRWKEFVRTLGLREAEIEAV 31 (77)
T ss_pred ccCChHHHHHHHHHcCCcHhHHHHH
Confidence 4445777788899999999886654
No 82
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=25.94 E-value=1.1e+02 Score=19.09 Aligned_cols=21 Identities=19% Similarity=0.409 Sum_probs=12.5
Q ss_pred HHHHHHHHcCCCHHHHHHHHH
Q psy2669 32 LTDQAFDILGFTKEEKENVYK 52 (166)
Q Consensus 32 ~~~~al~~lg~~~~e~~~i~~ 52 (166)
++.+.|..+||+.+.+-++|+
T Consensus 11 ~lVd~F~~mGF~~dkVvevlr 31 (55)
T PF09288_consen 11 DLVDQFENMGFERDKVVEVLR 31 (55)
T ss_dssp HHHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHcCCcHHHHHHHHH
Confidence 466777888888765555544
No 83
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=25.89 E-value=2.2e+02 Score=20.25 Aligned_cols=58 Identities=10% Similarity=0.044 Sum_probs=36.5
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCchhHHHHHhhhCCCHHHHH
Q psy2669 31 QLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLY 97 (166)
Q Consensus 31 ~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~ 97 (166)
..++......|++..+......|=-. ++++++ .+...++.+.+..+|..|||+++.|.
T Consensus 8 ~rlk~~R~~~gltq~~lA~~~gvs~~--~is~~E-------~g~~~p~~~~l~~la~~l~vs~~~l~ 65 (135)
T PRK09706 8 QRIRYRRKQLKLSQRSLAKAVKVSHV--SISQWE-------RDETEPTGKNLFALAKALQCSPTWLL 65 (135)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHH--HHHHHH-------cCCCCCCHHHHHHHHHHHCcCHHHHh
Confidence 45777888889998766655443211 111211 12234556779999999999998765
No 84
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=25.83 E-value=52 Score=19.24 Aligned_cols=21 Identities=24% Similarity=0.382 Sum_probs=17.1
Q ss_pred cCCchhHHHHHhhhCCCHHHH
Q psy2669 76 PDGTEEGDRVSKLLGVDSQQL 96 (166)
Q Consensus 76 v~~~~~l~~~a~LLgv~~~~L 96 (166)
.++.+.+..+|+.||++.+.|
T Consensus 35 ~~~~~~~~~ia~~l~~~~~~l 55 (55)
T PF01381_consen 35 NPSLDTLKKIAKALGVSPEYL 55 (55)
T ss_dssp TSBHHHHHHHHHHHTSEHHHH
T ss_pred CCCHHHHHHHHHHHCCCHHHC
Confidence 345678999999999998765
No 85
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=25.80 E-value=1.1e+02 Score=24.36 Aligned_cols=82 Identities=12% Similarity=0.159 Sum_probs=40.9
Q ss_pred CC-CHHHHHHHHHHHHHHHhhcCceEeecCCCCccccC-CchhHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCCh
Q psy2669 41 GF-TKEEKENVYKITASVMHMGGMKFKQRGREEQAEPD-GTEEGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNV 118 (166)
Q Consensus 41 g~-~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~-~~~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~ 118 (166)
|+ ++++...||.-++.- +.|.+. .+. +...+...|+ |.+.+++..+++... ..+++.+ +.
T Consensus 66 GY~Pee~~~~IF~Alc~a-----~~~dp~------~~r~dA~~l~~~a~--~~s~~~i~~~l~~~~-~~~~~~l----~l 127 (214)
T TIGR03060 66 GYRPEEHLDALFDALCNS-----NGFDPE------QLREDAKQLLEQAK--GKGLDEILSWLTQAN-LSNGGGD----TL 127 (214)
T ss_pred CCCChHHHHHHHHHHHHh-----cCCCHH------HHHHHHHHHHHHHh--cCCHHHHHHHHhccc-cCCcchh----HH
Confidence 77 556777787775432 222221 111 1222333333 778899999998665 1111111 10
Q ss_pred hHHHHhhhhhhHHHHHHHHHHHHHHH
Q psy2669 119 NQQAFDILGFTKEEKENVYKITASVM 144 (166)
Q Consensus 119 ~~A~~~rdalaK~lY~~LF~wiV~~I 144 (166)
...-+=.|.-|+|||.-=+-++
T Consensus 128 ----~~ia~n~~f~YSRl~AIGL~~L 149 (214)
T TIGR03060 128 ----QGIAGRHKFKYSRLFAIGLYSL 149 (214)
T ss_pred ----HHHhcCCCcchHHHHHHHHHHH
Confidence 1111224556999988644443
No 86
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=25.76 E-value=75 Score=19.50 Aligned_cols=22 Identities=32% Similarity=0.258 Sum_probs=17.5
Q ss_pred HHHHHhhhCCCHHHHHhhhccc
Q psy2669 82 GDRVSKLLGVDSQQLYTNLVKP 103 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L~~~ 103 (166)
+..+|+++||++..|..+.-..
T Consensus 3 i~eva~~~gvs~~tlr~y~~~g 24 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYEREG 24 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHTT
T ss_pred HHHHHHHHCcCHHHHHHHHHhc
Confidence 4679999999999998775433
No 87
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=25.75 E-value=40 Score=23.32 Aligned_cols=28 Identities=7% Similarity=0.157 Sum_probs=22.3
Q ss_pred CCCcHHHHHHHHHHHHHcCCCHHHHHHH
Q psy2669 23 GMDDGEEFQLTDQAFDILGFTKEEKENV 50 (166)
Q Consensus 23 ~~dD~~~f~~~~~al~~lg~~~~e~~~i 50 (166)
.+-+.-.+..+++..+.+|+++.+++.|
T Consensus 13 ~Ia~~~~~~~wK~faR~lglse~~Id~I 40 (97)
T cd08316 13 DIADVMTLKDVKKFVRKSGLSEPKIDEI 40 (97)
T ss_pred HHHHHcCHHHHHHHHHHcCCCHHHHHHH
Confidence 3345556778888999999999999887
No 88
>TIGR02675 tape_meas_nterm tape measure domain. Proteins containing this domain are strictly bacterial, including bacteriophage and prophage regions of bacterial genomes. Most members are 800 to 1800 amino acids long, making them among the longest predicted proteins of their respective phage genomes, where they are encoded in tail protein regions. This roughly 80-residue domain described here usually begins between residue 100 and 250. Many members are known or predicted to act as phage tail tape measure proteins, a minor tail component that regulates tail length.
Probab=25.59 E-value=1.6e+02 Score=19.05 Aligned_cols=68 Identities=15% Similarity=0.135 Sum_probs=49.9
Q ss_pred HHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHhhhcccee
Q psy2669 35 QAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYTNLVKPRI 105 (166)
Q Consensus 35 ~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~~L~~~~~ 105 (166)
+++...|.+.++...+..-++=.+--|-+.-.+-. ...=.-+..++.+|+=+|++..+|.+.+....+
T Consensus 3 ~a~~~~G~s~e~~~~~~~ql~Q~~~~Gkv~~ee~n---~~~e~~p~~~~~lAk~~G~t~~~l~~~~~~Gki 70 (75)
T TIGR02675 3 DAGAASGASAEEADGALIQLSQMLASGKLRGEEIN---SLLEALPGALQALAKAMGVTRGELRKMLSDGKL 70 (75)
T ss_pred hHHHHhCCCHHHHHHHHHHHHHHHHcCcccHHHHH---HHHHHhHHHHHHHHHHhCCCHHHHHHHHHCCCC
Confidence 57788899999999998888888888877633221 000013467888999999999999988766554
No 89
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=25.26 E-value=82 Score=18.09 Aligned_cols=22 Identities=23% Similarity=0.333 Sum_probs=16.5
Q ss_pred hhHHHHHhhhCCCHHHHHhhhc
Q psy2669 80 EEGDRVSKLLGVDSQQLYTNLV 101 (166)
Q Consensus 80 ~~l~~~a~LLgv~~~~L~~~L~ 101 (166)
..+..+|+.+||+...+.+.|-
T Consensus 22 ~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 22 MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp --HHHHHHHTTS-HHHHHHHHC
T ss_pred CCHHHHHHHHCcCHHHHHHHHh
Confidence 4578899999999999988763
No 90
>PRK13266 Thf1-like protein; Reviewed
Probab=24.98 E-value=1.3e+02 Score=24.10 Aligned_cols=84 Identities=13% Similarity=0.226 Sum_probs=41.6
Q ss_pred CC-CHHHHHHHHHHHHHHHhhcCceEeecCCCCcccc-CCchhHHHHHhhhCCCHHHHHhhhccceeeeCCeeEEecCCh
Q psy2669 41 GF-TKEEKENVYKITASVMHMGGMKFKQRGREEQAEP-DGTEEGDRVSKLLGVDSQQLYTNLVKPRIKVGNEFVTQGRNV 118 (166)
Q Consensus 41 g~-~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v-~~~~~l~~~a~LLgv~~~~L~~~L~~~~~~~~~e~~~~~~~~ 118 (166)
|+ ++++...||.-|+--+ .|.+. .+ .+...+...|+ |.+.+++..+|+...-..++ . .
T Consensus 66 GY~Pee~~~~IF~Alc~a~-----~~dp~------~~r~dA~~l~~~a~--~~s~~~i~~~l~~~~~~~~~-~------l 125 (225)
T PRK13266 66 GYRPEEHKDSIFNALCQAV-----GFDPE------QLRQDAERLLELAK--GKSLKEILSWLTQKALGEPG-G------L 125 (225)
T ss_pred CCCChHHHHHHHHHHHHHc-----CCCHH------HHHHHHHHHHHHHh--cCCHHHHHHHHhccccccch-h------H
Confidence 77 5567777877755332 22221 11 11122333333 78889999999865411110 0 1
Q ss_pred hHHHHhhhhhhHHHHHHHHHHHHHHH
Q psy2669 119 NQQAFDILGFTKEEKENVYKITASVM 144 (166)
Q Consensus 119 ~~A~~~rdalaK~lY~~LF~wiV~~I 144 (166)
......+-.=.+.-|+|||.-=+-++
T Consensus 126 ~~~l~~ia~~~~f~YSRl~AIGL~~L 151 (225)
T PRK13266 126 LATLLAIANNSKFKYSRLFAIGLYTL 151 (225)
T ss_pred HHHHHHHhcCCCCchHHHHHHHHHHH
Confidence 11112221225667999998644444
No 91
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=24.40 E-value=1.4e+02 Score=18.20 Aligned_cols=24 Identities=25% Similarity=0.120 Sum_probs=18.9
Q ss_pred HHHHHhhhCCCHHHHHhhhcccee
Q psy2669 82 GDRVSKLLGVDSQQLYTNLVKPRI 105 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L~~~~~ 105 (166)
+..+|+++||++..+..+.-...+
T Consensus 3 ~~eva~~~gvs~~tlr~~~~~gli 26 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYERIGLL 26 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCC
Confidence 467899999999999877654443
No 92
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=24.22 E-value=1e+02 Score=18.08 Aligned_cols=22 Identities=18% Similarity=0.232 Sum_probs=19.4
Q ss_pred HHHHHhhhCCCHHHHHhhhccc
Q psy2669 82 GDRVSKLLGVDSQQLYTNLVKP 103 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L~~~ 103 (166)
+..+|+..||+.....++|-.+
T Consensus 2 i~dIA~~agvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNGP 23 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTTC
T ss_pred HHHHHHHHCcCHHHHHHHHhCC
Confidence 5789999999999999999765
No 93
>PF11758 Bacteriocin_IIi: Aureocin-like type II bacteriocin; InterPro: IPR020968 This is a small family of type II bacteriocins usually encoded on a plasmid. Characteristically the members are small, cationic, rich in Lys and Try, and bring about a generalised membrane permeabilisation leading to leakage of ions. The family includes aureocin A, lacticins Q and Z, and BhtB [, ].
Probab=24.12 E-value=51 Score=20.11 Aligned_cols=12 Identities=0% Similarity=-0.119 Sum_probs=10.0
Q ss_pred HHHHHHHHHHhc
Q psy2669 135 NVYKITASVMHM 146 (166)
Q Consensus 135 ~LF~wiV~~IN~ 146 (166)
.-|+||+++|+.
T Consensus 36 ~a~dWI~~kI~~ 47 (51)
T PF11758_consen 36 MAIDWIVQKIKK 47 (51)
T ss_pred chHHHHHHHHHH
Confidence 458999999986
No 94
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=23.80 E-value=78 Score=19.51 Aligned_cols=19 Identities=26% Similarity=0.300 Sum_probs=16.0
Q ss_pred HHHHHhhhCCCHHHHHhhh
Q psy2669 82 GDRVSKLLGVDSQQLYTNL 100 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L 100 (166)
...+|+++||++..|..+-
T Consensus 3 i~evA~~~gvs~~tlR~~~ 21 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYE 21 (67)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4678999999999998764
No 95
>PF07804 HipA_C: HipA-like C-terminal domain; InterPro: IPR012893 The members of this entry are similar to a region close to the C terminus of the HipA protein expressed by various bacterial species (for example P23874 from SWISSPROT). This protein is known to be involved in high-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis []. When expressed alone, it is toxic to bacterial cells [], but it is usually tightly associated with HipB [], and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with cell division genes or their products []. ; PDB: 3AKL_D 3AKJ_B 3AKK_D 2WIU_C 3HZI_A 3DNT_B 3FBR_A 3DNU_A 3DNV_A.
Probab=23.35 E-value=1.4e+02 Score=19.14 Aligned_cols=41 Identities=10% Similarity=0.182 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHcCCC-HHHHHHHHHHHH-HH------HhhcCceEeec
Q psy2669 28 EEFQLTDQAFDILGFT-KEEKENVYKITA-SV------MHMGGMKFKQR 68 (166)
Q Consensus 28 ~~f~~~~~al~~lg~~-~~e~~~i~~ila-aI------LhLGNi~F~~~ 68 (166)
..|+.+.+++...+.. ..+...+|+.++ .+ .|++|+.|-..
T Consensus 20 ~s~~~~~~~l~~~~~~~~~~~~~l~~~~~fn~ligN~D~H~kN~s~l~~ 68 (79)
T PF07804_consen 20 PSYEDLAQALRQYSSDPAADVRELFRRLVFNYLIGNTDRHLKNFSFLYD 68 (79)
T ss_dssp -BHHHHHHHHCCSTTCHHHHHHHHHHHHHHHHHCTBS---CCCSEEEEE
T ss_pred cCHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHcCCcCCcCCEEEEEc
Confidence 6688899999998876 677777777653 33 38888888765
No 96
>PF10260 SAYSvFN: Uncharacterized conserved domain (SAYSvFN); InterPro: IPR019387 This domain of approximately 75 residues contains a highly conserved SATSv/iFN motif. The function is unknown but the domain is conserved from plants to humans.
Probab=23.28 E-value=82 Score=20.63 Aligned_cols=27 Identities=26% Similarity=0.454 Sum_probs=23.0
Q ss_pred CCCCccccccCCCCCCCCCCcHHHHHH
Q psy2669 6 NDIYDYYNVSQGKITIPGMDDGEEFQL 32 (166)
Q Consensus 6 ~~~~~y~yL~~~~~~~~~~dD~~~f~~ 32 (166)
++.+.|.--|.+|-.++|.=++++|+.
T Consensus 42 ge~SAYSVFN~~~~~i~Gtl~aE~~er 68 (71)
T PF10260_consen 42 GELSAYSVFNKGCERIPGTLTAEQFER 68 (71)
T ss_pred CCccchhhhCCCccccCCCCCHHHHHH
Confidence 357889999999989999889998874
No 97
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=23.27 E-value=75 Score=18.52 Aligned_cols=29 Identities=21% Similarity=0.284 Sum_probs=24.0
Q ss_pred cCCchhHHHHHhhhCCCHHHHHhhhccce
Q psy2669 76 PDGTEEGDRVSKLLGVDSQQLYTNLVKPR 104 (166)
Q Consensus 76 v~~~~~l~~~a~LLgv~~~~L~~~L~~~~ 104 (166)
-++.+....+|..+|++..++..++..++
T Consensus 24 ~P~~~~~~~la~~~~l~~~qV~~WF~nrR 52 (56)
T smart00389 24 YPSREEREELAAKLGLSERQVKVWFQNRR 52 (56)
T ss_pred CCCHHHHHHHHHHHCcCHHHHHHhHHHHh
Confidence 34667889999999999999998887664
No 98
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=23.04 E-value=71 Score=18.75 Aligned_cols=30 Identities=23% Similarity=0.286 Sum_probs=24.7
Q ss_pred cCCchhHHHHHhhhCCCHHHHHhhhcccee
Q psy2669 76 PDGTEEGDRVSKLLGVDSQQLYTNLVKPRI 105 (166)
Q Consensus 76 v~~~~~l~~~a~LLgv~~~~L~~~L~~~~~ 105 (166)
-++....+.+|..+|++..++..++..++.
T Consensus 24 ~P~~~~~~~la~~~~l~~~qV~~WF~nrR~ 53 (59)
T cd00086 24 YPSREEREELAKELGLTERQVKIWFQNRRA 53 (59)
T ss_pred CCCHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345677899999999999999999877653
No 99
>COG1924 Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism]
Probab=22.77 E-value=3.3e+02 Score=23.81 Aligned_cols=70 Identities=17% Similarity=0.125 Sum_probs=44.9
Q ss_pred CchhHHHHHhhhCCCHHHHHhhhccce--eeeCCeeEEecCC--hh-------HHHHhhhhhhHHHHHHHHHHHHHHHhc
Q psy2669 78 GTEEGDRVSKLLGVDSQQLYTNLVKPR--IKVGNEFVTQGRN--VN-------QQAFDILGFTKEEKENVYKITASVMHM 146 (166)
Q Consensus 78 ~~~~l~~~a~LLgv~~~~L~~~L~~~~--~~~~~e~~~~~~~--~~-------~A~~~rdalaK~lY~~LF~wiV~~IN~ 146 (166)
.-.=|+.+|+-||++-+++-+.=...+ +..++ ....... +- ...+..-+++.+++++.+..+..+++-
T Consensus 264 tGrFLE~~A~~Lgv~v~E~~~~A~~~~~~v~i~S-~CaVF~eSevi~~~~~G~~~EdI~AGl~~Sv~~~v~~~~~~~~~i 342 (396)
T COG1924 264 TGRFLEVIARRLGVDVEELGKLALKATPPVKINS-RCAVFAESEVISALAEGASPEDILAGLAYSVAENVAEKVIKRVDI 342 (396)
T ss_pred cchHHHHHHHHhCCCHHHHHHHHhcCCCCcccCC-eeEEEehHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHhhccCC
Confidence 346799999999999999966543322 22222 2222222 11 234667788888999999888888876
Q ss_pred cC
Q psy2669 147 GG 148 (166)
Q Consensus 147 ~~ 148 (166)
..
T Consensus 343 ~~ 344 (396)
T COG1924 343 EE 344 (396)
T ss_pred CC
Confidence 43
No 100
>PF03165 MH1: MH1 domain; InterPro: IPR003619 Mammalian dwarfins are phosphorylated in response to transforming growth factor beta and are implicated in control of cell growth []. The dwarfin family also includes the Drosophila protein MAD that is required for the function of decapentaplegic (DPP) and may play a role in DPP signalling. Drosophila Mad binds to DNA and directly mediates activation of vestigial by Dpp []. This domain is also found in nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF). This entry represents the MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localisation signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx [, , ].; GO: 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3QSV_A 1MHD_A 1OZJ_A 3KMP_B.
Probab=22.69 E-value=36 Score=23.85 Aligned_cols=46 Identities=13% Similarity=0.066 Sum_probs=24.5
Q ss_pred HHHHHhhhccceeeeCCeeEEecCCh--hHHHHhhhhhhHHHHHHHHHH
Q psy2669 93 SQQLYTNLVKPRIKVGNEFVTQGRNV--NQQAFDILGFTKEEKENVYKI 139 (166)
Q Consensus 93 ~~~L~~~L~~~~~~~~~e~~~~~~~~--~~A~~~rdalaK~lY~~LF~w 139 (166)
.+.|.+++.++.-. ...-+..|.+. .--...+..+...+|.|||.|
T Consensus 19 le~L~~Av~s~g~~-~t~CV~i~r~~dgrl~v~~~k~~phvl~crlwRw 66 (103)
T PF03165_consen 19 LEELLKAVESRGDP-PTKCVTIPRSLDGRLQVSGRKGLPHVLYCRLWRW 66 (103)
T ss_dssp HHHHHHHHHCTTTS-TS---EEE--TTS-EEETTEEE-HHHHHHHHHT-
T ss_pred HHHHHHHHhcCCCC-CCCcEEecCccCccccccccccCceEEEEEEech
Confidence 47888888865311 12234444322 111246778889999999999
No 101
>PF08809 DUF1799: Phage related hypothetical protein (DUF1799); InterPro: IPR014915 This entry is represented by the Bacteriophage TLS, TfmB. The characteristics of the protein distribution suggest prophage matches.
Probab=22.51 E-value=1.5e+02 Score=19.83 Aligned_cols=27 Identities=11% Similarity=0.401 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2669 28 EEFQLTDQAFDILGFTKEEKENVYKIT 54 (166)
Q Consensus 28 ~~f~~~~~al~~lg~~~~e~~~i~~il 54 (166)
=+|..+...|+..|++.++..++|.=|
T Consensus 46 LDY~al~~~~~~~gi~~~~~~~~~~~l 72 (83)
T PF08809_consen 46 LDYGALPAVMDLMGIDDEDRPELFDDL 72 (83)
T ss_pred ccHHHHHHHHHHcCCChhhHHHHHHHH
Confidence 357888899999999988887777543
No 102
>PF04609 MCR_C: Methyl-coenzyme M reductase operon protein C; InterPro: IPR007687 Methyl-coenzyme M reductase (MCR) catalyses the reduction of methyl-coenzyme M (CH3-SCoM) and coenzyme B (HS-CoB) to methane and the corresponding heterosulphide CoM-S-S-CoB (2.8.4.1 from EC), the final step in methane biosynthesis. This reaction proceeds under anaerobic conditions by methanogenic Archaea [], and requires a nickel-porphinoid prosthetic group, coenzyme F430, which is in the EPR-detectable Ni(I) oxidation state in the active enzyme. Studies on a catalytically inactive enzyme aerobically co-crystallized with coenzyme M displayed a fully occupied coenzyme M-binding site with no alternate conformations. The binding of coenzyme M appears to induce specific conformational changes that suggests a molecular mechanism by which the enzyme ensures that methyl-coenzyme M enters the substrate channel prior to coenzyme B, as required by the active-site geometry []. MCR is a hexamer composed of 2 alpha, 2 beta, and 2 gamma subunits with two identical nickel porphinoid active sites, which form two long active site channels with F430 embedded at the bottom [, ]. Genes encoding the beta (mcrB) and gamma (mcrG) subunits of MCR are separated by two open reading frames coding for two proteins C and D [, ]. The function of proteins C and D is unknown. This entry represents protein C.; GO: 0003824 catalytic activity, 0015948 methanogenesis
Probab=22.49 E-value=12 Score=30.68 Aligned_cols=27 Identities=33% Similarity=0.610 Sum_probs=23.8
Q ss_pred HHcCCCHHHHHHHHHHHHHHHhhcCce
Q psy2669 38 DILGFTKEEKENVYKITASVMHMGGMK 64 (166)
Q Consensus 38 ~~lg~~~~e~~~i~~ilaaILhLGNi~ 64 (166)
.+.|++++|++.|-+==.||+|+||+.
T Consensus 115 ~~~gl~~~E~~~I~~Hd~AV~~~Gn~~ 141 (268)
T PF04609_consen 115 RIFGLTPKEIEQINEHDLAVFHLGNFK 141 (268)
T ss_pred CccCCCHHHHHHHhhcCEEEEEeCCHH
Confidence 456899999999998889999999985
No 103
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=22.35 E-value=67 Score=29.40 Aligned_cols=58 Identities=17% Similarity=0.288 Sum_probs=40.9
Q ss_pred cCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHhhhcc
Q psy2669 40 LGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYTNLVK 102 (166)
Q Consensus 40 lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~~L~~ 102 (166)
+|+..----.+++||-||-..|+..-.+.. .. ..+...+.+.+++|++++.+.++|..
T Consensus 510 ~g~~~PVtP~~~rVL~Ai~~~g~lyvKe~K----vR-i~pk~~ke~~K~sgL~~e~f~kaL~~ 567 (591)
T PF04458_consen 510 LGFGFPVTPTIYRVLKAIREVGTLYVKEKK----VR-ILPKNIKEAIKLSGLTPEEFKKALEV 567 (591)
T ss_pred cccCCCCCHHHHHHHHHHHHhhhhhhhhhh----hh-cCccchHHHHHhcCCCHHHHHHHHHH
Confidence 344433456789999999999998654331 11 12344566889999999999999864
No 104
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=22.27 E-value=1.2e+02 Score=18.52 Aligned_cols=22 Identities=14% Similarity=0.158 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHhccCccccc
Q psy2669 132 EKENVYKITASVMHMGGMKFKQ 153 (166)
Q Consensus 132 lY~~LF~wiV~~IN~~~~~~~~ 153 (166)
+|..++++|...|-.+..++.+
T Consensus 1 l~~~i~~~l~~~I~~g~~~~g~ 22 (64)
T PF00392_consen 1 LYEQIYDQLRQAILSGRLPPGD 22 (64)
T ss_dssp HHHHHHHHHHHHHHTTSS-TTS
T ss_pred CHHHHHHHHHHHHHcCCCCCCC
Confidence 6889999999999988776644
No 105
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=21.72 E-value=1.2e+02 Score=22.90 Aligned_cols=59 Identities=8% Similarity=0.216 Sum_probs=38.3
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCceEeecCCCCccccCCchhHHHHHhhhCCCHHHHHh
Q psy2669 31 QLTDQAFDILGFTKEEKENVYKITASVMHMGGMKFKQRGREEQAEPDGTEEGDRVSKLLGVDSQQLYT 98 (166)
Q Consensus 31 ~~~~~al~~lg~~~~e~~~i~~ilaaILhLGNi~F~~~~~~~~~~v~~~~~l~~~a~LLgv~~~~L~~ 98 (166)
..++.+.+..|++..+......+-.+ .+++++ .....++...+..+|..||++.+.|..
T Consensus 10 ~~l~~~R~~~glt~~elA~~~gis~~--~is~~E-------~g~~~p~~~~l~~ia~~l~v~~~~l~~ 68 (185)
T PRK09943 10 KRLSEIRQQQGLSQRRAAELSGLTHS--AISTIE-------QDKVSPAISTLQKLLKVYGLSLSEFFS 68 (185)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHH--HHHHHH-------cCCCCCCHHHHHHHHHHhCCCHHHHcc
Confidence 56778888999998776655433111 122222 112234567899999999999988763
No 106
>PF05099 TerB: Tellurite resistance protein TerB; InterPro: IPR007791 The prokaryotic heat shock protein DnaJ interacts with the chaperone hsp70-like DnaK protein []. Structurally, the DnaJ protein consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acids, a glycine-rich region ('G' domain') of about 30 residues, a central domain containing four repeats of a CXXCXGXG motif ('CRR' domain) and a C-terminal region of 120 to 170 residues. Direct interaction between DnaK and djlA is needed for the induction of the wcaABCDE operon which is involved in the synthesis of a colanic acid polysaccharide capsule. The colanic acid capsule may help the bacterium survive conditions outside the host [, ]; PDB: 2H5N_D 2JXU_A.
Probab=21.23 E-value=1.2e+02 Score=21.41 Aligned_cols=20 Identities=20% Similarity=0.351 Sum_probs=13.2
Q ss_pred chhHHHHHhhhCCCHHHHHh
Q psy2669 79 TEEGDRVSKLLGVDSQQLYT 98 (166)
Q Consensus 79 ~~~l~~~a~LLgv~~~~L~~ 98 (166)
...+..++.+||++.+++..
T Consensus 118 ~~~l~~ia~~L~i~~~~~~~ 137 (140)
T PF05099_consen 118 QEFLRRIAEALGISEEDFQR 137 (140)
T ss_dssp HHHHHHHHHHCTS-SS----
T ss_pred HHHHHHHHHHcCCCHHHHhc
Confidence 46799999999999887754
No 107
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=21.20 E-value=98 Score=19.14 Aligned_cols=19 Identities=21% Similarity=0.139 Sum_probs=15.9
Q ss_pred HHHHHhhhCCCHHHHHhhh
Q psy2669 82 GDRVSKLLGVDSQQLYTNL 100 (166)
Q Consensus 82 l~~~a~LLgv~~~~L~~~L 100 (166)
+..+|+++||++..|..+-
T Consensus 3 i~e~A~~~gVs~~tlr~ye 21 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWE 21 (68)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4679999999999998664
No 108
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=20.90 E-value=1.6e+02 Score=15.86 Aligned_cols=19 Identities=21% Similarity=0.331 Sum_probs=12.8
Q ss_pred HHHHHHHHcCCCHHHHHHH
Q psy2669 32 LTDQAFDILGFTKEEKENV 50 (166)
Q Consensus 32 ~~~~al~~lg~~~~e~~~i 50 (166)
+..+.|..+||+.++....
T Consensus 3 ~~v~~L~~mGf~~~~~~~A 21 (38)
T cd00194 3 EKLEQLLEMGFSREEARKA 21 (38)
T ss_pred HHHHHHHHcCCCHHHHHHH
Confidence 4566777889997655443
No 109
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=20.73 E-value=1.1e+02 Score=17.48 Aligned_cols=22 Identities=23% Similarity=0.276 Sum_probs=16.2
Q ss_pred hhHHHHHhhhCCCHHHHHhhhc
Q psy2669 80 EEGDRVSKLLGVDSQQLYTNLV 101 (166)
Q Consensus 80 ~~l~~~a~LLgv~~~~L~~~L~ 101 (166)
.....+|+.|||+...+.+++-
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 3567899999999998888764
No 110
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=20.16 E-value=60 Score=19.24 Aligned_cols=28 Identities=25% Similarity=0.369 Sum_probs=22.6
Q ss_pred CCchhHHHHHhhhCCCHHHHHhhhccce
Q psy2669 77 DGTEEGDRVSKLLGVDSQQLYTNLVKPR 104 (166)
Q Consensus 77 ~~~~~l~~~a~LLgv~~~~L~~~L~~~~ 104 (166)
++.+..+.+|.-|||+...+..++..+.
T Consensus 25 p~~~~~~~la~~l~l~~~~V~~WF~nrR 52 (57)
T PF00046_consen 25 PSKEEREELAKELGLTERQVKNWFQNRR 52 (57)
T ss_dssp CHHHHHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred ccccccccccccccccccccccCHHHhH
Confidence 3456788899999999999998887654
No 111
>PF13105 DUF3959: Protein of unknown function (DUF3959)
Probab=20.15 E-value=1e+02 Score=24.21 Aligned_cols=18 Identities=17% Similarity=0.043 Sum_probs=15.1
Q ss_pred hhhHHHHHHHHHHHHHHH
Q psy2669 127 GFTKEEKENVYKITASVM 144 (166)
Q Consensus 127 alaK~lY~~LF~wiV~~I 144 (166)
-+||-+|+|+-+||..-+
T Consensus 36 YfaKk~ySRiCSWiAYap 53 (239)
T PF13105_consen 36 YFAKKIYSRICSWIAYAP 53 (239)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 379999999999997643
Done!