Query psy18112
Match_columns 107
No_of_seqs 152 out of 1040
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 22:50:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy18112.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/18112hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00014 myosin-A; Provisional 100.0 7.3E-33 1.6E-37 228.7 7.2 100 1-105 261-364 (821)
2 COG5022 Myosin heavy chain [Cy 100.0 4.5E-33 9.8E-38 234.9 5.1 100 1-105 232-336 (1463)
3 cd01381 MYSc_type_VII Myosin m 100.0 1.2E-31 2.5E-36 218.2 7.4 100 1-105 162-266 (671)
4 cd01380 MYSc_type_V Myosin mot 100.0 1.2E-31 2.6E-36 218.8 7.4 100 1-105 168-272 (691)
5 cd01383 MYSc_type_VIII Myosin 100.0 1.2E-31 2.5E-36 218.4 7.3 101 1-106 167-272 (677)
6 cd01377 MYSc_type_II Myosin mo 100.0 1.5E-31 3.3E-36 218.2 7.9 100 1-105 177-281 (693)
7 cd01384 MYSc_type_XI Myosin mo 100.0 4E-31 8.7E-36 215.2 7.5 99 1-105 168-271 (674)
8 cd01387 MYSc_type_XV Myosin mo 100.0 3.7E-31 8E-36 215.5 7.2 101 1-106 163-268 (677)
9 cd01378 MYSc_type_I Myosin mot 100.0 4.5E-31 9.7E-36 214.9 7.6 100 1-105 165-269 (674)
10 cd01385 MYSc_type_IX Myosin mo 100.0 8.1E-31 1.8E-35 213.9 7.9 101 1-106 173-278 (692)
11 cd00124 MYSc Myosin motor doma 100.0 8.8E-31 1.9E-35 213.4 7.8 101 1-106 163-268 (679)
12 smart00242 MYSc Myosin. Large 100.0 1.5E-30 3.2E-35 212.0 7.6 101 1-106 171-276 (677)
13 cd01382 MYSc_type_VI Myosin mo 100.0 1.6E-30 3.4E-35 212.9 7.6 100 1-105 167-297 (717)
14 KOG0164|consensus 100.0 1.8E-30 4E-35 208.8 5.8 99 2-105 176-279 (1001)
15 PF00063 Myosin_head: Myosin h 100.0 8.5E-30 1.8E-34 207.6 6.9 101 1-106 166-271 (689)
16 cd01386 MYSc_type_XVIII Myosin 100.0 1.2E-29 2.5E-34 208.8 7.6 101 1-106 164-270 (767)
17 cd01379 MYSc_type_III Myosin m 100.0 1.6E-29 3.4E-34 205.3 7.2 100 1-105 163-272 (653)
18 KOG0162|consensus 100.0 3.2E-29 6.9E-34 202.1 5.0 99 2-105 184-287 (1106)
19 KOG0161|consensus 99.9 3.7E-27 7.9E-32 205.0 5.0 101 1-106 251-356 (1930)
20 KOG0163|consensus 99.9 1.5E-25 3.3E-30 181.6 4.5 100 1-105 220-350 (1259)
21 KOG0160|consensus 99.9 3.6E-25 7.7E-30 182.4 6.2 99 1-105 172-275 (862)
22 KOG4229|consensus 99.8 1.8E-19 4E-24 151.6 1.9 100 1-105 225-330 (1062)
23 PF07499 RuvA_C: RuvA, C-termi 83.7 1.7 3.7E-05 23.8 2.9 25 76-100 3-27 (47)
24 PF11181 YflT: Heat induced st 62.9 10 0.00022 23.9 2.9 28 78-105 72-99 (103)
25 smart00027 EH Eps15 homology d 61.4 12 0.00027 22.9 3.1 30 73-102 26-55 (96)
26 PF13833 EF-hand_8: EF-hand do 60.5 16 0.00036 19.6 3.2 27 76-102 7-36 (54)
27 PF09288 UBA_3: Fungal ubiquit 60.4 8.3 0.00018 22.2 1.9 29 78-106 11-39 (55)
28 cd00052 EH Eps15 homology doma 56.8 19 0.00041 19.8 3.1 27 75-101 17-43 (67)
29 PF10440 WIYLD: Ubiquitin-bind 55.0 20 0.00044 21.2 3.0 25 74-98 9-33 (65)
30 PF02119 FlgI: Flagellar P-rin 54.4 18 0.00039 28.2 3.5 35 72-106 301-336 (342)
31 PRK13908 putative recombinatio 51.1 18 0.0004 26.1 2.8 31 73-103 173-203 (204)
32 PF08671 SinI: Anti-repressor 48.7 29 0.00063 17.3 2.6 25 74-98 3-27 (30)
33 PF01244 Peptidase_M19: Membra 44.8 28 0.0006 26.5 3.2 31 67-97 280-310 (320)
34 COG2355 Zn-dependent dipeptida 42.9 27 0.00059 26.9 2.8 32 67-98 269-300 (313)
35 KOG0064|consensus 39.4 20 0.00043 30.2 1.7 69 32-102 524-593 (728)
36 PF01152 Bac_globin: Bacterial 39.2 41 0.0009 21.2 3.0 24 77-100 87-110 (120)
37 PF09278 MerR-DNA-bind: MerR, 38.3 37 0.00079 19.1 2.4 22 78-99 5-26 (65)
38 cd01301 rDP_like renal dipepti 37.3 38 0.00082 25.7 2.9 31 68-98 273-303 (309)
39 PRK05303 flgI flagellar basal 36.6 50 0.0011 26.1 3.4 35 72-106 326-361 (367)
40 PF11103 DUF2887: Protein of u 35.8 33 0.00072 24.7 2.2 28 30-57 3-32 (200)
41 cd08315 Death_TRAILR_DR4_DR5 D 33.9 42 0.00092 21.1 2.3 25 73-97 16-40 (96)
42 PRK12789 flgI flagellar basal 32.5 58 0.0013 25.7 3.3 33 74-106 328-361 (367)
43 cd08313 Death_TNFR1 Death doma 31.5 51 0.0011 20.1 2.3 22 75-96 10-31 (80)
44 cd00194 UBA Ubiquitin Associat 31.1 65 0.0014 16.0 2.4 22 78-99 3-24 (38)
45 cd08784 Death_DRs Death Domain 31.1 54 0.0012 19.7 2.3 23 75-97 10-32 (79)
46 smart00165 UBA Ubiquitin assoc 31.1 66 0.0014 15.9 2.4 22 78-99 3-24 (37)
47 PF03979 Sigma70_r1_1: Sigma-7 30.7 69 0.0015 19.3 2.8 27 75-101 23-49 (82)
48 PRK14606 ruvA Holliday junctio 29.5 59 0.0013 23.0 2.7 26 75-100 142-167 (188)
49 cd08316 Death_FAS_TNFRSF6 Deat 29.5 34 0.00074 21.7 1.3 28 70-97 14-41 (97)
50 PF08809 DUF1799: Phage relate 27.6 72 0.0016 19.6 2.5 28 72-99 44-71 (83)
51 PRK14604 ruvA Holliday junctio 27.4 68 0.0015 22.8 2.7 25 76-100 149-173 (195)
52 PHA02414 hypothetical protein 26.2 34 0.00073 22.1 0.8 12 25-36 56-67 (111)
53 PRK14603 ruvA Holliday junctio 26.0 74 0.0016 22.6 2.6 26 75-100 151-176 (197)
54 PF02526 GBP_repeat: Glycophor 25.0 48 0.001 17.2 1.1 15 27-41 21-35 (38)
55 PRK14600 ruvA Holliday junctio 24.9 80 0.0017 22.3 2.7 26 75-100 144-169 (186)
56 PRK00116 ruvA Holliday junctio 24.7 81 0.0018 22.1 2.7 25 76-100 149-173 (192)
57 PF07126 DUF1379: Protein of u 23.9 77 0.0017 21.8 2.3 28 69-96 30-57 (153)
58 PRK13901 ruvA Holliday junctio 23.9 1E+02 0.0022 22.1 3.0 26 75-100 143-168 (196)
59 COG0599 Uncharacterized homolo 23.8 95 0.0021 20.0 2.7 24 76-100 74-97 (124)
60 cd08815 Death_TNFRSF25_DR3 Dea 23.4 83 0.0018 19.2 2.2 23 73-95 8-30 (77)
61 PF12616 DUF3775: Protein of u 22.8 77 0.0017 19.2 1.9 18 87-104 12-29 (75)
62 TIGR00084 ruvA Holliday juncti 22.7 89 0.0019 22.1 2.5 26 75-100 146-171 (191)
63 PF05054 DUF673: Protein of un 22.6 90 0.0019 24.6 2.7 31 70-100 231-261 (357)
64 PF03874 RNA_pol_Rpb4: RNA pol 22.5 1.4E+02 0.003 18.8 3.3 31 69-99 52-82 (117)
65 cd04777 HTH_MerR-like_sg1 Heli 22.5 1.1E+02 0.0024 19.1 2.7 27 75-101 43-69 (107)
66 PF13877 RPAP3_C: Potential Mo 21.5 1E+02 0.0022 18.7 2.4 35 72-107 45-80 (94)
67 COG4365 Uncharacterized protei 21.2 96 0.0021 25.3 2.6 29 73-101 483-511 (537)
68 PRK14602 ruvA Holliday junctio 21.1 1E+02 0.0023 21.9 2.7 26 75-100 154-179 (203)
69 cd00807 GlnRS_core catalytic c 20.7 2.2E+02 0.0047 21.1 4.3 24 79-102 189-212 (238)
70 cd08330 CARD_ASC_NALP1 Caspase 20.5 70 0.0015 19.4 1.4 25 23-47 57-81 (82)
71 cd01671 CARD Caspase activatio 20.0 77 0.0017 18.3 1.5 19 22-40 54-72 (80)
No 1
>PTZ00014 myosin-A; Provisional
Probab=99.97 E-value=7.3e-33 Score=228.67 Aligned_cols=100 Identities=23% Similarity=0.338 Sum_probs=96.6
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCccccccCCchhhhhHHHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHTCYTVATTSVDTIFPSSR 80 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~~~~~~~~~d~~~f~~l~ 80 (107)
|+||+|++|| |||||||+|++||||||||||||+|++++++++|+|.++..|+| |+++|.+++++||+++|++++
T Consensus 261 i~Ga~I~~YL---LEKSRVv~q~~gERNfHIFYqLl~G~~~~~~~~l~L~~~~~y~y--L~~~~~~~~~~dD~~~f~~~~ 335 (821)
T PTZ00014 261 IRYGSIVAFL---LEKSRVVTQEDDERSYHIFYQLLKGANDEMKEKYKLKSLEEYKY--INPKCLDVPGIDDVKDFEEVM 335 (821)
T ss_pred EeeEEEEEEe---ccCceeeecCCCCCCEeHHHHHHhCCCHHHHHHcCCCChHhccc--cCCCCccCCCCchHHHHHHHH
Confidence 5799999999 99999999999999999999999999999999999999999999 998888899999999999999
Q ss_pred HhhccCCCChHHHHHHHHHH----hcCCC
Q psy18112 81 RDYDPTDEPLREEDRIWFRE----ELGKL 105 (107)
Q Consensus 81 ~al~~lGf~~~e~~~I~~il----~~~~~ 105 (107)
+||++|||+++|+..||+|| .|||+
T Consensus 336 ~A~~~lg~s~~e~~~If~ilaaILhLGNi 364 (821)
T PTZ00014 336 ESFDSMGLSESQIEDIFSILSGVLLLGNV 364 (821)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHhhcce
Confidence 99999999999999999987 89987
No 2
>COG5022 Myosin heavy chain [Cytoskeleton]
Probab=99.97 E-value=4.5e-33 Score=234.89 Aligned_cols=100 Identities=26% Similarity=0.424 Sum_probs=94.9
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCc-cccccCCchhhhhHHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHT-CYTVATTSVDTIFPSS 79 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~-~~~~~~~~d~~~f~~l 79 (107)
|+||.|++|| |||||||+|..+||||||||||++|.+...++.+++.+|.+|.| ++++ |..++|+||+++|+.|
T Consensus 232 I~GA~I~~YL---LEKSRVV~Q~~~ERNYHIFYQll~G~~~~~k~~~~~~~~~dY~Y--l~~~~~~~I~gIdD~kefk~t 306 (1463)
T COG5022 232 ICGAKIETYL---LEKSRVVHQNKNERNYHIFYQLLAGDPEELKKLLLLQNPKDYIY--LSQGGCDKIDGIDDAKEFKIT 306 (1463)
T ss_pred eechhhhhhh---hhhhhhccCCCCccchhhhhhHhcCChHHHHHHhhccChHhhHh--HhhcCCCcCCCcccHHHHHHH
Confidence 6899999999 99999999999999999999999997777778888889999999 9998 8899999999999999
Q ss_pred HHhhccCCCChHHHHHHHHHH----hcCCC
Q psy18112 80 RRDYDPTDEPLREEDRIWFRE----ELGKL 105 (107)
Q Consensus 80 ~~al~~lGf~~~e~~~I~~il----~~~~~ 105 (107)
++||+++||+++|+..||+|| ++|||
T Consensus 307 ~~AlktiGi~~eeq~~IF~iLAaILhiGNI 336 (1463)
T COG5022 307 LDALKTIGIDEEEQDQIFKILAAILHIGNI 336 (1463)
T ss_pred HHHHHHhCCChHHHHHHHHHHHHHHhhcce
Confidence 999999999999999999987 89987
No 3
>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=99.97 E-value=1.2e-31 Score=218.24 Aligned_cols=100 Identities=25% Similarity=0.341 Sum_probs=95.6
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCc-cccccCCchhhhhHHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHT-CYTVATTSVDTIFPSS 79 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~-~~~~~~~~d~~~f~~l 79 (107)
|+||+|++|| ||||||++|++|||||||||||++|++++++++|+|.++..|+| |+++ +..+++++|+++|+++
T Consensus 162 i~Ga~i~~yL---LEksRV~~q~~gERnfHIFYqLl~g~~~~~~~~l~L~~~~~y~y--L~~~~~~~~~~~dD~~~f~~~ 236 (671)
T cd01381 162 IEGAKIEQYL---LEKSRIVRQARDERNYHIFYCMLAGLSTDEKERLKLGEASDYHY--LAQGGCITCEGRDDAKDFADI 236 (671)
T ss_pred EEEEEEEEEe---ccCCceeecCCCCCcHHHHHHHHcCCCHHHHHHcCCCChhhcee--ecCCCCccCCCccHHHHHHHH
Confidence 5799999999 99999999999999999999999999999999999999999999 9987 6778899999999999
Q ss_pred HHhhccCCCChHHHHHHHHHH----hcCCC
Q psy18112 80 RRDYDPTDEPLREEDRIWFRE----ELGKL 105 (107)
Q Consensus 80 ~~al~~lGf~~~e~~~I~~il----~~~~~ 105 (107)
++||++|||+++|+..||+|| .|||+
T Consensus 237 ~~al~~lG~~~~e~~~i~~ilaaILhLGni 266 (671)
T cd01381 237 RSAMKVLMFTDQEIWEIFKLLAAILHIGNL 266 (671)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHhhcce
Confidence 999999999999999999987 89987
No 4
>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=99.97 E-value=1.2e-31 Score=218.78 Aligned_cols=100 Identities=26% Similarity=0.426 Sum_probs=95.3
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCc-cccccCCchhhhhHHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHT-CYTVATTSVDTIFPSS 79 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~-~~~~~~~~d~~~f~~l 79 (107)
|+||+|++|| |||||||+|++|||||||||||++|+++++++.|+|.++..|+| |+++ +..+++++|+++|+++
T Consensus 168 i~Ga~i~~yL---LEksRv~~~~~gErnfHIFYqLl~g~~~~~~~~l~L~~~~~y~y--l~~~~~~~~~~~~d~~~f~~~ 242 (691)
T cd01380 168 IIGANMRTYL---LEKSRVVFQAPGERNYHIFYQLCAGAPSQELKELHLGHADKFNY--LNQGGAPTIEGVDDAEDFNAT 242 (691)
T ss_pred EEEEEEEEee---ccccceeecCCCCChhHHHHHHHhCCCHHHHHHhCCCCHHHCcc--ccCCCCccCCCCChHHHHHHH
Confidence 5799999999 99999999999999999999999999999999999999999999 9987 6678899999999999
Q ss_pred HHhhccCCCChHHHHHHHHHH----hcCCC
Q psy18112 80 RRDYDPTDEPLREEDRIWFRE----ELGKL 105 (107)
Q Consensus 80 ~~al~~lGf~~~e~~~I~~il----~~~~~ 105 (107)
++||++|||+++|+..||+|| .|||+
T Consensus 243 ~~al~~lg~s~~e~~~I~~iLaaILhLGni 272 (691)
T cd01380 243 VQALTLLGISEEQQMDIFKLLAALLHLGNI 272 (691)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHhccce
Confidence 999999999999999999987 89986
No 5
>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=99.97 E-value=1.2e-31 Score=218.37 Aligned_cols=101 Identities=26% Similarity=0.449 Sum_probs=95.8
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCc-cccccCCchhhhhHHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHT-CYTVATTSVDTIFPSS 79 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~-~~~~~~~~d~~~f~~l 79 (107)
|+||+|++|| ||||||++|++||||||||||||+|++++++++|+|.++..|+| |+++ |.++++++|+++|+++
T Consensus 167 i~ga~i~~yL---LEksRv~~q~~gErNfHIFYqLl~g~~~~~~~~l~L~~~~~y~y--L~~~~~~~~~~~dd~~~f~~~ 241 (677)
T cd01383 167 ISGAKIQTFL---LEKSRVVQCARGERSYHIFYQLCAGAPPALKEKLNLKSASEYKY--LKQSCCYSINGVDDAQRFHTL 241 (677)
T ss_pred EEEEEEEEEe---cCCCceeccCCCCchhHHHHHHHcCCCHHHHHHhCCCCHHHCce--ecCCCcccCCCccHHHHHHHH
Confidence 5799999999 99999999999999999999999999999999999999999999 9987 6778899999999999
Q ss_pred HHhhccCCCChHHHHHHHHHH----hcCCCC
Q psy18112 80 RRDYDPTDEPLREEDRIWFRE----ELGKLN 106 (107)
Q Consensus 80 ~~al~~lGf~~~e~~~I~~il----~~~~~~ 106 (107)
++||++|||+++|+..||+|| .|||+.
T Consensus 242 ~~al~~lG~~~~e~~~I~~iLaaILhLGNi~ 272 (677)
T cd01383 242 VEALDIVHISKEDQENVFAMLAAVLWLGNVS 272 (677)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHhhcceE
Confidence 999999999999999999987 899863
No 6
>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=99.97 E-value=1.5e-31 Score=218.18 Aligned_cols=100 Identities=32% Similarity=0.489 Sum_probs=94.8
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCC-ccccccccCCccccccCCchhhhhHHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEP-MRFRFGRLQHTCYTVATTSVDTIFPSS 79 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~-~~y~y~~l~~~~~~~~~~~d~~~f~~l 79 (107)
|+||+|++|| |||||||+|++|||||||||||++|+++++++.|+|.++ ..|+| |++++..+++++|+++|+++
T Consensus 177 i~Ga~i~~yL---LEksRVv~q~~gERNfHIFYqLl~G~~~~~~~~l~L~~~~~~y~y--L~~~~~~~~~~~d~~~f~~~ 251 (693)
T cd01377 177 IAGADIETYL---LEKSRVVFQASGERNYHIFYQLLSGADPELKSMLLLTGNPNDYRY--LSQGELTIPGVDDAEEFKLT 251 (693)
T ss_pred EEEEEEEEEe---cccCceeecCCCCCcHHHHHHHHcCCCHHHHHHcCCCCchhcCee--eCCCCccCCCCcHHHHHHHH
Confidence 5799999999 999999999999999999999999999999999999965 99999 99886668899999999999
Q ss_pred HHhhccCCCChHHHHHHHHHH----hcCCC
Q psy18112 80 RRDYDPTDEPLREEDRIWFRE----ELGKL 105 (107)
Q Consensus 80 ~~al~~lGf~~~e~~~I~~il----~~~~~ 105 (107)
+.||+.|||+++++..||+|| .|||+
T Consensus 252 ~~al~~lG~~~~e~~~i~~iLaaILhLGni 281 (693)
T cd01377 252 DEAFDILGFSDEEKNSIFKIVAAILHLGNI 281 (693)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHhhcce
Confidence 999999999999999999987 89987
No 7
>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=99.97 E-value=4e-31 Score=215.15 Aligned_cols=99 Identities=25% Similarity=0.439 Sum_probs=94.2
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCc-cccccCCchhhhhHHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHT-CYTVATTSVDTIFPSS 79 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~-~~~~~~~~d~~~f~~l 79 (107)
|+||+|++|| ||||||++|++|||||||||||++| ++++++.|+|.++..|+| |+++ +..+++++|+++|+++
T Consensus 168 i~Ga~i~~yL---LEksRv~~~~~gErnfHIFYqLl~g-~~~~~~~l~L~~~~~y~y--L~~~~~~~~~~~~D~~~f~~~ 241 (674)
T cd01384 168 ISGAAIRTYL---LERSRVCQISDPERNYHCFYQLCAA-PPEDVKKYKLGDPKEFHY--LNQSNCFELDGVDDAEEYLAT 241 (674)
T ss_pred EEEEEEEEEe---cccCceeecCCCCCchhHHHHHHcC-CHHHHHHcCCCChHhCcc--ccCCCCccccccchHHHHHHH
Confidence 5799999999 9999999999999999999999999 888999999999999999 9987 6778899999999999
Q ss_pred HHhhccCCCChHHHHHHHHHH----hcCCC
Q psy18112 80 RRDYDPTDEPLREEDRIWFRE----ELGKL 105 (107)
Q Consensus 80 ~~al~~lGf~~~e~~~I~~il----~~~~~ 105 (107)
++||+.|||+++++..||+|| .|||+
T Consensus 242 ~~al~~lG~~~~e~~~I~~iLaaILhLGni 271 (674)
T cd01384 242 RRAMDVVGISEEEQDAIFRVVAAILHLGNI 271 (674)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHhccce
Confidence 999999999999999999987 89987
No 8
>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=99.97 E-value=3.7e-31 Score=215.48 Aligned_cols=101 Identities=24% Similarity=0.349 Sum_probs=95.0
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCc-cccccCCchhhhhHHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHT-CYTVATTSVDTIFPSS 79 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~-~~~~~~~~d~~~f~~l 79 (107)
|+||+|++|| |||||||+|++|||||||||||++|+++++++.|+|.++..|+| |+++ +..+++.+|+++|+++
T Consensus 163 i~Ga~i~~yL---LEksRvv~q~~gErnfHIFYqll~g~~~~~~~~~~L~~~~~y~y--L~~~~~~~~~~~~d~~~f~~~ 237 (677)
T cd01387 163 IVGAITSQYL---LEKSRIVFQAKNERNYHIFYELLAGLPAQLRQAFSLQEAETYYY--LNQGGNCEIAGKSDADDFRRL 237 (677)
T ss_pred EeEEEEEEEe---cCCCceeecCCCCchHHHHHHHHhCCCHHHHHHhcCCCHHhCch--hcCCCcccCCCcCHHHHHHHH
Confidence 5799999999 99999999999999999999999999999999999999999999 9987 5557788999999999
Q ss_pred HHhhccCCCChHHHHHHHHHH----hcCCCC
Q psy18112 80 RRDYDPTDEPLREEDRIWFRE----ELGKLN 106 (107)
Q Consensus 80 ~~al~~lGf~~~e~~~I~~il----~~~~~~ 106 (107)
++||++|||+++|++.||+|| .|||+.
T Consensus 238 ~~al~~lg~~~~e~~~i~~iLaaILhLGni~ 268 (677)
T cd01387 238 LAAMEVLGFSSEDQDSIFRILASILHLGNVY 268 (677)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHhhcCeE
Confidence 999999999999999999987 899873
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=99.97 E-value=4.5e-31 Score=214.93 Aligned_cols=100 Identities=34% Similarity=0.511 Sum_probs=95.3
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCc-cccccCCchhhhhHHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHT-CYTVATTSVDTIFPSS 79 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~-~~~~~~~~d~~~f~~l 79 (107)
|+||+|++|| |||||||+|++|||||||||||++|+++++++.|+|.++..|+| |+++ +.++++++|+++|+++
T Consensus 165 i~ga~i~~yL---LEksRVv~~~~gErnfHIFYqll~g~~~~~~~~l~L~~~~~y~y--L~~~~~~~~~~~~d~~~f~~~ 239 (674)
T cd01378 165 PVGGKITNYL---LEKSRVVSQNKGERNFHIFYQLLAGASEQLLRELGLQKPEYYYY--LNQSQCYTVDGIDDKKDFKET 239 (674)
T ss_pred EeeEEEEEee---cCCCceeecCCCCchhHHHHHHHcCCCHHHHHHhCCCChhhCee--ecCCCccCCCCccHHHHHHHH
Confidence 5799999999 99999999999999999999999999999999999999999999 9987 5578899999999999
Q ss_pred HHhhccCCCChHHHHHHHHHH----hcCCC
Q psy18112 80 RRDYDPTDEPLREEDRIWFRE----ELGKL 105 (107)
Q Consensus 80 ~~al~~lGf~~~e~~~I~~il----~~~~~ 105 (107)
++||++|||+++|+..||+|| .|||+
T Consensus 240 ~~al~~lG~s~~e~~~i~~ilaaILhLGni 269 (674)
T cd01378 240 QNAMKVIGFSEDEQDEIFRIVAAILHLGNV 269 (674)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHhhcce
Confidence 999999999999999999987 89986
No 10
>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=99.97 E-value=8.1e-31 Score=213.88 Aligned_cols=101 Identities=19% Similarity=0.257 Sum_probs=93.7
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCccc-cccCCchhhhhHHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHTCY-TVATTSVDTIFPSS 79 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~~~-~~~~~~d~~~f~~l 79 (107)
|+||+|++|| ||||||++|++||||||||||||+|++++++++++|.++.+|+| |++++. ..++++|+++|+++
T Consensus 173 i~Ga~i~~yL---LEksRV~~q~~gERNfHIFYqll~G~~~~~~~~~~l~~~~~y~y--L~~~~~~~~~~~dd~~~f~~~ 247 (692)
T cd01385 173 VRGAVVEKYL---LEKSRIVSQEKDERNYHVFYYLLLGASEEERKQEFLLKQPDYFY--LNQHNLKIEDGEDEKHEFERL 247 (692)
T ss_pred EEEEEEEEee---cccceeeecCCCCchhHHHHHHHcCCCHHHHHHhcCCChhcCCe--eCCCCCccCCCCCHHHHHHHH
Confidence 5799999999 99999999999999999999999999999999999998889999 998743 34688999999999
Q ss_pred HHhhccCCCChHHHHHHHHHH----hcCCCC
Q psy18112 80 RRDYDPTDEPLREEDRIWFRE----ELGKLN 106 (107)
Q Consensus 80 ~~al~~lGf~~~e~~~I~~il----~~~~~~ 106 (107)
++||+++||++++++.||+|| .|||+.
T Consensus 248 ~~al~~lG~~~~~~~~i~~iLaaILhLGni~ 278 (692)
T cd01385 248 KQAMEMVGFLAATQKQIFAVLSAVLLLGNVT 278 (692)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHhccCce
Confidence 999999999999999999987 899874
No 11
>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=99.97 E-value=8.8e-31 Score=213.44 Aligned_cols=101 Identities=31% Similarity=0.479 Sum_probs=95.1
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCc-cccccCCchhhhhHHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHT-CYTVATTSVDTIFPSS 79 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~-~~~~~~~~d~~~f~~l 79 (107)
|+||+|++|| ||||||++|++|||||||||||++|+++++++.|+|.++..|+| |+++ +..+++++|+++|+++
T Consensus 163 i~ga~i~~yL---LEksRv~~~~~gErnfHIFYqll~g~~~~~~~~l~L~~~~~y~y--L~~~~~~~~~~~~d~~~f~~~ 237 (679)
T cd00124 163 ISGAKITTYL---LEKSRVVSQEPGERNFHIFYQLLAGASPEERKKLGLKRPESYRY--LNQGGCNDVDGIDDAEEFEEL 237 (679)
T ss_pred EeEEEEEEEE---cccceeeccCCCCCchhHHHHHHcCCCHHHHHhcCCCCcccCee--eCCCCcccCCCCCHHHHHHHH
Confidence 5799999999 99999999999999999999999999999999999999999999 9987 4455889999999999
Q ss_pred HHhhccCCCChHHHHHHHHHH----hcCCCC
Q psy18112 80 RRDYDPTDEPLREEDRIWFRE----ELGKLN 106 (107)
Q Consensus 80 ~~al~~lGf~~~e~~~I~~il----~~~~~~ 106 (107)
+.||++|||+++++..||+|| .|||+.
T Consensus 238 ~~al~~lg~~~~e~~~i~~iLaaILhLGni~ 268 (679)
T cd00124 238 KEALKSLGFSEEEIESIFRILAAILHLGNIE 268 (679)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHhhcCee
Confidence 999999999999999999987 899874
No 12
>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=99.96 E-value=1.5e-30 Score=212.04 Aligned_cols=101 Identities=31% Similarity=0.484 Sum_probs=95.8
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCc-cccccCCchhhhhHHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHT-CYTVATTSVDTIFPSS 79 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~-~~~~~~~~d~~~f~~l 79 (107)
|.||+|++|| ||||||++|++|||||||||||++|+++++++.|+|.++..|+| |+++ +..+++.+|+++|+++
T Consensus 171 i~ga~i~~yL---LEksRv~~~~~gErnfHIFYqLl~g~~~~~~~~l~L~~~~~y~y--L~~~~~~~~~~~~d~~~f~~~ 245 (677)
T smart00242 171 IVGAKIETYL---LEKSRVVSQAKGERNYHIFYQLLAGASEELKKELGLKSPEDYRY--LNQGGCLSVDGIDDAEEFKET 245 (677)
T ss_pred EeEEEEEEee---cCCceEEecCCCCCchHHHHHHHcCCCHHHHHhcCCCChhhCce--eCCCCCccCCCCCHHHHHHHH
Confidence 5799999999 99999999999999999999999999999999999999999999 9987 6778889999999999
Q ss_pred HHhhccCCCChHHHHHHHHHH----hcCCCC
Q psy18112 80 RRDYDPTDEPLREEDRIWFRE----ELGKLN 106 (107)
Q Consensus 80 ~~al~~lGf~~~e~~~I~~il----~~~~~~ 106 (107)
++||+.|||+++|+..||+|| .|||+.
T Consensus 246 ~~al~~lG~~~~e~~~I~~iLaaILhLGni~ 276 (677)
T smart00242 246 LNAMRVLGFSEEEQESIFKILAAILHLGNIE 276 (677)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHhhccee
Confidence 999999999999999999987 899873
No 13
>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=99.96 E-value=1.6e-30 Score=212.88 Aligned_cols=100 Identities=22% Similarity=0.307 Sum_probs=92.5
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCccc---------------
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHTCY--------------- 65 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~~~--------------- 65 (107)
|+||+|++|| |||||||+|++||||||||||||+|+++++++.|+|.++..|+| |++++.
T Consensus 167 i~Ga~i~~yL---LEksRVv~~~~gErNfHIFYqLl~G~~~~~~~~l~L~~~~~y~y--L~~~~~~~~~~~~~~~~~~~~ 241 (717)
T cd01382 167 VVGGFVSHYL---LEKSRICVQSAEERNYHIFYRLCAGASEDIREKLHLSSPDDFRY--LNRGCTRYFANKETDKQILQN 241 (717)
T ss_pred EeEEEEEEEe---ccCCceEecCCCCCchHHHHHHHhCCCHHHHHHhcCCChhhCee--ecCCccccccccccccccccc
Confidence 5799999999 99999999999999999999999999999999999999999999 986532
Q ss_pred ------------cccCCchhhhhHHHHHhhccCCCChHHHHHHHHHH----hcCCC
Q psy18112 66 ------------TVATTSVDTIFPSSRRDYDPTDEPLREEDRIWFRE----ELGKL 105 (107)
Q Consensus 66 ------------~~~~~~d~~~f~~l~~al~~lGf~~~e~~~I~~il----~~~~~ 105 (107)
..++++|+++|+++++||++|||+++++..||+|| .|||+
T Consensus 242 ~~s~~~~~~~~~~~~~~dD~~~f~~~~~Al~~lg~s~~e~~~i~~iLaaILhLGni 297 (717)
T cd01382 242 RKSPEHLKKGALKDPLLDDYGDFQRMCVALKKIGLDDTEKLDLFRVVAGVLHLGNI 297 (717)
T ss_pred ccccccccccccCCCCCcHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCce
Confidence 24567899999999999999999999999999987 89986
No 14
>KOG0164|consensus
Probab=99.96 E-value=1.8e-30 Score=208.77 Aligned_cols=99 Identities=29% Similarity=0.453 Sum_probs=95.1
Q ss_pred ccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCC-CCccccccccCCccccccCCchhhhhHHHH
Q psy18112 2 SSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMA-EPMRFRFGRLQHTCYTVATTSVDTIFPSSR 80 (107)
Q Consensus 2 ~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~-~~~~y~y~~l~~~~~~~~~~~d~~~f~~l~ 80 (107)
+|+.|.+|| |||||||+|.+|||||||||||+.|+++++..+|+|+ ++..|+| |++++..+.+++|+.+|..++
T Consensus 176 vGG~I~nYL---LEKSRVv~Q~~GERNFH~FYQLL~G~~e~~Lr~l~Ler~~~~Y~y--lnqg~~~v~sinD~~dfk~V~ 250 (1001)
T KOG0164|consen 176 VGGHITNYL---LEKSRVVKQQPGERNFHIFYQLLRGGEEQLLRQLGLERNPQSYNY--LNQGSAKVSSINDASDFKAVQ 250 (1001)
T ss_pred ccchHhHHH---HhhhhhhhcCcCcchHHHHHHHHcCCcHHHHHHhccccCcchhhh--hhhhhhhhcccccHHHHHHHH
Confidence 589999999 9999999999999999999999999999999999999 9999999 999988889999999999999
Q ss_pred HhhccCCCChHHHHHHHHHH----hcCCC
Q psy18112 81 RDYDPTDEPLREEDRIWFRE----ELGKL 105 (107)
Q Consensus 81 ~al~~lGf~~~e~~~I~~il----~~~~~ 105 (107)
+||.++||+++|+..+|+|+ .|||+
T Consensus 251 ~Am~vIgFs~eEVe~v~~iiAavLhLGNv 279 (1001)
T KOG0164|consen 251 KAMRVIGFSEEEVESVLSIIAAVLHLGNV 279 (1001)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHhccce
Confidence 99999999999999999976 89986
No 15
>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=99.96 E-value=8.5e-30 Score=207.59 Aligned_cols=101 Identities=32% Similarity=0.493 Sum_probs=86.7
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCc-cccccCCchhhhhHHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHT-CYTVATTSVDTIFPSS 79 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~-~~~~~~~~d~~~f~~l 79 (107)
|+||+|++|| ||||||+.|++|||||||||||++|+++++++.|+|.+++.|+| |+++ +.++++.+|.++|+++
T Consensus 166 ~~g~~i~~yl---LEksRv~~~~~~ErnfhiFYqll~G~~~~~~~~l~L~~~~~~~y--L~~~~~~~~~~~~d~~~f~~l 240 (689)
T PF00063_consen 166 IVGAKIETYL---LEKSRVVRQPPGERNFHIFYQLLAGADDEERKELRLNDASDYRY--LNQSGCSTIPGIDDAEEFQEL 240 (689)
T ss_dssp EEEEEEEEEE---E-GGGGT---TTS-SBHHHHHHHHTSSHHHHHHTT-S-GGGSTT--CCTTSSSSBTTCTHHHHHHHH
T ss_pred ccccceeccc---ccccceeeccccccccchhhhhhhccchhhhhcccccccccccc--eecccccccCCccCHHHhhhh
Confidence 4799999999 99999999999999999999999999999999999999999999 9986 6677889999999999
Q ss_pred HHhhccCCCChHHHHHHHHHH----hcCCCC
Q psy18112 80 RRDYDPTDEPLREEDRIWFRE----ELGKLN 106 (107)
Q Consensus 80 ~~al~~lGf~~~e~~~I~~il----~~~~~~ 106 (107)
++||++|||+++++..||+|| .|||+.
T Consensus 241 ~~al~~lg~~~~e~~~I~~iLaaILhLGni~ 271 (689)
T PF00063_consen 241 KDALKTLGFSDEEIDDIFRILAAILHLGNIE 271 (689)
T ss_dssp HHHHHHTT--HHHHHHHHHHHHHHHHHTTSS
T ss_pred hhhhccccCchhHHHHHHHHHHHHhhhcccc
Confidence 999999999999999999987 899874
No 16
>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=99.96 E-value=1.2e-29 Score=208.76 Aligned_cols=101 Identities=21% Similarity=0.256 Sum_probs=87.2
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCc--cccccCCchhhhhHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHT--CYTVATTSVDTIFPS 78 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~--~~~~~~~~d~~~f~~ 78 (107)
|+||+|++|| |||||||+|++||||||||||||+|++++++++|+|.++..+.+ .... +.+.++++|+++|++
T Consensus 164 i~Ga~i~~yL---LEKSRVv~q~~gERNFHIFYqLlaG~~~~~~~~l~L~~~~~~~~--~~~~~~~~~~d~~~D~~~f~~ 238 (767)
T cd01386 164 IASASLQTML---LERSRVARRPNGETNFVVFSQLLAGVDGDLRTELHLEQMAESSS--FGMGGLSKPEDKQKAAIDFSR 238 (767)
T ss_pred EeEEEEEEEe---cccCceeecCCCCCcchhHHHHHhCCCHHHHHHhcCCCccccch--hhcCCCCCCcCcccHHHHHHH
Confidence 5799999999 99999999999999999999999999999999999985544322 2221 233567899999999
Q ss_pred HHHhhccCCCChHHHHHHHHHH----hcCCCC
Q psy18112 79 SRRDYDPTDEPLREEDRIWFRE----ELGKLN 106 (107)
Q Consensus 79 l~~al~~lGf~~~e~~~I~~il----~~~~~~ 106 (107)
+++||++|||+++|+..||+|| .|||+.
T Consensus 239 ~~~Al~~lGfs~~e~~~If~iLaaILhLGNi~ 270 (767)
T cd01386 239 LQQAMEVLGISEGEQRAIWRVLAAIYHLGAAG 270 (767)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHhccCce
Confidence 9999999999999999999987 899873
No 17
>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=99.96 E-value=1.6e-29 Score=205.30 Aligned_cols=100 Identities=24% Similarity=0.307 Sum_probs=89.3
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHH-HHccCCCCccccccccCCcc-ccccCCc----hhh
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLL-RVVNMAEPMRFRFGRLQHTC-YTVATTS----VDT 74 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~-~~l~L~~~~~y~y~~l~~~~-~~~~~~~----d~~ 74 (107)
|+||+|++|| ||||||++|++|||||||||||++|++++++ +.++|.++..|+| |++++ ..+++++ |++
T Consensus 163 i~Ga~i~~yL---LEksRVv~q~~gERNfHIFYqLl~G~~~~~~~~~~~L~~~~~~~y--L~~~~~~~~~~~~~~~~~~~ 237 (653)
T cd01379 163 VVGARISEYL---LEKSRVVHQAEGEKNFHIFYYIYAGLAEEKKLAEYKLPESKTPRY--LQNEATRVVQDITSNKFYKD 237 (653)
T ss_pred EEEEEEEEEe---ccCCceeccCCCCCceeeHHHHHhCCCHHHHHHhcCCCCccccCc--cCCCCccccCCCccchhHHH
Confidence 5799999999 9999999999999999999999999997765 7899998899999 98873 3344443 578
Q ss_pred hhHHHHHhhccCCCChHHHHHHHHHH----hcCCC
Q psy18112 75 IFPSSRRDYDPTDEPLREEDRIWFRE----ELGKL 105 (107)
Q Consensus 75 ~f~~l~~al~~lGf~~~e~~~I~~il----~~~~~ 105 (107)
+|+++++||++|||++++++.||+|| .|||+
T Consensus 238 ~f~~~~~al~~lg~~~~e~~~I~~iLaaILhLGNi 272 (653)
T cd01379 238 QFEQIEQCFRVIGFTDEEVGSVYRILAAILNLGDI 272 (653)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcce
Confidence 99999999999999999999999987 89986
No 18
>KOG0162|consensus
Probab=99.95 E-value=3.2e-29 Score=202.10 Aligned_cols=99 Identities=28% Similarity=0.423 Sum_probs=95.2
Q ss_pred ccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCc-cccccCCchhhhhHHHH
Q psy18112 2 SSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHT-CYTVATTSVDTIFPSSR 80 (107)
Q Consensus 2 ~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~-~~~~~~~~d~~~f~~l~ 80 (107)
+|+.|++|| |||||||.|.++||||||||||+.|++.+.|..+++..|+.|.| ++.+ |..+++.||.++|+++.
T Consensus 184 ~ggkisNfL---LEKsRVV~q~~neRnFHIfYQ~~kgAs~~~r~t~Gi~~pe~Y~Y--~~~sg~~s~D~idd~kdfq~Tl 258 (1106)
T KOG0162|consen 184 DGGKISNFL---LEKSRVVMQNENERNFHIFYQLTKGASQEYRQTFGIQEPEYYVY--LNASGCYSVDDIDDRKDFQETL 258 (1106)
T ss_pred CcchhhHHH---HhhhhhhhccCCccceeeehhhhcCccHHHHhhhCcCCchheee--eccccceeccccchHHHHHHHH
Confidence 689999999 99999999999999999999999999999999999999999999 8876 88999999999999999
Q ss_pred HhhccCCCChHHHHHHHHHH----hcCCC
Q psy18112 81 RDYDPTDEPLREEDRIWFRE----ELGKL 105 (107)
Q Consensus 81 ~al~~lGf~~~e~~~I~~il----~~~~~ 105 (107)
.||+++|+.++||+.||++| +|||+
T Consensus 259 ~AM~vIGi~~~eQ~~v~rmva~IL~lGNI 287 (1106)
T KOG0162|consen 259 HAMKVIGINQEEQDEVLRMVAGILHLGNI 287 (1106)
T ss_pred HHheeccCChHHHHHHHHHHHHHHhccce
Confidence 99999999999999999976 99997
No 19
>KOG0161|consensus
Probab=99.93 E-value=3.7e-27 Score=205.02 Aligned_cols=101 Identities=33% Similarity=0.452 Sum_probs=96.1
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCC-CCccccccccCCccccccCCchhhhhHHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMA-EPMRFRFGRLQHTCYTVATTSVDTIFPSS 79 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~-~~~~y~y~~l~~~~~~~~~~~d~~~f~~l 79 (107)
|+||.|++|| ||||||++|+++|||||||||+++|.++.++..|.|+ ++.+|.| ++++..++++++|+++|+.|
T Consensus 251 i~~a~Ie~yL---LEKsRv~~Q~~~Er~yhiFyqlls~~~~~l~~~l~L~~~~~~Y~f--~~~~~~~i~g~dd~eef~~t 325 (1930)
T KOG0161|consen 251 IAGADIETYL---LEKSRVIRQAPGERNYHIFYQLLSGADPELKEELLLSDNVKDYKF--LSNGESTIPGVDDAEEFQET 325 (1930)
T ss_pred cchhhHHHHH---HHHhHhhccCcchhHHHHHHHHHhCCCHHHHHHHhhcccchhhhh--hccccCCCCCcchHHHHHHH
Confidence 6899999999 9999999999999999999999999999999999999 6999999 99886689999999999999
Q ss_pred HHhhccCCCChHHHHHHHHHH----hcCCCC
Q psy18112 80 RRDYDPTDEPLREEDRIWFRE----ELGKLN 106 (107)
Q Consensus 80 ~~al~~lGf~~~e~~~I~~il----~~~~~~ 106 (107)
..||++|||+++|+.+||+|+ .+||++
T Consensus 326 ~~a~~ilgfs~~E~~~~~~i~sailhlGn~~ 356 (1930)
T KOG0161|consen 326 DEAMDILGFSEEEKISIFRIVSAILHLGNIK 356 (1930)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHHHhcchh
Confidence 999999999999999999988 788875
No 20
>KOG0163|consensus
Probab=99.91 E-value=1.5e-25 Score=181.59 Aligned_cols=100 Identities=27% Similarity=0.428 Sum_probs=90.3
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCcccc----------c---
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHTCYT----------V--- 67 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~~~~----------~--- 67 (107)
++|+-+++|| ||||||+.|+.+||||||||+|++|+++++++.|+|..|++|+| |+.+|.. +
T Consensus 220 VvGGyvSHYL---LEkSRiC~Qaa~ERNYHiFY~LiAGas~dl~~kL~L~~pd~f~Y--L~rG~t~yFan~~t~~ki~~n 294 (1259)
T KOG0163|consen 220 VVGGYVSHYL---LEKSRICRQAAEERNYHIFYQLIAGASPDLRKKLSLGKPDDFRY--LKRGCTQYFANAKTEQKIPGN 294 (1259)
T ss_pred eechhhhHHH---HHHhHHHHhhhcccchhHHHHHHcCCCHHHHHHhccCCchhhhH--HhcchhhhccCcchhhcCccc
Confidence 4789999999 99999999999999999999999999999999999999999999 9876421 1
Q ss_pred --------------cCCchhhhhHHHHHhhccCCCChHHHHHHHHHH----hcCCC
Q psy18112 68 --------------ATTSVDTIFPSSRRDYDPTDEPLREEDRIWFRE----ELGKL 105 (107)
Q Consensus 68 --------------~~~~d~~~f~~l~~al~~lGf~~~e~~~I~~il----~~~~~ 105 (107)
+-+||-.+|..+..||+.+|++++|...||+++ +|||+
T Consensus 295 r~S~~~~~~~~~kD~iidD~~dF~rl~~Al~~~Glsd~Ekl~i~s~vA~vLHLGNi 350 (1259)
T KOG0163|consen 295 RKSKNHQQKGSLKDPIIDDYQDFHRLEKALKLLGLSDTEKLFIWSTVAAVLHLGNI 350 (1259)
T ss_pred ccCccccccCcccCcccccHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHcccc
Confidence 125788999999999999999999999999965 89997
No 21
>KOG0160|consensus
Probab=99.91 E-value=3.6e-25 Score=182.40 Aligned_cols=99 Identities=27% Similarity=0.386 Sum_probs=94.8
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCc-cccccCCchhhhhHHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHT-CYTVATTSVDTIFPSS 79 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~-~~~~~~~~d~~~f~~l 79 (107)
|.||.|++|| ||||||+.++++|||||||||+++|.+ +++.+|+|.++..|.| ++++ |..+++++|+.+|..+
T Consensus 172 I~GA~~~TYL---LekSRv~~~~~~ernyhiFyQlca~~~-~~~~~l~L~~~~~f~y--l~q~~~~~i~~v~d~~e~~~t 245 (862)
T KOG0160|consen 172 ISGAKIRTYL---LEKSRVVQLSAPERNYHIFYQLCAGAP-EELEKLKLGTLRRFSY--LNQSACVLISGVSDAEEFLST 245 (862)
T ss_pred cccceeeeEE---eecceeeecCccccchHHHHHHhcCCc-hhhhccCcCcccccee--cccccchhhcccccHHHHHHH
Confidence 6899999999 999999999999999999999999999 8899999999999999 9998 7789999999999999
Q ss_pred HHhhccCCCChHHHHHHHHHH----hcCCC
Q psy18112 80 RRDYDPTDEPLREEDRIWFRE----ELGKL 105 (107)
Q Consensus 80 ~~al~~lGf~~~e~~~I~~il----~~~~~ 105 (107)
+.||..+|++.++|..||+++ +|||+
T Consensus 246 ~~A~~~vgi~~~~q~~if~lla~ilhlGni 275 (862)
T KOG0160|consen 246 TEAMLFVGISESHQELIFRLLAAILHLGNI 275 (862)
T ss_pred HHHHHHhcCChHHHHHHHHHHHHHhccCce
Confidence 999999999999999999988 88875
No 22
>KOG4229|consensus
Probab=99.75 E-value=1.8e-19 Score=151.57 Aligned_cols=100 Identities=23% Similarity=0.340 Sum_probs=93.3
Q ss_pred CccceehhhhccCCCcceecccCCCCcchhHHHHHhcCCCHHHHHHccCCCCccccccccCCc-cccc-cCCchhhhhHH
Q psy18112 1 MSSYDIEMRIATGASMSRVTYQAPGERNFHIFYQLLVGADVHLLRVVNMAEPMRFRFGRLQHT-CYTV-ATTSVDTIFPS 78 (107)
Q Consensus 1 ~~ga~i~~yL~~~LEKSRVv~q~~gErnfHIFY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~-~~~~-~~~~d~~~f~~ 78 (107)
+.||.|..|| ||||||+.|+.+||||||||++++|++.+++..+.|..+++|.| |+++ +.++ ++.++...|..
T Consensus 225 i~Gaki~~yl---lEKsr~~~q~~~e~nyhify~~~agl~~~e~~~~~l~~~e~y~y--L~~~~~~~~~d~~~~~~~~~~ 299 (1062)
T KOG4229|consen 225 IEGAKIVEYL---LEKSRLVIQAGGERNYHIFYYLLAGLSENELKAFVLGEAENYEY--LEQGALFTISDGEDDVAQFIR 299 (1062)
T ss_pred CCcchHHHHH---HHHHHHHHhcCCCcccccchhheeccchhhhhHHhhcCCCCHHH--hhccccccccchHHHHHhHHH
Confidence 5799999999 99999999999999999999999999998899999999999999 9988 5566 88899999999
Q ss_pred HHHhhccCCCChHHHHHHHHHH----hcCCC
Q psy18112 79 SRRDYDPTDEPLREEDRIWFRE----ELGKL 105 (107)
Q Consensus 79 l~~al~~lGf~~~e~~~I~~il----~~~~~ 105 (107)
+..||+++||+.+++..|++++ ++||+
T Consensus 300 l~~~m~v~~f~~~~~~si~~~la~il~~gni 330 (1062)
T KOG4229|consen 300 LEAAMSVVGFTDKVLGSIFKSLAAILHIGNI 330 (1062)
T ss_pred HHHHHHHhccchhHHHHHHHhcccceeecce
Confidence 9999999999999999999987 77765
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=83.66 E-value=1.7 Score=23.76 Aligned_cols=25 Identities=4% Similarity=-0.100 Sum_probs=20.3
Q ss_pred hHHHHHhhccCCCChHHHHHHHHHH
Q psy18112 76 FPSSRRDYDPTDEPLREEDRIWFRE 100 (107)
Q Consensus 76 f~~l~~al~~lGf~~~e~~~I~~il 100 (107)
.+++..||..|||++.|+..+.+-+
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 5688999999999999998876654
No 24
>PF11181 YflT: Heat induced stress protein YflT
Probab=62.94 E-value=10 Score=23.89 Aligned_cols=28 Identities=18% Similarity=0.156 Sum_probs=25.1
Q ss_pred HHHHhhccCCCChHHHHHHHHHHhcCCC
Q psy18112 78 SSRRDYDPTDEPLREEDRIWFREELGKL 105 (107)
Q Consensus 78 ~l~~al~~lGf~~~e~~~I~~il~~~~~ 105 (107)
.+...|..||+++++...-.+-+.-|++
T Consensus 72 ~~~~~l~~lGl~~~ea~~y~~~l~~Gki 99 (103)
T PF11181_consen 72 ELRSKLESLGLSEDEAERYEEELDQGKI 99 (103)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHCCCE
Confidence 5788999999999999999998888875
No 25
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=61.36 E-value=12 Score=22.91 Aligned_cols=30 Identities=10% Similarity=0.102 Sum_probs=24.2
Q ss_pred hhhhHHHHHhhccCCCChHHHHHHHHHHhc
Q psy18112 73 DTIFPSSRRDYDPTDEPLREEDRIWFREEL 102 (107)
Q Consensus 73 ~~~f~~l~~al~~lGf~~~e~~~I~~il~~ 102 (107)
.-.+.++..+|..+|++++++..+++.+..
T Consensus 26 ~Is~~el~~~l~~~~~~~~ev~~i~~~~d~ 55 (96)
T smart00027 26 TVTGAQAKPILLKSGLPQTLLAKIWNLADI 55 (96)
T ss_pred eEeHHHHHHHHHHcCCCHHHHHHHHHHhcC
Confidence 346677888888899999999999988743
No 26
>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=60.49 E-value=16 Score=19.59 Aligned_cols=27 Identities=19% Similarity=0.112 Sum_probs=19.3
Q ss_pred hHHHHHhhccCC---CChHHHHHHHHHHhc
Q psy18112 76 FPSSRRDYDPTD---EPLREEDRIWFREEL 102 (107)
Q Consensus 76 f~~l~~al~~lG---f~~~e~~~I~~il~~ 102 (107)
.++++.+|..+| +++++...||.....
T Consensus 7 ~~~~~~~l~~~g~~~~s~~e~~~l~~~~D~ 36 (54)
T PF13833_consen 7 REEFRRALSKLGIKDLSEEEVDRLFREFDT 36 (54)
T ss_dssp HHHHHHHHHHTTSSSSCHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHhccc
Confidence 445566666554 889999999988743
No 27
>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=60.43 E-value=8.3 Score=22.15 Aligned_cols=29 Identities=7% Similarity=0.025 Sum_probs=16.8
Q ss_pred HHHHhhccCCCChHHHHHHHHHHhcCCCC
Q psy18112 78 SSRRDYDPTDEPLREEDRIWFREELGKLN 106 (107)
Q Consensus 78 ~l~~al~~lGf~~~e~~~I~~il~~~~~~ 106 (107)
++.+.|..+||+.+.+-.+++-+..-+.|
T Consensus 11 ~lVd~F~~mGF~~dkVvevlrrlgik~~n 39 (55)
T PF09288_consen 11 DLVDQFENMGFERDKVVEVLRRLGIKSMN 39 (55)
T ss_dssp HHHHHHHHHT--HHHHHHHHHHS--SS--
T ss_pred HHHHHHHHcCCcHHHHHHHHHHhCCCCCC
Confidence 46677778888888887777776554443
No 28
>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=56.83 E-value=19 Score=19.83 Aligned_cols=27 Identities=15% Similarity=0.090 Sum_probs=20.9
Q ss_pred hhHHHHHhhccCCCChHHHHHHHHHHh
Q psy18112 75 IFPSSRRDYDPTDEPLREEDRIWFREE 101 (107)
Q Consensus 75 ~f~~l~~al~~lGf~~~e~~~I~~il~ 101 (107)
..+++..+|..+|++.+++..|++.+.
T Consensus 17 ~~~el~~~l~~~g~~~~~~~~i~~~~d 43 (67)
T cd00052 17 SGDEARPFLGKSGLPRSVLAQIWDLAD 43 (67)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHHHHhc
Confidence 445666777778999999999988774
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=54.99 E-value=20 Score=21.22 Aligned_cols=25 Identities=0% Similarity=-0.129 Sum_probs=20.5
Q ss_pred hhhHHHHHhhccCCCChHHHHHHHH
Q psy18112 74 TIFPSSRRDYDPTDEPLREEDRIWF 98 (107)
Q Consensus 74 ~~f~~l~~al~~lGf~~~e~~~I~~ 98 (107)
..+..-.+||+.+||+++.+..+..
T Consensus 9 ~R~daA~dam~~lG~~~~~v~~vl~ 33 (65)
T PF10440_consen 9 ERIDAALDAMRQLGFSKKQVRPVLK 33 (65)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 5677778999999999999886544
No 30
>PF02119 FlgI: Flagellar P-ring protein; InterPro: IPR001782 The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body []. In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament []. The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively. The sequences of the FlgH, FlgI and FliF gene products have been determined []. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences [, ]. FlgH is predicted to have an extensive beta-sheet structure, in keeping with other outer membrane proteins, and FlgI is thought to have even more beta-structure content []. Several aspects of the DNA sequence of these genes and their surrounds suggest complex regulation of the flagellar gene system.; GO: 0005198 structural molecule activity, 0001539 ciliary or flagellar motility, 0009428 bacterial-type flagellum basal body, distal rod, P ring, 0030288 outer membrane-bounded periplasmic space
Probab=54.43 E-value=18 Score=28.17 Aligned_cols=35 Identities=14% Similarity=0.076 Sum_probs=30.4
Q ss_pred hhhhhHHHHHhhccCCCChHHHHHHHHHH-hcCCCC
Q psy18112 72 VDTIFPSSRRDYDPTDEPLREEDRIWFRE-ELGKLN 106 (107)
Q Consensus 72 d~~~f~~l~~al~~lGf~~~e~~~I~~il-~~~~~~ 106 (107)
.....+++.+||..+|.++.++-.|++-+ .-|.|+
T Consensus 301 ~~~tl~~lV~aLN~lg~~p~DlI~Ilqaik~aGAL~ 336 (342)
T PF02119_consen 301 EGATLQDLVRALNALGATPRDLIAILQAIKAAGALH 336 (342)
T ss_pred CCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCc
Confidence 46678999999999999999999999877 677765
No 31
>PRK13908 putative recombination protein RecO; Provisional
Probab=51.06 E-value=18 Score=26.08 Aligned_cols=31 Identities=13% Similarity=-0.062 Sum_probs=24.3
Q ss_pred hhhhHHHHHhhccCCCChHHHHHHHHHHhcC
Q psy18112 73 DTIFPSSRRDYDPTDEPLREEDRIWFREELG 103 (107)
Q Consensus 73 ~~~f~~l~~al~~lGf~~~e~~~I~~il~~~ 103 (107)
.+...++-+.=+++-++++|++.+|.|+.+|
T Consensus 173 ~~ki~~~f~~k~t~~l~D~Evd~Lw~il~~G 203 (204)
T PRK13908 173 LEKIKEFFRTKSTIFLEDEEVEELWRILLEG 203 (204)
T ss_pred HHHHHHHHHhCCceecChHHHHHHHHHHHcc
Confidence 3444555566677889999999999999887
No 32
>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=48.75 E-value=29 Score=17.35 Aligned_cols=25 Identities=4% Similarity=-0.093 Sum_probs=18.2
Q ss_pred hhhHHHHHhhccCCCChHHHHHHHH
Q psy18112 74 TIFPSSRRDYDPTDEPLREEDRIWF 98 (107)
Q Consensus 74 ~~f~~l~~al~~lGf~~~e~~~I~~ 98 (107)
++|-.+..--..+|++.+|+...+.
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 4777888878889999999887654
No 33
>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=44.80 E-value=28 Score=26.53 Aligned_cols=31 Identities=6% Similarity=0.010 Sum_probs=26.8
Q ss_pred ccCCchhhhhHHHHHhhccCCCChHHHHHHH
Q psy18112 67 VATTSVDTIFPSSRRDYDPTDEPLREEDRIW 97 (107)
Q Consensus 67 ~~~~~d~~~f~~l~~al~~lGf~~~e~~~I~ 97 (107)
.++..+..++..+.++|..-|++++++..|+
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 4567788999999999999999999999876
No 34
>COG2355 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]
Probab=42.92 E-value=27 Score=26.87 Aligned_cols=32 Identities=9% Similarity=-0.139 Sum_probs=28.9
Q ss_pred ccCCchhhhhHHHHHhhccCCCChHHHHHHHH
Q psy18112 67 VATTSVDTIFPSSRRDYDPTDEPLREEDRIWF 98 (107)
Q Consensus 67 ~~~~~d~~~f~~l~~al~~lGf~~~e~~~I~~ 98 (107)
.++..|..+++.+.++|..-|++++++..|+.
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 46788999999999999999999999998875
No 35
>KOG0064|consensus
Probab=39.38 E-value=20 Score=30.15 Aligned_cols=69 Identities=13% Similarity=0.167 Sum_probs=48.0
Q ss_pred HHHHhcCCCHHHHHHccCCCCccccccccCCcc-ccccCCchhhhhHHHHHhhccCCCChHHHHHHHHHHhc
Q psy18112 32 FYQLLVGADVHLLRVVNMAEPMRFRFGRLQHTC-YTVATTSVDTIFPSSRRDYDPTDEPLREEDRIWFREEL 102 (107)
Q Consensus 32 FY~Ll~g~~~~~~~~l~L~~~~~y~y~~l~~~~-~~~~~~~d~~~f~~l~~al~~lGf~~~e~~~I~~il~~ 102 (107)
.+-++.|..|--...|....+..-.| ++|-. .......|.--|.+..+-|+-=|+++.|...|..++.|
T Consensus 524 LfRILggLWPvy~g~L~~P~~~~mFY--IPQRPYms~gtlRDQIIYPdS~e~~~~kg~~d~dL~~iL~~v~L 593 (728)
T KOG0064|consen 524 LFRILGGLWPVYNGLLSIPRPNNIFY--IPQRPYMSGGTLRDQIIYPDSSEQMKRKGYTDQDLEAILDIVHL 593 (728)
T ss_pred HHHHHhccCcccCCeeecCCCcceEe--ccCCCccCcCcccceeecCCcHHHHHhcCCCHHHHHHHHHHhhH
Confidence 34566777776555666666777778 87762 23333456666666667777779999999999999865
No 36
>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=39.21 E-value=41 Score=21.23 Aligned_cols=24 Identities=17% Similarity=0.097 Sum_probs=20.7
Q ss_pred HHHHHhhccCCCChHHHHHHHHHH
Q psy18112 77 PSSRRDYDPTDEPLREEDRIWFRE 100 (107)
Q Consensus 77 ~~l~~al~~lGf~~~e~~~I~~il 100 (107)
+.+.+||+.+|++++.+..++..+
T Consensus 87 ~~~~~al~~~~v~~~~~~~~~~~~ 110 (120)
T PF01152_consen 87 ELLKQALDELGVPEELIDELLARL 110 (120)
T ss_dssp HHHHHHHHHTTCTHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHH
Confidence 446789999999999999998876
No 37
>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=38.33 E-value=37 Score=19.05 Aligned_cols=22 Identities=14% Similarity=-0.068 Sum_probs=16.2
Q ss_pred HHHHhhccCCCChHHHHHHHHH
Q psy18112 78 SSRRDYDPTDEPLREEDRIWFR 99 (107)
Q Consensus 78 ~l~~al~~lGf~~~e~~~I~~i 99 (107)
.....++.+|||-+|+..++.+
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 3567888999999999998855
No 38
>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=37.30 E-value=38 Score=25.73 Aligned_cols=31 Identities=10% Similarity=-0.076 Sum_probs=27.4
Q ss_pred cCCchhhhhHHHHHhhccCCCChHHHHHHHH
Q psy18112 68 ATTSVDTIFPSSRRDYDPTDEPLREEDRIWF 98 (107)
Q Consensus 68 ~~~~d~~~f~~l~~al~~lGf~~~e~~~I~~ 98 (107)
++..|..++..+.++|..-||+++++..|+.
T Consensus 273 ~gl~~~~~~~~l~~~L~~rG~s~~~i~~i~g 303 (309)
T cd01301 273 GGLEDVSDLPNLTAELLERGYSEEEIEKIAG 303 (309)
T ss_pred cccCCHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 4577899999999999999999999998763
No 39
>PRK05303 flgI flagellar basal body P-ring protein; Provisional
Probab=36.58 E-value=50 Score=26.06 Aligned_cols=35 Identities=14% Similarity=0.080 Sum_probs=29.3
Q ss_pred hhhhhHHHHHhhccCCCChHHHHHHHHHH-hcCCCC
Q psy18112 72 VDTIFPSSRRDYDPTDEPLREEDRIWFRE-ELGKLN 106 (107)
Q Consensus 72 d~~~f~~l~~al~~lGf~~~e~~~I~~il-~~~~~~ 106 (107)
.....+++.+||..+|.++.++-.|++-+ .-|.|+
T Consensus 326 ~~~~l~~lV~aLN~lG~tp~DlIaILqalk~aGAL~ 361 (367)
T PRK05303 326 EGATLADLVRALNALGATPRDLIAILQALKAAGALH 361 (367)
T ss_pred CCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCc
Confidence 34678999999999999999999998877 666654
No 40
>PF11103 DUF2887: Protein of unknown function (DUF2887); InterPro: IPR022573 This bacterial group of proteins has no known function.
Probab=35.80 E-value=33 Score=24.68 Aligned_cols=28 Identities=21% Similarity=0.490 Sum_probs=21.5
Q ss_pred hHHHHHhcCCCHHHHHHccCC--CCccccc
Q psy18112 30 HIFYQLLVGADVHLLRVVNMA--EPMRFRF 57 (107)
Q Consensus 30 HIFY~Ll~g~~~~~~~~l~L~--~~~~y~y 57 (107)
+|||.|+...+....+-++.. .++.|+|
T Consensus 3 ~iFY~lf~~~P~~~feLi~~~~~~a~~Y~F 32 (200)
T PF11103_consen 3 SIFYRLFQSFPSIFFELIGGPPEEAENYQF 32 (200)
T ss_pred hHHHHHHHHChHHHHHHcCCCcccccceEE
Confidence 699999988776666777765 5677888
No 41
>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=33.91 E-value=42 Score=21.06 Aligned_cols=25 Identities=20% Similarity=-0.013 Sum_probs=19.3
Q ss_pred hhhhHHHHHhhccCCCChHHHHHHH
Q psy18112 73 DTIFPSSRRDYDPTDEPLREEDRIW 97 (107)
Q Consensus 73 ~~~f~~l~~al~~lGf~~~e~~~I~ 97 (107)
.-.+....+-+..||+++.+++.|-
T Consensus 16 ~V~~~~Wk~laR~LGLse~~I~~i~ 40 (96)
T cd08315 16 EVPFDSWNRLMRQLGLSENEIDVAK 40 (96)
T ss_pred HCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 3346667788899999999988763
No 42
>PRK12789 flgI flagellar basal body P-ring protein; Reviewed
Probab=32.54 E-value=58 Score=25.67 Aligned_cols=33 Identities=12% Similarity=0.002 Sum_probs=28.1
Q ss_pred hhhHHHHHhhccCCCChHHHHHHHHHH-hcCCCC
Q psy18112 74 TIFPSSRRDYDPTDEPLREEDRIWFRE-ELGKLN 106 (107)
Q Consensus 74 ~~f~~l~~al~~lGf~~~e~~~I~~il-~~~~~~ 106 (107)
...+++.+||..+|.++.++-.|++-+ .-|.|+
T Consensus 328 ~tl~~lV~aLN~lG~tp~DlIsILqalk~aGAL~ 361 (367)
T PRK12789 328 SDLQTLVRGLNQIGLKPSDIIAILQAIKTAGALQ 361 (367)
T ss_pred CCHHHHHHHHHHcCCChHHHHHHHHHHHhcCccc
Confidence 478999999999999999999998877 556554
No 43
>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=31.50 E-value=51 Score=20.11 Aligned_cols=22 Identities=9% Similarity=-0.155 Sum_probs=17.3
Q ss_pred hhHHHHHhhccCCCChHHHHHH
Q psy18112 75 IFPSSRRDYDPTDEPLREEDRI 96 (107)
Q Consensus 75 ~f~~l~~al~~lGf~~~e~~~I 96 (107)
.+.+.++.++.+|+++.+++.|
T Consensus 10 ~~~~wk~~~R~LGlse~~Id~i 31 (80)
T cd08313 10 PPRRWKEFVRRLGLSDNEIERV 31 (80)
T ss_pred CHHHHHHHHHHcCCCHHHHHHH
Confidence 4555667888999999988876
No 44
>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=31.10 E-value=65 Score=15.99 Aligned_cols=22 Identities=5% Similarity=-0.151 Sum_probs=14.3
Q ss_pred HHHHhhccCCCChHHHHHHHHH
Q psy18112 78 SSRRDYDPTDEPLREEDRIWFR 99 (107)
Q Consensus 78 ~l~~al~~lGf~~~e~~~I~~i 99 (107)
+..+.|..+||+.++.......
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~ 24 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRA 24 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHH
Confidence 3456677789997766655443
No 45
>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=31.09 E-value=54 Score=19.66 Aligned_cols=23 Identities=13% Similarity=-0.029 Sum_probs=17.3
Q ss_pred hhHHHHHhhccCCCChHHHHHHH
Q psy18112 75 IFPSSRRDYDPTDEPLREEDRIW 97 (107)
Q Consensus 75 ~f~~l~~al~~lGf~~~e~~~I~ 97 (107)
.+....+....|||++.++..|-
T Consensus 10 ~~~~Wk~laR~LGls~~~I~~ie 32 (79)
T cd08784 10 PFDQHKRFFRKLGLSDNEIKVAE 32 (79)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHH
Confidence 45556677788999999988763
No 46
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=31.05 E-value=66 Score=15.89 Aligned_cols=22 Identities=5% Similarity=-0.221 Sum_probs=14.6
Q ss_pred HHHHhhccCCCChHHHHHHHHH
Q psy18112 78 SSRRDYDPTDEPLREEDRIWFR 99 (107)
Q Consensus 78 ~l~~al~~lGf~~~e~~~I~~i 99 (107)
+..+.|..+||++++.....+.
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~ 24 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRA 24 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHH
Confidence 3456677789998876655443
No 47
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=30.65 E-value=69 Score=19.27 Aligned_cols=27 Identities=15% Similarity=0.105 Sum_probs=17.7
Q ss_pred hhHHHHHhhccCCCChHHHHHHHHHHh
Q psy18112 75 IFPSSRRDYDPTDEPLREEDRIWFREE 101 (107)
Q Consensus 75 ~f~~l~~al~~lGf~~~e~~~I~~il~ 101 (107)
.|.++.++|....++++.+..|+..|+
T Consensus 23 T~~eI~~~L~~~~~~~e~id~i~~~L~ 49 (82)
T PF03979_consen 23 TYDEINDALPEDDLDPEQIDEIYDTLE 49 (82)
T ss_dssp BHHHHHHH-S-S---HHHHHHHHHHHH
T ss_pred CHHHHHHHcCccCCCHHHHHHHHHHHH
Confidence 577788888888888888888888773
No 48
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.54 E-value=59 Score=22.98 Aligned_cols=26 Identities=12% Similarity=0.043 Sum_probs=21.7
Q ss_pred hhHHHHHhhccCCCChHHHHHHHHHH
Q psy18112 75 IFPSSRRDYDPTDEPLREEDRIWFRE 100 (107)
Q Consensus 75 ~f~~l~~al~~lGf~~~e~~~I~~il 100 (107)
.+.+...||..|||++.|.....+-+
T Consensus 142 ~~~e~~~AL~~LGy~~~ea~~av~~~ 167 (188)
T PRK14606 142 IYHESLEALVSLGYPEKQAREAVKHV 167 (188)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 46789999999999999988766544
No 49
>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=29.52 E-value=34 Score=21.67 Aligned_cols=28 Identities=7% Similarity=-0.082 Sum_probs=20.8
Q ss_pred CchhhhhHHHHHhhccCCCChHHHHHHH
Q psy18112 70 TSVDTIFPSSRRDYDPTDEPLREEDRIW 97 (107)
Q Consensus 70 ~~d~~~f~~l~~al~~lGf~~~e~~~I~ 97 (107)
+.+.-.+.+.++....+|+++.+++.|-
T Consensus 14 Ia~~~~~~~wK~faR~lglse~~Id~I~ 41 (97)
T cd08316 14 IADVMTLKDVKKFVRKSGLSEPKIDEIK 41 (97)
T ss_pred HHHHcCHHHHHHHHHHcCCCHHHHHHHH
Confidence 3445566677788889999998888763
No 50
>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=27.63 E-value=72 Score=19.62 Aligned_cols=28 Identities=4% Similarity=-0.090 Sum_probs=22.8
Q ss_pred hhhhhHHHHHhhccCCCChHHHHHHHHH
Q psy18112 72 VDTIFPSSRRDYDPTDEPLREEDRIWFR 99 (107)
Q Consensus 72 d~~~f~~l~~al~~lGf~~~e~~~I~~i 99 (107)
-.-+|..+...|+..|++.++...+|.=
T Consensus 44 ~GLDY~al~~~~~~~gi~~~~~~~~~~~ 71 (83)
T PF08809_consen 44 TGLDYGALPAVMDLMGIDDEDRPELFDD 71 (83)
T ss_pred ccccHHHHHHHHHHcCCChhhHHHHHHH
Confidence 3457888999999999999888777753
No 51
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=27.36 E-value=68 Score=22.82 Aligned_cols=25 Identities=4% Similarity=-0.332 Sum_probs=21.5
Q ss_pred hHHHHHhhccCCCChHHHHHHHHHH
Q psy18112 76 FPSSRRDYDPTDEPLREEDRIWFRE 100 (107)
Q Consensus 76 f~~l~~al~~lGf~~~e~~~I~~il 100 (107)
+.+...||..|||++.|...+..-+
T Consensus 149 ~~e~~~aL~~LGy~~~ea~~ai~~i 173 (195)
T PRK14604 149 DRELSEILISLGYSAAEAAAAIAAL 173 (195)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 5789999999999999988876654
No 52
>PHA02414 hypothetical protein
Probab=26.24 E-value=34 Score=22.06 Aligned_cols=12 Identities=42% Similarity=0.839 Sum_probs=9.5
Q ss_pred CCcchhHHHHHh
Q psy18112 25 GERNFHIFYQLL 36 (107)
Q Consensus 25 gErnfHIFY~Ll 36 (107)
.|.--|||||+-
T Consensus 56 sEKqshi~yQi~ 67 (111)
T PHA02414 56 SEKQSHIYYQIE 67 (111)
T ss_pred HHHhhHHHHHHH
Confidence 466779999984
No 53
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=26.02 E-value=74 Score=22.65 Aligned_cols=26 Identities=0% Similarity=-0.311 Sum_probs=21.6
Q ss_pred hhHHHHHhhccCCCChHHHHHHHHHH
Q psy18112 75 IFPSSRRDYDPTDEPLREEDRIWFRE 100 (107)
Q Consensus 75 ~f~~l~~al~~lGf~~~e~~~I~~il 100 (107)
...+...||..|||++.|.....+=+
T Consensus 151 ~~~ea~~AL~~LGy~~~ea~~al~~i 176 (197)
T PRK14603 151 AAEDAVLALLALGFREAQVRSVVAEL 176 (197)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 46789999999999999988766644
No 54
>PF02526 GBP_repeat: Glycophorin-binding protein; InterPro: IPR003681 The glycophorin-binding protein contains a tandem repeat. The repeated sequence determines the binding domain for an erythrocyte receptor binding protein of Plasmodium falciparum, the malarial parasite []. Erythrocyte invasion by the malarial merozoite is a receptor-mediated process, an obligatory step in the development of the parasite. The P. falciparum protein binds to the erythrocyte receptor glycophorin.
Probab=25.03 E-value=48 Score=17.18 Aligned_cols=15 Identities=27% Similarity=0.742 Sum_probs=11.3
Q ss_pred cchhHHHHHhcCCCH
Q psy18112 27 RNFHIFYQLLVGADV 41 (107)
Q Consensus 27 rnfHIFY~Ll~g~~~ 41 (107)
....||||+|.-.++
T Consensus 21 kh~~v~yqil~~tdp 35 (38)
T PF02526_consen 21 KHLNVLYQILTNTDP 35 (38)
T ss_pred HHHHHHHHHHccCCC
Confidence 456899999987654
No 55
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.94 E-value=80 Score=22.28 Aligned_cols=26 Identities=4% Similarity=-0.248 Sum_probs=21.2
Q ss_pred hhHHHHHhhccCCCChHHHHHHHHHH
Q psy18112 75 IFPSSRRDYDPTDEPLREEDRIWFRE 100 (107)
Q Consensus 75 ~f~~l~~al~~lGf~~~e~~~I~~il 100 (107)
..++...||..|||++.|...+.+=+
T Consensus 144 ~~~e~~~aL~~LGy~~~ea~~al~~v 169 (186)
T PRK14600 144 INDDALAALISLGYEKTKAFNAIQKI 169 (186)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 35788999999999999988766543
No 56
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=24.71 E-value=81 Score=22.14 Aligned_cols=25 Identities=4% Similarity=-0.068 Sum_probs=22.5
Q ss_pred hHHHHHhhccCCCChHHHHHHHHHH
Q psy18112 76 FPSSRRDYDPTDEPLREEDRIWFRE 100 (107)
Q Consensus 76 f~~l~~al~~lGf~~~e~~~I~~il 100 (107)
..++..+|..+||++.+...+++-+
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 6889999999999999999888765
No 57
>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=23.94 E-value=77 Score=21.82 Aligned_cols=28 Identities=4% Similarity=0.130 Sum_probs=24.9
Q ss_pred CCchhhhhHHHHHhhccCCCChHHHHHH
Q psy18112 69 TTSVDTIFPSSRRDYDPTDEPLREEDRI 96 (107)
Q Consensus 69 ~~~d~~~f~~l~~al~~lGf~~~e~~~I 96 (107)
.++|++-|....+.+..+.++++++..|
T Consensus 30 svdDA~~y~~f~E~l~~l~ls~~~~~el 57 (153)
T PF07126_consen 30 SVDDAALYQTFKEQLRQLDLSDAQRAEL 57 (153)
T ss_pred cHHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence 4689999999999999999999998765
No 58
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=23.86 E-value=1e+02 Score=22.13 Aligned_cols=26 Identities=4% Similarity=-0.192 Sum_probs=21.7
Q ss_pred hhHHHHHhhccCCCChHHHHHHHHHH
Q psy18112 75 IFPSSRRDYDPTDEPLREEDRIWFRE 100 (107)
Q Consensus 75 ~f~~l~~al~~lGf~~~e~~~I~~il 100 (107)
.+++...||..|||++.|...+.+-+
T Consensus 143 ~~~ea~~AL~~LGy~~~ea~~al~~v 168 (196)
T PRK13901 143 KFKELEQSIVNMGFDRKLVNSAIKEI 168 (196)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 46789999999999999988776644
No 59
>COG0599 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]
Probab=23.79 E-value=95 Score=20.01 Aligned_cols=24 Identities=8% Similarity=-0.110 Sum_probs=20.0
Q ss_pred hHHHHHhhccCCCChHHHHHHHHHH
Q psy18112 76 FPSSRRDYDPTDEPLREEDRIWFRE 100 (107)
Q Consensus 76 f~~l~~al~~lGf~~~e~~~I~~il 100 (107)
--.++.|++. |.+++|+..+..++
T Consensus 74 ~~H~~~Al~~-GaT~eEI~e~i~~~ 97 (124)
T COG0599 74 KVHVRAALEN-GATKEEIAEAIAVA 97 (124)
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHH
Confidence 3458899977 99999999988776
No 60
>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=23.37 E-value=83 Score=19.25 Aligned_cols=23 Identities=4% Similarity=-0.252 Sum_probs=16.6
Q ss_pred hhhhHHHHHhhccCCCChHHHHH
Q psy18112 73 DTIFPSSRRDYDPTDEPLREEDR 95 (107)
Q Consensus 73 ~~~f~~l~~al~~lGf~~~e~~~ 95 (107)
.-.|....+-|+.||+++.++..
T Consensus 8 ~VP~~~wk~F~R~LGLsdn~Ie~ 30 (77)
T cd08815 8 AVPARRWKEFVRTLGLREAEIEA 30 (77)
T ss_pred cCChHHHHHHHHHcCCcHhHHHH
Confidence 33456667788899999988654
No 61
>PF12616 DUF3775: Protein of unknown function (DUF3775); InterPro: IPR022254 This domain family is found in bacteria, and is approximately 80 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=22.80 E-value=77 Score=19.17 Aligned_cols=18 Identities=17% Similarity=0.091 Sum_probs=15.2
Q ss_pred CCChHHHHHHHHHHhcCC
Q psy18112 87 DEPLREEDRIWFREELGK 104 (107)
Q Consensus 87 Gf~~~e~~~I~~il~~~~ 104 (107)
+++++|+..+..+.++|+
T Consensus 12 ~l~~deqaeLvALmwiGR 29 (75)
T PF12616_consen 12 DLNEDEQAELVALMWIGR 29 (75)
T ss_pred hCCHHHHHHHHHHHHhcC
Confidence 468889999999999885
No 62
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=22.65 E-value=89 Score=22.06 Aligned_cols=26 Identities=4% Similarity=-0.240 Sum_probs=21.4
Q ss_pred hhHHHHHhhccCCCChHHHHHHHHHH
Q psy18112 75 IFPSSRRDYDPTDEPLREEDRIWFRE 100 (107)
Q Consensus 75 ~f~~l~~al~~lGf~~~e~~~I~~il 100 (107)
..+++..||..|||++.+......=+
T Consensus 146 ~~~e~~~aL~~LGy~~~e~~~ai~~~ 171 (191)
T TIGR00084 146 ARDELFEALVSLGYKPQEIQQALKKI 171 (191)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 35789999999999999988766544
No 63
>PF05054 DUF673: Protein of unknown function (DUF673); InterPro: IPR007748 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf109; it is a family of uncharacterised viral proteins.
Probab=22.60 E-value=90 Score=24.56 Aligned_cols=31 Identities=0% Similarity=-0.252 Sum_probs=25.2
Q ss_pred CchhhhhHHHHHhhccCCCChHHHHHHHHHH
Q psy18112 70 TSVDTIFPSSRRDYDPTDEPLREEDRIWFRE 100 (107)
Q Consensus 70 ~~d~~~f~~l~~al~~lGf~~~e~~~I~~il 100 (107)
.-+...++-++.|++.||++...+..|..++
T Consensus 231 ~~nr~Sl~Yik~a~elL~i~~~~i~sv~~~v 261 (357)
T PF05054_consen 231 IVNRPSLQYIKDAQELLGIDDSSIQSVHDLV 261 (357)
T ss_pred eechHHHHHHHHHHHHhCCCcchHHHHHHHH
Confidence 3467889999999999999999977665544
No 64
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=22.51 E-value=1.4e+02 Score=18.82 Aligned_cols=31 Identities=10% Similarity=-0.169 Sum_probs=20.9
Q ss_pred CCchhhhhHHHHHhhccCCCChHHHHHHHHH
Q psy18112 69 TTSVDTIFPSSRRDYDPTDEPLREEDRIWFR 99 (107)
Q Consensus 69 ~~~d~~~f~~l~~al~~lGf~~~e~~~I~~i 99 (107)
...+.+....+.+.|...|+++.|...|..+
T Consensus 52 ~~~~~e~~~~l~~~L~~~~L~~~E~~qi~Nl 82 (117)
T PF03874_consen 52 KFQNPESIKELREELKKFGLTEFEILQIINL 82 (117)
T ss_dssp SSSSHHHHHHHHHHHTTSTS-HHHHHHHHHH
T ss_pred cCCCHHHHHHHHHHHhcccCCHHHHHHHhcC
Confidence 4455667777888888888887777666544
No 65
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=22.47 E-value=1.1e+02 Score=19.07 Aligned_cols=27 Identities=11% Similarity=-0.123 Sum_probs=22.5
Q ss_pred hhHHHHHhhccCCCChHHHHHHHHHHh
Q psy18112 75 IFPSSRRDYDPTDEPLREEDRIWFREE 101 (107)
Q Consensus 75 ~f~~l~~al~~lGf~~~e~~~I~~il~ 101 (107)
.+-.....++.+||+-+|+..++....
T Consensus 43 ~~l~~I~~lr~~G~sL~eI~~~l~~~~ 69 (107)
T cd04777 43 DDLEFILELKGLGFSLIEIQKIFSYKR 69 (107)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHhcc
Confidence 566678999999999999999887643
No 66
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=21.54 E-value=1e+02 Score=18.74 Aligned_cols=35 Identities=11% Similarity=0.051 Sum_probs=22.5
Q ss_pred hhhhhHHHHHhhccCCCChHHHHHHHHHH-hcCCCCC
Q psy18112 72 VDTIFPSSRRDYDPTDEPLREEDRIWFRE-ELGKLNR 107 (107)
Q Consensus 72 d~~~f~~l~~al~~lGf~~~e~~~I~~il-~~~~~~~ 107 (107)
+.+-+.++..++..- +.+++...|+.+| .|.+..|
T Consensus 45 ~~~~L~~il~~l~~~-~~~~~~~~i~~~L~~L~~~~R 80 (94)
T PF13877_consen 45 EPEFLSEILEALNEH-FIPEDPEFIFEILEALSKVKR 80 (94)
T ss_pred CHHHHHHHHHHHHHH-HccCCHHHHHHHHHHhcCCCC
Confidence 566777788888765 3333445777777 6666554
No 67
>COG4365 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.17 E-value=96 Score=25.28 Aligned_cols=29 Identities=7% Similarity=-0.152 Sum_probs=26.7
Q ss_pred hhhhHHHHHhhccCCCChHHHHHHHHHHh
Q psy18112 73 DTIFPSSRRDYDPTDEPLREEDRIWFREE 101 (107)
Q Consensus 73 ~~~f~~l~~al~~lGf~~~e~~~I~~il~ 101 (107)
-+.|.+..+.++.+|-.++.++.+.++|+
T Consensus 483 lk~f~eiq~~lkP~g~lQERiwn~~q~LN 511 (537)
T COG4365 483 LKQFREIQETLKPMGGLQERIWNPLQILN 511 (537)
T ss_pred HHHHHHHHHhhCcccchHHhhhhHHHHHH
Confidence 57899999999999999999999999983
No 68
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=21.08 E-value=1e+02 Score=21.94 Aligned_cols=26 Identities=8% Similarity=-0.010 Sum_probs=21.0
Q ss_pred hhHHHHHhhccCCCChHHHHHHHHHH
Q psy18112 75 IFPSSRRDYDPTDEPLREEDRIWFRE 100 (107)
Q Consensus 75 ~f~~l~~al~~lGf~~~e~~~I~~il 100 (107)
...+...||..|||++.|.....+=+
T Consensus 154 ~~~ea~~AL~~LGy~~~ea~~av~~~ 179 (203)
T PRK14602 154 VFRDALAGLANLGYGEEEARPVLKEV 179 (203)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 46789999999999999988755433
No 69
>cd00807 GlnRS_core catalytic core domain of glutaminyl-tRNA synthetase. Glutaminyl-tRNA synthetase (GlnRS) cataytic core domain. These enzymes attach Gln to the appropriate tRNA. Like other class I tRNA synthetases, they aminoacylate the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. GlnRS contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. These enzymes function as monomers. Archaea and most bacteria lack GlnRS. In these organisms, the "non-discriminating" form of GluRS aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu, which is converted to Gln when appropriate by a transamidation enzyme.
Probab=20.74 E-value=2.2e+02 Score=21.05 Aligned_cols=24 Identities=8% Similarity=0.088 Sum_probs=19.1
Q ss_pred HHHhhccCCCChHHHHHHHHHHhc
Q psy18112 79 SRRDYDPTDEPLREEDRIWFREEL 102 (107)
Q Consensus 79 l~~al~~lGf~~~e~~~I~~il~~ 102 (107)
+..++...|+.++.+.+.+..+-+
T Consensus 189 ~~~~l~~~G~~peal~~~l~~lG~ 212 (238)
T cd00807 189 TLRGLRRRGVTPEAIRQFILRQGV 212 (238)
T ss_pred HHHHHHHcCCCHHHHHHHHHHhCC
Confidence 678899999999988887765533
No 70
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. 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 PYRIN and DED (Death Effector Domain). They se
Probab=20.50 E-value=70 Score=19.39 Aligned_cols=25 Identities=28% Similarity=0.363 Sum_probs=19.5
Q ss_pred CCCCcchhHHHHHhcCCCHHHHHHc
Q psy18112 23 APGERNFHIFYQLLVGADVHLLRVV 47 (107)
Q Consensus 23 ~~gErnfHIFY~Ll~g~~~~~~~~l 47 (107)
..|.+.|.+||..|....+.+...|
T Consensus 57 ~kG~~A~~~F~~~L~e~~p~L~~~L 81 (82)
T cd08330 57 SWGASCKDIFYQILREEEPYLVEDL 81 (82)
T ss_pred ccCHHHHHHHHHHHHHhChHHHhHc
Confidence 5799999999999987777655443
No 71
>cd01671 CARD Caspase activation and recruitment domain: a protein-protein interaction domain. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form mutliprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. In general, 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 PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=20.02 E-value=77 Score=18.35 Aligned_cols=19 Identities=32% Similarity=0.510 Sum_probs=15.4
Q ss_pred cCCCCcchhHHHHHhcCCC
Q psy18112 22 QAPGERNFHIFYQLLVGAD 40 (107)
Q Consensus 22 q~~gErnfHIFY~Ll~g~~ 40 (107)
+..|++.|.+|+..|....
T Consensus 54 ~~kg~~af~~F~~~L~~~~ 72 (80)
T cd01671 54 PRKGPKAFQSFLQALQETD 72 (80)
T ss_pred HhcChHHHHHHHHHHHhcC
Confidence 4589999999999987554
Done!