Query psy312
Match_columns 90
No_of_seqs 61 out of 63
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 16:56:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy312.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/312hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3304|consensus 100.0 1.1E-44 2.4E-49 258.1 11.4 90 1-90 57-146 (148)
2 PF06179 Med22: Surfeit locus 99.9 2.6E-24 5.6E-29 144.9 2.9 79 2-80 31-109 (109)
3 PRK07033 hypothetical protein; 73.0 6.9 0.00015 32.2 4.6 44 18-61 49-92 (427)
4 PF15463 ECM11: Extracellular 67.2 13 0.00029 25.9 4.4 56 19-74 75-136 (139)
5 PRK08126 hypothetical protein; 66.4 14 0.0003 30.6 5.0 44 18-61 64-107 (432)
6 PF09753 Use1: Membrane fusion 65.1 56 0.0012 24.5 8.8 58 21-87 168-225 (251)
7 PF09340 NuA4: Histone acetylt 62.1 31 0.00066 22.3 5.1 31 52-86 4-34 (80)
8 PF09278 MerR-DNA-bind: MerR, 61.0 31 0.00067 20.1 7.2 40 29-70 17-56 (65)
9 PRK07034 hypothetical protein; 57.7 26 0.00056 30.2 5.2 43 18-61 144-186 (536)
10 cd04779 HTH_MerR-like_sg4 Heli 55.4 68 0.0015 22.3 6.6 41 29-69 59-100 (134)
11 KOG4196|consensus 52.2 47 0.001 24.0 5.1 38 50-89 74-111 (135)
12 PF01920 Prefoldin_2: Prefoldi 49.8 55 0.0012 20.6 4.7 47 36-86 55-101 (106)
13 cd04769 HTH_MerR2 Helix-Turn-H 43.7 94 0.002 20.5 6.6 39 29-67 59-103 (116)
14 KOG2678|consensus 43.6 1.2E+02 0.0026 23.9 6.5 58 21-87 156-213 (244)
15 PF08295 Sin3_corepress: Sin3 39.7 65 0.0014 21.8 4.0 32 3-34 62-93 (101)
16 cd01107 HTH_BmrR Helix-Turn-He 39.5 1.1E+02 0.0023 20.0 6.7 43 29-71 61-103 (108)
17 PF10768 FliX: Class II flagel 38.4 1.5E+02 0.0032 21.3 6.2 58 14-73 68-126 (139)
18 TIGR00153 conserved hypothetic 38.1 1.5E+02 0.0034 21.4 7.6 44 14-61 122-165 (216)
19 cd04782 HTH_BltR Helix-Turn-He 38.0 1.1E+02 0.0024 19.6 5.2 29 29-57 60-88 (97)
20 KOG0977|consensus 37.0 73 0.0016 27.6 4.8 63 20-82 293-367 (546)
21 PF01484 Col_cuticle_N: Nemato 35.9 68 0.0015 18.0 3.2 29 34-62 21-49 (53)
22 cd00890 Prefoldin Prefoldin is 35.6 1.2E+02 0.0027 19.6 6.5 43 40-82 84-126 (129)
23 PRK12817 flgG flagellar basal 35.2 61 0.0013 24.6 3.7 26 5-33 234-259 (260)
24 PF08831 MHCassoc_trimer: Clas 34.5 48 0.001 21.6 2.6 35 32-66 7-45 (72)
25 PRK04654 sec-independent trans 34.4 2.2E+02 0.0047 22.0 8.6 61 17-82 24-86 (214)
26 smart00742 Hr1 Rho effector or 34.0 1E+02 0.0022 18.1 5.0 42 17-74 15-56 (57)
27 PHA00743 helix-turn-helix prot 33.8 1.1E+02 0.0025 18.6 5.1 20 24-43 10-29 (51)
28 COG4847 Uncharacterized protei 33.5 1.6E+02 0.0035 20.3 7.4 50 18-67 52-101 (103)
29 COG1392 Phosphate transport re 33.5 2.1E+02 0.0045 21.5 8.1 61 14-84 121-181 (217)
30 PF09850 DUF2077: Uncharacteri 33.4 84 0.0018 22.3 4.1 61 17-77 2-72 (206)
31 PF02996 Prefoldin: Prefoldin 33.3 1.4E+02 0.0029 19.3 6.2 43 42-84 76-118 (120)
32 PF08606 Prp19: Prp19/Pso4-lik 31.9 1.4E+02 0.0031 19.2 6.0 36 47-82 12-47 (70)
33 KOG1466|consensus 31.0 2.3E+02 0.005 23.1 6.4 57 18-75 73-129 (313)
34 TIGR00512 salvage_mtnA S-methy 30.8 2.8E+02 0.0062 22.3 7.3 53 15-73 87-139 (331)
35 PF05321 HHA: Haemolysin expre 30.8 88 0.0019 19.5 3.3 36 21-56 8-43 (57)
36 KOG1507|consensus 30.6 1.5E+02 0.0032 24.7 5.4 42 41-86 68-109 (358)
37 PF00512 HisKA: His Kinase A ( 30.0 99 0.0021 17.6 3.3 25 12-36 39-63 (68)
38 KOG0119|consensus 29.2 1.1E+02 0.0024 26.7 4.6 59 22-80 54-122 (554)
39 PF05700 BCAS2: Breast carcino 29.2 2.4E+02 0.0052 20.9 6.2 48 40-87 140-187 (221)
40 PRK02506 dihydroorotate dehydr 29.0 97 0.0021 24.1 4.0 46 4-49 252-305 (310)
41 PF02185 HR1: Hr1 repeat; Int 28.9 1.4E+02 0.003 18.1 4.6 43 17-75 15-58 (70)
42 cd04784 HTH_CadR-PbrR Helix-Tu 28.3 1.8E+02 0.004 19.3 6.4 36 29-64 60-100 (127)
43 cd04777 HTH_MerR-like_sg1 Heli 27.7 1.7E+02 0.0038 18.8 5.5 11 29-39 58-68 (107)
44 TIGR02047 CadR-PbrR Cd(II)/Pb( 27.7 2E+02 0.0042 19.4 5.8 42 29-70 60-106 (127)
45 cd04776 HTH_GnyR Helix-Turn-He 27.3 2E+02 0.0042 19.2 6.7 43 29-71 58-108 (118)
46 PF11945 WASH_WAHD: WAHD domai 27.0 3.2E+02 0.007 21.7 7.3 44 18-73 23-66 (297)
47 cd01282 HTH_MerR-like_sg3 Heli 27.0 1.9E+02 0.0041 19.0 6.4 39 29-67 59-105 (112)
48 PF11690 DUF3287: Protein of u 26.4 1.6E+02 0.0034 20.4 4.3 37 46-84 45-81 (109)
49 PF02561 FliS: Flagellar prote 26.3 1.5E+02 0.0032 19.7 4.1 73 5-80 4-81 (122)
50 PRK07565 dihydroorotate dehydr 25.9 61 0.0013 25.2 2.4 46 5-50 251-304 (334)
51 cd00584 Prefoldin_alpha Prefol 25.7 2.1E+02 0.0045 19.0 6.5 43 40-82 84-126 (129)
52 KOG3499|consensus 25.5 51 0.0011 21.2 1.5 11 28-38 4-14 (69)
53 COG2841 Uncharacterized protei 25.1 1.9E+02 0.0041 18.8 4.2 53 27-79 7-68 (72)
54 PF01627 Hpt: Hpt domain; Int 24.8 1.5E+02 0.0033 17.2 7.6 61 21-81 28-88 (90)
55 COG1382 GimC Prefoldin, chaper 24.8 2.5E+02 0.0055 19.7 5.1 33 46-78 80-112 (119)
56 smart00761 HDAC_interact Histo 24.7 1.6E+02 0.0035 20.1 4.0 31 3-33 63-93 (102)
57 PF11598 COMP: Cartilage oligo 24.7 1.6E+02 0.0034 17.3 3.5 20 16-35 4-23 (45)
58 PRK12692 flgG flagellar basal 24.6 1.1E+02 0.0023 23.5 3.5 26 5-33 236-261 (262)
59 PF11932 DUF3450: Protein of u 24.3 2.3E+02 0.005 21.1 5.2 40 24-64 106-145 (251)
60 PF06791 TMP_2: Prophage tail 24.0 2.8E+02 0.0061 20.4 5.6 46 39-84 152-197 (210)
61 cd00632 Prefoldin_beta Prefold 23.6 2.2E+02 0.0047 18.5 6.9 45 35-79 55-99 (105)
62 cd04770 HTH_HMRTR Helix-Turn-H 23.6 2.2E+02 0.0048 18.6 6.2 40 29-68 60-104 (123)
63 PF15136 UPF0449: Uncharacteri 22.8 2.6E+02 0.0055 19.1 5.2 32 41-72 62-93 (97)
64 PF15272 BBP1_C: Spindle pole 22.5 3.3E+02 0.0071 20.7 5.7 55 26-82 8-62 (196)
65 TIGR00511 ribulose_e2b2 ribose 22.4 3.8E+02 0.0082 20.9 6.9 49 18-73 64-112 (301)
66 PF10960 DUF2762: Protein of u 22.1 2.2E+02 0.0048 18.1 7.8 56 25-82 5-60 (71)
67 PF00611 FCH: Fes/CIP4, and EF 22.0 1.9E+02 0.0042 17.3 4.5 20 39-58 9-28 (91)
68 PF07350 DUF1479: Protein of u 21.9 2.1E+02 0.0047 24.0 5.0 37 28-64 6-44 (416)
69 PRK13752 putative transcriptio 21.8 2.9E+02 0.0062 19.3 6.8 42 29-70 67-111 (144)
70 PF04111 APG6: Autophagy prote 21.7 4.1E+02 0.0088 20.9 6.5 41 46-87 60-100 (314)
71 PRK08334 translation initiatio 21.6 4.5E+02 0.0098 21.5 7.1 53 17-73 105-157 (356)
72 PF03410 Peptidase_M44: Protei 21.5 64 0.0014 28.2 1.8 15 71-85 102-116 (590)
73 PF07889 DUF1664: Protein of u 21.1 3E+02 0.0066 19.3 10.0 64 13-81 36-99 (126)
74 KOG0977|consensus 21.0 4E+02 0.0086 23.3 6.5 49 35-83 147-195 (546)
75 PF05600 DUF773: Protein of un 20.8 2.7E+02 0.0059 23.6 5.4 36 49-88 130-165 (507)
76 KOG2196|consensus 20.6 4.4E+02 0.0095 20.9 8.0 64 18-81 139-202 (254)
77 TIGR02425 decarb_PcaC 4-carbox 20.3 2.9E+02 0.0063 18.8 5.3 51 5-57 71-121 (123)
78 cd01109 HTH_YyaN Helix-Turn-He 20.3 2.6E+02 0.0056 18.2 6.8 43 29-71 60-107 (113)
79 COG1564 THI80 Thiamine pyropho 20.3 19 0.0004 27.4 -1.4 36 32-67 42-83 (212)
80 TIGR01220 Pmev_kin_Gr_pos phos 20.1 4.1E+02 0.0088 21.0 6.0 34 25-58 254-287 (358)
No 1
>KOG3304|consensus
Probab=100.00 E-value=1.1e-44 Score=258.09 Aligned_cols=90 Identities=67% Similarity=1.044 Sum_probs=88.7
Q ss_pred ChhhHHHHHHHHHhHHHHHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q psy312 1 MTQCELDLYEMHVRAGNIVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDL 80 (90)
Q Consensus 1 ~tq~~qe~fem~vRAa~mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eL 80 (90)
+|||+||+|||+|||+|||||||||||||+|||||||||||+|+|++|++++.+|++.+++|+++++.|+||+|.+||||
T Consensus 57 ~tq~~q~a~eM~vRAa~mVrA~dsLlKLvsdLKqflIl~dFhsln~~I~q~~aq~~~t~~e~~r~l~~l~de~s~~L~eL 136 (148)
T KOG3304|consen 57 ATQGEQDAYEMHVRAANMVRAGDSLLKLVSDLKQFLILNDFHSLNEAIDQRNAQFRQTQEECDRKLITLRDEVSIDLYEL 136 (148)
T ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhccC
Q psy312 81 EEEYYTSVYK 90 (90)
Q Consensus 81 E~eYYsS~~k 90 (90)
|+|||+|.||
T Consensus 137 E~eyyss~~r 146 (148)
T KOG3304|consen 137 EEEYYSSAYR 146 (148)
T ss_pred HHHHHHHHHh
Confidence 9999999985
No 2
>PF06179 Med22: Surfeit locus protein 5 subunit 22 of Mediator complex; PDB: 3R84_P 3RJ1_K.
Probab=99.89 E-value=2.6e-24 Score=144.91 Aligned_cols=79 Identities=37% Similarity=0.642 Sum_probs=53.1
Q ss_pred hhhHHHHHHHHHhHHHHHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q psy312 2 TQCELDLYEMHVRAGNIVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDL 80 (90)
Q Consensus 2 tq~~qe~fem~vRAa~mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eL 80 (90)
++++++.|+|++||++||||||+||+||++||+++|||||+++|+.++.+...++...++|++++..|+++++.+|++|
T Consensus 31 ~~~a~~~~~m~~~a~~lira~e~LL~Ltr~LKe~wll~d~~~~~e~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~l~el 109 (109)
T PF06179_consen 31 TQAAQESFQMEVRAAQLIRAAEDLLSLTRELKELWLLGDFPPLNEDIDEQEERLDQEQEEVDKLLNALRDELMRELAEL 109 (109)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHB-----------------TT------THHHHSTTTTTTT--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 6899999999999999999999999999999999999999999999999999999999999999999999999999986
No 3
>PRK07033 hypothetical protein; Provisional
Probab=73.04 E-value=6.9 Score=32.21 Aligned_cols=44 Identities=23% Similarity=0.394 Sum_probs=40.6
Q ss_pred HHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHH
Q psy312 18 IVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTE 61 (90)
Q Consensus 18 mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~ 61 (90)
+|.||--||.|+..|+...-..|...+-+.+...++.|++....
T Consensus 49 Lv~AA~pLL~l~~~lr~~~~~~d~~~Lr~~l~~~i~~fe~~~~~ 92 (427)
T PRK07033 49 LVAAANPLLNLIPQIRSTVHHPDPASLREQLLDEIRQFEERAQQ 92 (427)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999998889999999999999999876654
No 4
>PF15463 ECM11: Extracellular mutant protein 11
Probab=67.21 E-value=13 Score=25.86 Aligned_cols=56 Identities=20% Similarity=0.392 Sum_probs=42.9
Q ss_pred HHhHhhHHH----HHHHHHHH--HHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHH
Q psy312 19 VRAGESLLK----LVSDIKQY--LILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMA 74 (90)
Q Consensus 19 VrAaesLLk----LvseLKq~--LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~ 74 (90)
..+|+.|++ |+..||.. -.-.=|..++..|..|...++.+...++++|..|+..-.
T Consensus 75 e~~Gd~~l~qf~~l~~kl~~~R~~~r~~~~~fe~eI~~R~eav~~~~~~l~~kL~~mk~~G~ 136 (139)
T PF15463_consen 75 EEAGDWFLEQFSELMQKLKEARRKLRKKFAVFEDEINRRAEAVRAQGEQLDRKLEKMKEGGK 136 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 567777764 45555442 234557888999999999999999999999999997654
No 5
>PRK08126 hypothetical protein; Provisional
Probab=66.41 E-value=14 Score=30.63 Aligned_cols=44 Identities=16% Similarity=0.307 Sum_probs=40.6
Q ss_pred HHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHH
Q psy312 18 IVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTE 61 (90)
Q Consensus 18 mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~ 61 (90)
+|.||-.||.|+..|+..+-..|...|-+.+-..+..|++....
T Consensus 64 Ll~aA~pLL~l~~~lr~~~~~~~~~~Lr~~l~~ei~~fe~~~~~ 107 (432)
T PRK08126 64 LLEAARPLLRALADMPATLDSAAVEQLRTLLVREVRLFQKLCEQ 107 (432)
T ss_pred HHHHHHHHHHHHHHhhcccCcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999998999999999999999999886654
No 6
>PF09753 Use1: Membrane fusion protein Use1; InterPro: IPR019150 This entry represents a family of proteins, approximately 300 residues in length, involved in vesicle transport. They have a single C-terminal transmembrane domain and a SNARE [soluble NSF (N-ethylmaleimide-sensitive fusion protein) attachment protein receptor] domain of approximately 60 residues. The SNARE domains are essential for membrane fusion and are conserved from yeasts to humans. Use1 is one of the three protein subunits that make up the SNARE complex and it is specifically required for Golgi-endoplasmic reticulum retrograde transport [].
Probab=65.14 E-value=56 Score=24.50 Aligned_cols=58 Identities=19% Similarity=0.356 Sum_probs=47.3
Q ss_pred hHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhh
Q psy312 21 AGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEEEYYTS 87 (90)
Q Consensus 21 AaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~eYYsS 87 (90)
=+++|++|+..||+... .++..|..-...+.......++.+..|..+-.. |+.+++.+
T Consensus 168 L~~em~~La~~LK~~s~-----~~~~~l~~D~~~L~~~~~~~d~n~~~l~~~~~r----l~~~~~~~ 225 (251)
T PF09753_consen 168 LTEEMLSLARQLKENSL-----AFSQILKEDNKVLDRTEEGLDRNLSSLKRESKR----LKEHSSKS 225 (251)
T ss_pred HHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHhc
Confidence 47899999999999875 468899999999999999999999988877554 56555443
No 7
>PF09340 NuA4: Histone acetyltransferase subunit NuA4; InterPro: IPR015418 The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast []. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control [].
Probab=62.07 E-value=31 Score=22.25 Aligned_cols=31 Identities=23% Similarity=0.412 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhh
Q psy312 52 SKLFRTKQTECDQKLMNLRDDMAADLYDLEEEYYT 86 (90)
Q Consensus 52 ~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~eYYs 86 (90)
..++.++..+++..|. .+-..+|++|..|..
T Consensus 4 L~~l~~~k~~Le~~L~----~lE~qIy~~Et~YL~ 34 (80)
T PF09340_consen 4 LKELLQKKKKLEKDLA----ALEKQIYDKETSYLE 34 (80)
T ss_pred HHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHH
Confidence 3455555666666655 555668999999987
No 8
>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=60.97 E-value=31 Score=20.11 Aligned_cols=40 Identities=20% Similarity=0.371 Sum_probs=26.1
Q ss_pred HHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHH
Q psy312 29 VSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLR 70 (90)
Q Consensus 29 vseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lr 70 (90)
+.|+|+++-+.|-+ +.........+..+.++.++++..+.
T Consensus 17 L~eI~~~l~l~~~~--~~~~~~~~~~l~~~~~~i~~~i~~L~ 56 (65)
T PF09278_consen 17 LEEIRELLELYDQG--DPPCADRRALLEEKLEEIEEQIAELQ 56 (65)
T ss_dssp HHHHHHHHHHCCSH--CHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhccCCC--CCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 58999999886653 33344444666777777777666543
No 9
>PRK07034 hypothetical protein; Provisional
Probab=57.69 E-value=26 Score=30.22 Aligned_cols=43 Identities=21% Similarity=0.355 Sum_probs=39.5
Q ss_pred HHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHH
Q psy312 18 IVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTE 61 (90)
Q Consensus 18 mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~ 61 (90)
+|.||-.||.|+..|+...- .|...+-+.+...++.|++....
T Consensus 144 Lv~AA~pLL~l~~~lr~~~~-~~~~~Lr~~l~~eI~~fe~~~~~ 186 (536)
T PRK07034 144 YIAAAMPLLLLVENIRSWPT-RNAAEVRPPIVRELQYFQQHLQK 186 (536)
T ss_pred HHHHHHHHHHHHHHHhcccc-cCHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999988 59999999999999999987754
No 10
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). 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=55.38 E-value=68 Score=22.30 Aligned_cols=41 Identities=17% Similarity=0.209 Sum_probs=23.3
Q ss_pred HHHHHHHHHhcCh-hhHHHHHHHhHHHHHHHHHHHHHHHHhH
Q psy312 29 VSDIKQYLILNDF-PSVNEAITQNSKLFRTKQTECDQKLMNL 69 (90)
Q Consensus 29 vseLKq~LIL~DF-~~lne~i~~~~~~~~~~~~~~d~~l~~l 69 (90)
++++|.++-..+. ....+.+.++.+.+..+..+.+.++..|
T Consensus 59 L~eI~~~l~~~~~~~~~~~~~~~~~~~l~~~i~~Le~~l~~L 100 (134)
T cd04779 59 LAEIKDQLEEVQRSDKEQREVAQEVQLVCDQIDGLEHRLKQL 100 (134)
T ss_pred HHHHHHHHHhhccccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3578888766553 2334445555555666655555555444
No 11
>KOG4196|consensus
Probab=52.23 E-value=47 Score=23.98 Aligned_cols=38 Identities=21% Similarity=0.320 Sum_probs=28.5
Q ss_pred HhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhhcc
Q psy312 50 QNSKLFRTKQTECDQKLMNLRDDMAADLYDLEEEYYTSVY 89 (90)
Q Consensus 50 ~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~eYYsS~~ 89 (90)
++-.+++.+.....+.+..|+.|.+.. -+|-.||.+.|
T Consensus 74 ~Qk~eLE~~k~~L~qqv~~L~~e~s~~--~~E~da~k~k~ 111 (135)
T KOG4196|consen 74 QQKHELEKEKAELQQQVEKLKEENSRL--RRELDAYKSKY 111 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHH
Confidence 345678888889999999999999887 45556665544
No 12
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=49.81 E-value=55 Score=20.57 Aligned_cols=47 Identities=15% Similarity=0.296 Sum_probs=34.3
Q ss_pred HHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhh
Q psy312 36 LILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEEEYYT 86 (90)
Q Consensus 36 LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~eYYs 86 (90)
+|..|-+.+-..+..+...+......+...+..+.. .+.+++...|.
T Consensus 55 fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~----~l~~~~~~l~~ 101 (106)
T PF01920_consen 55 FVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEK----KLKELKKKLYE 101 (106)
T ss_dssp EEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHC
T ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH
Confidence 566777888888888888888888888888775544 44556665553
No 13
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=43.74 E-value=94 Score=20.51 Aligned_cols=39 Identities=18% Similarity=0.271 Sum_probs=21.3
Q ss_pred HHHHHHHHHhcChhh------HHHHHHHhHHHHHHHHHHHHHHHH
Q psy312 29 VSDIKQYLILNDFPS------VNEAITQNSKLFRTKQTECDQKLM 67 (90)
Q Consensus 29 vseLKq~LIL~DF~~------lne~i~~~~~~~~~~~~~~d~~l~ 67 (90)
++|+|+++-..|.+. +-+.+..+.+.+.++..+..+.+.
T Consensus 59 l~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~ 103 (116)
T cd04769 59 LAELKAIFAGHEGRAVLPWPHLQQALEDKKQEIRAQITELQQLLA 103 (116)
T ss_pred HHHHHHHHhccccCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 688999988887753 223344444444444444443333
No 14
>KOG2678|consensus
Probab=43.56 E-value=1.2e+02 Score=23.92 Aligned_cols=58 Identities=21% Similarity=0.276 Sum_probs=43.2
Q ss_pred hHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhh
Q psy312 21 AGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEEEYYTS 87 (90)
Q Consensus 21 AaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~eYYsS 87 (90)
-+|||++|+..||+..+ +--.+|+.-++.+.......|.....|++.=. -+|.+=|++
T Consensus 156 Laesll~LArslKtnal-----AfqsalkeDnQvl~~~~k~~D~N~~~L~~~Se----rve~y~ksk 213 (244)
T KOG2678|consen 156 LAESLLKLARSLKTNAL-----AFQSALKEDNQVLGAAEKGIDVNSQGLMDVSE----RVEKYDKSK 213 (244)
T ss_pred HHHHHHHHHHHHHHhHH-----HHHHHHHhhHHHHHHHHHHHhHHHHHHHhhhH----HHHHHHHhh
Confidence 48999999999999764 44567788888888888888888887776532 456665554
No 15
>PF08295 Sin3_corepress: Sin3 family co-repressor; InterPro: IPR013194 This domain is found on transcriptional regulators. It forms interactions with histone deacetylases [].
Probab=39.70 E-value=65 Score=21.75 Aligned_cols=32 Identities=19% Similarity=0.271 Sum_probs=27.3
Q ss_pred hhHHHHHHHHHhHHHHHHhHhhHHHHHHHHHH
Q psy312 3 QCELDLYEMHVRAGNIVRAGESLLKLVSDIKQ 34 (90)
Q Consensus 3 q~~qe~fem~vRAa~mVrAaesLLkLvseLKq 34 (90)
.|+-|.||+.+.-....++.+.|-.|...|.+
T Consensus 62 ~~EDeR~E~D~~ie~~~~tI~~Le~l~~~i~~ 93 (101)
T PF08295_consen 62 RCEDERFELDMLIESNRSTIKLLEELQEKIQD 93 (101)
T ss_pred HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 57889999999999999999988888777653
No 16
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=39.51 E-value=1.1e+02 Score=20.00 Aligned_cols=43 Identities=16% Similarity=0.205 Sum_probs=28.8
Q ss_pred HHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHH
Q psy312 29 VSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRD 71 (90)
Q Consensus 29 vseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrd 71 (90)
++++|..+-..+.+.+...+..+.+.++++..+.......|.+
T Consensus 61 l~~i~~l~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~ 103 (108)
T cd01107 61 LEEIKEILDADNDDELRKLLREKLAELEAEIEELQRILRLLED 103 (108)
T ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4778877766776666666777777777776666666555543
No 17
>PF10768 FliX: Class II flagellar assembly regulator; InterPro: IPR019704 The FliX protein is possibly a transient component of the flagellum that is required for the assembly process. FliX may contribute to the targeting or assembly of the P- and L-ring protein monomers at the cell pole. The family carries a potential N-terminal signal sequence and at least one transmembrane domain indicating that it might function either in or in association with the cell membrane [].
Probab=38.40 E-value=1.5e+02 Score=21.31 Aligned_cols=58 Identities=22% Similarity=0.431 Sum_probs=38.6
Q ss_pred hHHHHHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHH-HHHHHhHHHHH
Q psy312 14 RAGNIVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTEC-DQKLMNLRDDM 73 (90)
Q Consensus 14 RAa~mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~-d~~l~~lrdel 73 (90)
|--+.||-|+.||-...+||--|+-+.++- .....=...++++.+.+ |-.|..+.+||
T Consensus 68 rRrRav~Rg~~lLD~Ld~Lk~~LL~G~v~~--~~L~~L~~~~~~~r~~s~Dp~L~~vL~eI 126 (139)
T PF10768_consen 68 RRRRAVRRGHDLLDVLDELKIGLLSGTVPR--GDLERLARAVRERRESSGDPRLDAVLDEI 126 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCCCH--HHHHHHHHHHHHhhccCCCchHHHHHHHH
Confidence 445679999999999999999999987763 22222223333444444 56666666665
No 18
>TIGR00153 conserved hypothetical protein TIGR00153. An apparent homolog with a suggested function is Pit accessory protein from Sinorhizobium meliloti, which may be involved in phosphate (Pi) transport.
Probab=38.13 E-value=1.5e+02 Score=21.41 Aligned_cols=44 Identities=18% Similarity=0.147 Sum_probs=26.4
Q ss_pred hHHHHHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHH
Q psy312 14 RAGNIVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTE 61 (90)
Q Consensus 14 RAa~mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~ 61 (90)
=+..++.+++.+...|..|+ .-+||..+.+.+ .++..++.+.+.
T Consensus 122 l~~~i~~~~~~l~~av~~l~---~~~~~~~i~~~~-~~I~~lE~e~D~ 165 (216)
T TIGR00153 122 VLKITVDMIQHLHRVVEVIE---LETDLSLANDII-KEIKDLEDEIDV 165 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHH---HhccHHHHHHHH-HHHHHHHHHHHH
Confidence 34567889999999998873 357777444422 233444443333
No 19
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=38.04 E-value=1.1e+02 Score=19.64 Aligned_cols=29 Identities=21% Similarity=0.307 Sum_probs=14.8
Q ss_pred HHHHHHHHHhcChhhHHHHHHHhHHHHHH
Q psy312 29 VSDIKQYLILNDFPSVNEAITQNSKLFRT 57 (90)
Q Consensus 29 vseLKq~LIL~DF~~lne~i~~~~~~~~~ 57 (90)
+.++|.++-..|.+.+.+.+..+...+++
T Consensus 60 l~eI~~~l~~~~~~~~~~~l~~~~~~l~~ 88 (97)
T cd04782 60 LKEIKDYLDNRNPDELIELLKKQEKEIKE 88 (97)
T ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Confidence 37778777666554433333333333333
No 20
>KOG0977|consensus
Probab=37.00 E-value=73 Score=27.64 Aligned_cols=63 Identities=19% Similarity=0.263 Sum_probs=43.3
Q ss_pred HhHhhHHHHHHHHHHH-HHhcChhhHHHHHHHhHHHH-----------HHHHHHHHHHHHhHHHHHHHHHHHHHH
Q psy312 20 RAGESLLKLVSDIKQY-LILNDFPSVNEAITQNSKLF-----------RTKQTECDQKLMNLRDDMAADLYDLEE 82 (90)
Q Consensus 20 rAaesLLkLvseLKq~-LIL~DF~~lne~i~~~~~~~-----------~~~~~~~d~~l~~lrdel~~~L~eLE~ 82 (90)
.|=|.|+++.+.+=.+ .=|+|.++-|....++++.+ ++...+-+..+..||++|...+-||+.
T Consensus 293 ~~rEEl~~~R~~i~~Lr~klselE~~n~~L~~~I~dL~~ql~e~~r~~e~~L~~kd~~i~~mReec~~l~~Elq~ 367 (546)
T KOG0977|consen 293 YAREELRRIRSRISGLRAKLSELESRNSALEKRIEDLEYQLDEDQRSFEQALNDKDAEIAKMREECQQLSVELQK 367 (546)
T ss_pred HHHHHHHHHHhcccchhhhhccccccChhHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 3556676665433221 23677777766666666554 455677889999999999999999875
No 21
>PF01484 Col_cuticle_N: Nematode cuticle collagen N-terminal domain; InterPro: IPR002486 The function of this domain is unknown. It is found in the N-terminal region of nematode cuticle collagens (see IPR008160 from INTERPRO). Cuticle is a tough elastic structure secreted by hypodermal cells and is primarily composed of collagen proteins [, ].; GO: 0042302 structural constituent of cuticle
Probab=35.91 E-value=68 Score=17.99 Aligned_cols=29 Identities=14% Similarity=0.243 Sum_probs=21.6
Q ss_pred HHHHhcChhhHHHHHHHhHHHHHHHHHHH
Q psy312 34 QYLILNDFPSVNEAITQNSKLFRTKQTEC 62 (90)
Q Consensus 34 q~LIL~DF~~lne~i~~~~~~~~~~~~~~ 62 (90)
-..|++|...+.+.++...+.|+...++.
T Consensus 21 ~p~i~~~i~~~~~~~~~em~~fk~~s~d~ 49 (53)
T PF01484_consen 21 VPSIYNDIQNFQSELDDEMEEFKEISDDA 49 (53)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677888888888888888887776653
No 22
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=35.55 E-value=1.2e+02 Score=19.58 Aligned_cols=43 Identities=12% Similarity=0.230 Sum_probs=33.0
Q ss_pred ChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q psy312 40 DFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEE 82 (90)
Q Consensus 40 DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~ 82 (90)
+++..-..++.+...+....+.++..+..+.+++..--..+..
T Consensus 84 ~~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~l~~ 126 (129)
T cd00890 84 SLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQEELQQ 126 (129)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556667788888888888888888888888888776666654
No 23
>PRK12817 flgG flagellar basal body rod protein FlgG; Reviewed
Probab=35.18 E-value=61 Score=24.64 Aligned_cols=26 Identities=0% Similarity=0.429 Sum_probs=21.1
Q ss_pred HHHHHHHHHhHHHHHHhHhhHHHHHHHHH
Q psy312 5 ELDLYEMHVRAGNIVRAGESLLKLVSDIK 33 (90)
Q Consensus 5 ~qe~fem~vRAa~mVrAaesLLkLvseLK 33 (90)
.|-+|||..|+ ++.++.+.+.+.+||
T Consensus 234 ~qRaye~n~k~---i~t~d~~~~~~~~l~ 259 (260)
T PRK12817 234 TQRAFQLSSKG---IKTADEMWGIINNMR 259 (260)
T ss_pred HHHHHHHHHHH---HHHHHHHHHHHHHhh
Confidence 57789988765 556899999999887
No 24
>PF08831 MHCassoc_trimer: Class II MHC-associated invariant chain trimerisation domain; InterPro: IPR011988 This entry represents the trimerisation domain of the MHC class II-associated invariant chain (Ii). Ii plays a critical role in the assembly of the MHC, as well as in MHC II antigen processing by stabilising peptide-free class II alpha/beta heterodimers in a complex soon after their synthesis and directing transport of the complex from the endoplasmic reticulum to compartments where peptide loading of class II takes place []. In antigen-presenting cells (APCs), loading of MHC II molecules with peptides is regulated by Ii, which blocks MHC II antigen-binding sites in pre-endosomal compartments []. Several molecules then act upon MHC II molecules in endosomes to facilitate peptide loading: Ii-degrading proteases, the peptide exchange factor, human leukocyte antigen-DM (HLA-DM), and its modulator, HLA-DO (DO). The Invariant chain contains a single transmembrane domain. Ii first assembles into a trimer and then associates with three class II alpha/beta MHC heterodimers. Although the membrane-proximal region of the Ii luminal domain is structurally disordered, the C-terminal segment of the luminal domain is largely alpha-helical and contains a major interaction site for the Ii trimer []. More information about these proteins can be found at Protein of the Month: MHC [].; GO: 0042289 MHC class II protein binding, 0006886 intracellular protein transport, 0006955 immune response, 0019882 antigen processing and presentation, 0016020 membrane; PDB: 1IIE_C.
Probab=34.51 E-value=48 Score=21.57 Aligned_cols=35 Identities=29% Similarity=0.494 Sum_probs=22.2
Q ss_pred HHHHHHhcC----hhhHHHHHHHhHHHHHHHHHHHHHHH
Q psy312 32 IKQYLILND----FPSVNEAITQNSKLFRTKQTECDQKL 66 (90)
Q Consensus 32 LKq~LIL~D----F~~lne~i~~~~~~~~~~~~~~d~~l 66 (90)
.|-.|.=+| ||.+|+..-.+.+.+++..++.+.+.
T Consensus 7 Vk~LL~~~~P~k~~P~~n~tf~~NL~~LK~~M~~~~Wk~ 45 (72)
T PF08831_consen 7 VKHLLLKSDPLKVYPQFNGTFLENLKHLKNQMNESDWKS 45 (72)
T ss_dssp HHHHHHHH-TT-------S-HHHHHHHHHHHS-HHHHHH
T ss_pred HHHHHhccChhhhccccchHHHHHHHHHHHhcchhhHHH
Confidence 455566668 99999999999999999999998874
No 25
>PRK04654 sec-independent translocase; Provisional
Probab=34.44 E-value=2.2e+02 Score=22.02 Aligned_cols=61 Identities=11% Similarity=0.193 Sum_probs=42.4
Q ss_pred HHHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHH--hHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q psy312 17 NIVRAGESLLKLVSDIKQYLILNDFPSVNEAITQ--NSKLFRTKQTECDQKLMNLRDDMAADLYDLEE 82 (90)
Q Consensus 17 ~mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~--~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~ 82 (90)
++=.++.+|-+.|-.+|.+ |..+.+.+.+ ..+++++...+....+..+++++-....++++
T Consensus 24 rLPe~aRtlGk~irk~R~~-----~~~vk~El~~El~~~ELrk~l~~~~~~i~~~~~~lk~~~~el~q 86 (214)
T PRK04654 24 RLPKAARFAGLWVRRARMQ-----WDSVKQELERELEAEELKRSLQDVQASLREAEDQLRNTQQQVEQ 86 (214)
T ss_pred HHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445677778888888853 4555554443 34567777777777888888888888888874
No 26
>smart00742 Hr1 Rho effector or protein kinase C-related kinase homology region 1 homologues. Alpha-helical domain found in vertebrate PRK1 and yeast PKC1 protein kinases C. The HR1 in rhophilin bind RhoGTP; those in PRK1 bind RhoA and RhoB. Also called RBD - Rho-binding domain
Probab=33.98 E-value=1e+02 Score=18.13 Aligned_cols=42 Identities=21% Similarity=0.286 Sum_probs=30.0
Q ss_pred HHHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHH
Q psy312 17 NIVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMA 74 (90)
Q Consensus 17 ~mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~ 74 (90)
.|..+|+.++++.+.=+ ...........++++++.-|++.+.
T Consensus 15 ~i~~Gae~m~~~~~~~~----------------k~~~~a~~~l~es~~ki~~L~~~L~ 56 (57)
T smart00742 15 KVKEGAENMRKLTSNDR----------------KVLSEAQSMLRESNQKLDLLKEELE 56 (57)
T ss_pred HHHHHHHHHHHHHcCcH----------------HHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 46778888888876511 3455677777888888888887663
No 27
>PHA00743 helix-turn-helix protein
Probab=33.77 E-value=1.1e+02 Score=18.63 Aligned_cols=20 Identities=25% Similarity=0.507 Sum_probs=17.6
Q ss_pred hHHHHHHHHHHHHHhcChhh
Q psy312 24 SLLKLVSDIKQYLILNDFPS 43 (90)
Q Consensus 24 sLLkLvseLKq~LIL~DF~~ 43 (90)
.||++||++|==+|++..+.
T Consensus 10 eLLs~iheIKID~i~~~~~k 29 (51)
T PHA00743 10 ELLSIIHEIKIDIITQSYDK 29 (51)
T ss_pred HHHHHHHHHhhhhhcccCCH
Confidence 69999999999999988654
No 28
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=33.55 E-value=1.6e+02 Score=20.32 Aligned_cols=50 Identities=18% Similarity=0.217 Sum_probs=44.5
Q ss_pred HHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHH
Q psy312 18 IVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLM 67 (90)
Q Consensus 18 mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~ 67 (90)
.++|-.-|+.++-=+|..-.+-+=+-+.+.|++..+.++...-+..+++.
T Consensus 52 ll~a~~ll~~~ivllkel~~~Aeseeake~irq~rq~~EklAg~lTkki~ 101 (103)
T COG4847 52 LLLANLLLLYLIVLLKELAVIAESEEAKESIRQVRQEVEKLAGDLTKKIE 101 (103)
T ss_pred HHHHHHHHHHHHHHHHHHhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 47888889999999999999999999999999999999988888777764
No 29
>COG1392 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]
Probab=33.52 E-value=2.1e+02 Score=21.54 Aligned_cols=61 Identities=13% Similarity=0.170 Sum_probs=36.5
Q ss_pred hHHHHHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q psy312 14 RAGNIVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEEEY 84 (90)
Q Consensus 14 RAa~mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~eY 84 (90)
=+.+.+.|++.+.+.|..|.+.+-= ..+...+-.+.+........+-.++-..||.+|.+.
T Consensus 121 ~~~~~~~a~~~~~~ai~~L~~~~e~----------~~~~~~i~~eI~~~E~e~D~i~~~l~k~Lf~~e~~~ 181 (217)
T COG1392 121 LVDLSLKAAELLAEAIELLEDLLES----------ADRLLEIIKEIEALEHECDDIQRELLKKLFSLETEI 181 (217)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh----------HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhccccc
Confidence 3567789999999988888765432 222333333333333334444456667788887765
No 30
>PF09850 DUF2077: Uncharacterized protein conserved in bacteria (DUF2077); InterPro: IPR017732 At least two distinct groups of proteins, often encoded by adjacent genes, show sequence similarity due to homology between type IV secretion systems and type VI secretion systems. One is the IcmF family (IPR017731 from INTERPRO). The other group is the DotU family, defined by this N-terminal domain, which includes DotU from the Legionella pneumophila type IV secretion system. Many of the proteins in this entry from type VI secretion systems have an additional C-terminal domain with OmpA/MotB homology IPR017733 from INTERPRO.; PDB: 4ACL_B 4ACK_B 3U66_A.
Probab=33.42 E-value=84 Score=22.30 Aligned_cols=61 Identities=21% Similarity=0.235 Sum_probs=39.5
Q ss_pred HHHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHH----------HHHHHHhHHHHHHHHH
Q psy312 17 NIVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTE----------CDQKLMNLRDDMAADL 77 (90)
Q Consensus 17 ~mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~----------~d~~l~~lrdel~~~L 77 (90)
.++.++.-|+.+|..|++-.-..|...+-+.+....+.++++..+ ..=-+.++-||+.-..
T Consensus 2 ~L~~~~~pll~~~~~l~~~~~~~~~~~lr~~~~~~l~~~~~~~~~~~~~~~~~~~a~yalca~iDE~vl~~ 72 (206)
T PF09850_consen 2 PLLDAARPLLLLVLRLRQGSSPPDIEELRERLIDLLERFEQRLREAGYSPEDIEDARYALCALIDEAVLNS 72 (206)
T ss_dssp ----HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHHHHHHHHCH
T ss_pred chHHHHHHHHHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 368889999999999999666677788888888888777776432 2223455666665433
No 31
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=33.28 E-value=1.4e+02 Score=19.32 Aligned_cols=43 Identities=14% Similarity=0.198 Sum_probs=33.1
Q ss_pred hhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q psy312 42 PSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEEEY 84 (90)
Q Consensus 42 ~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~eY 84 (90)
+.--+-++.|...++...+++...+..+.+.+......++.-|
T Consensus 76 ~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~~~~l~~~~ 118 (120)
T PF02996_consen 76 EEAIEFLKKRIKELEEQLEKLEKELAELQAQIEQLEQTLQQLY 118 (120)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445667788888888888888888888888887777776543
No 32
>PF08606 Prp19: Prp19/Pso4-like; InterPro: IPR013915 This region is found specifically in PRP19-like protein. The region represented by this protein covers the sequence implicated in self-interaction and a coiled-coiled motif []. PRP19-like proteins form an oligomer that is necessary for spliceosome assembly [].
Probab=31.94 E-value=1.4e+02 Score=19.20 Aligned_cols=36 Identities=11% Similarity=0.241 Sum_probs=23.7
Q ss_pred HHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q psy312 47 AITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEE 82 (90)
Q Consensus 47 ~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~ 82 (90)
....+=..+--+.=.+++++...|.|+|..||+-+.
T Consensus 12 ~lQnEWDa~mLE~f~LRk~l~~~rqELs~aLYq~DA 47 (70)
T PF08606_consen 12 TLQNEWDALMLENFTLRKQLDQTRQELSHALYQHDA 47 (70)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 333333444444556778888889999999987653
No 33
>KOG1466|consensus
Probab=30.96 E-value=2.3e+02 Score=23.05 Aligned_cols=57 Identities=18% Similarity=0.353 Sum_probs=45.8
Q ss_pred HHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHH
Q psy312 18 IVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAA 75 (90)
Q Consensus 18 mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~ 75 (90)
+.-+||=.++.|+-= -.|-..||++.-+..-+|-+.|-++...++++++.+..+.-.
T Consensus 73 l~agcdlF~Rfvtr~-slld~~Df~~ck~~l~erg~~F~~~~~~sR~~IA~l~~~Fi~ 129 (313)
T KOG1466|consen 73 LRAGCDLFMRFVTRA-SLLDYEDFEQCKQHLLERGELFIERARKSRQKIAMLAQDFIT 129 (313)
T ss_pred hhhhhHHHHHHHHhh-hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHhh
Confidence 455677777777532 256778999999999999999999999999999988776543
No 34
>TIGR00512 salvage_mtnA S-methyl-5-thioribose-1-phosphate isomerase. The delineation of this family was based in part on a discussion and neighbor-joining phylogenetic study, by Kyrpides and Woese, of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. This clade is now recognized to include the methionine salvage pathway enzyme MtnA.
Probab=30.79 E-value=2.8e+02 Score=22.27 Aligned_cols=53 Identities=11% Similarity=0.122 Sum_probs=40.0
Q ss_pred HHHHHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHH
Q psy312 15 AGNIVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDM 73 (90)
Q Consensus 15 Aa~mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel 73 (90)
|-||-.|++.+.+.++.+ -|+..+-+.+-.+.+.+.++....++++.....+.
T Consensus 87 avnL~~A~~~~~~~i~~~------~~~~~~k~~l~e~a~~~~~e~~~~~~~I~~~g~~~ 139 (331)
T TIGR00512 87 AVNLSWALDRMRAALEAA------KTVADIKEALLAEAERILEEDLEDNRAIGENGAAL 139 (331)
T ss_pred HhhHHHHHHHHHHHHhcc------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 446777777776666551 68889999888899999988888888887665544
No 35
>PF05321 HHA: Haemolysin expression modulating protein; InterPro: IPR007985 This family consists of haemolysin expression modulating protein (Hha) from Escherichia coli and its enterobacterial homologues, such as YmoA from Yersinia enterocolitica, and RmoA encoded on the R100 plasmid. These proteins act as modulators of bacterial gene expression. Members of the Hha/YmoA/RmoA family act in conjunction with members of the H-NS family, participating in the thermoregulation of different virulence factors and in plasmid transfer []. Hha, along with the chromatin-associated protein H-NS, is involved in the regulation of expression of the toxin alpha-haemolysin in response to osmolarity and temperature []. YmoA modulates the expression of various virulence factors, such as Yop proteins and YadA adhesin, in response to temperature. RmoA is a plasmid R100 modulator involved in plasmid transfer []. The HHA family of proteins display striking similarity to the oligomerization domain of the H-NS proteins.; PDB: 1JW2_A 2K5S_A 2JQT_A.
Probab=30.77 E-value=88 Score=19.48 Aligned_cols=36 Identities=14% Similarity=0.182 Sum_probs=29.8
Q ss_pred hHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHH
Q psy312 21 AGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFR 56 (90)
Q Consensus 21 AaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~ 56 (90)
.-|+|=|+++-++-.|=-+++..+|.+.|-|..++.
T Consensus 8 s~dtLEkv~e~~~~~L~~~e~~~f~~AaDHR~AEL~ 43 (57)
T PF05321_consen 8 SLDTLEKVIEHNRYKLTDDELEAFNSAADHRRAELT 43 (57)
T ss_dssp -HHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHH
T ss_pred CHhhHHHHHHHhhCcCCHHHHHHHHHHHHHHHHHHH
Confidence 458899999999999999999999999998877653
No 36
>KOG1507|consensus
Probab=30.57 E-value=1.5e+02 Score=24.66 Aligned_cols=42 Identities=19% Similarity=0.362 Sum_probs=33.5
Q ss_pred hhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhh
Q psy312 41 FPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEEEYYT 86 (90)
Q Consensus 41 F~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~eYYs 86 (90)
..+|...|..|+..++..+.+|+..=. ..-..+++||..|+.
T Consensus 68 v~~Lp~~Vk~Rv~aLk~lQ~~~~~ie~----~F~~e~~~LE~ky~~ 109 (358)
T KOG1507|consen 68 VENLPPAVKNRVLALKNLQLECDEIEA----KFQEEVHELERKYAK 109 (358)
T ss_pred hhhcCHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHH
Confidence 357889999999999999988876555 445567899999963
No 37
>PF00512 HisKA: His Kinase A (phospho-acceptor) domain; InterPro: IPR003661 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents the dimerisation and phosphoacceptor domain found in histidine kinases. It has been found in bacterial sensor protein/histidine kinases. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms []. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and the phosphotransfer from aspartyl phosphate back to ADP or to water []. The homodimeric domain includes the site of histidine autophosphorylation and phosphate transfer reactions. The structure of the homodimeric domain comprises a closed, four-helical bundle with a left-handed twist, formed by two identical alpha-hairpin subunits.; GO: 0000155 two-component sensor activity, 0007165 signal transduction, 0016020 membrane; PDB: 3DGE_A 2C2A_A 3A0R_A 4EW8_A 2LFS_B 2LFR_B 3JZ3_A 1JOY_B 3ZRW_C 3ZRV_A ....
Probab=29.95 E-value=99 Score=17.59 Aligned_cols=25 Identities=20% Similarity=0.305 Sum_probs=19.5
Q ss_pred HHhHHHHHHhHhhHHHHHHHHHHHH
Q psy312 12 HVRAGNIVRAGESLLKLVSDIKQYL 36 (90)
Q Consensus 12 ~vRAa~mVrAaesLLkLvseLKq~L 36 (90)
.--...|.++++.+.++|++|-.|.
T Consensus 39 ~~~l~~i~~~~~~l~~li~~ll~~s 63 (68)
T PF00512_consen 39 REYLDRIRSAADRLNELINDLLDFS 63 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345678999999999999987653
No 38
>KOG0119|consensus
Probab=29.25 E-value=1.1e+02 Score=26.68 Aligned_cols=59 Identities=22% Similarity=0.322 Sum_probs=50.0
Q ss_pred HhhHHHHHHHHHHHHHhcCh----------hhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q psy312 22 GESLLKLVSDIKQYLILNDF----------PSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDL 80 (90)
Q Consensus 22 aesLLkLvseLKq~LIL~DF----------~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eL 80 (90)
+=+|.-.+.|++.+|=.+|| ++.+.-++.+-+++..+....+++|..-|.++...+-++
T Consensus 54 ~y~l~~~iee~t~kLrt~d~~~p~~~e~rSPsp~p~yda~g~R~ntRe~R~r~~Le~er~e~I~~~lk~ 122 (554)
T KOG0119|consen 54 SYSLNLRIEEITRKLRTGDVGVPPPRELRSPSPEPVYDAKGKRLNTREQRARKKLEDERHEIIEEILKL 122 (554)
T ss_pred hhhHHHHHHHhhhhhccccCCCCCCccccCCCcchhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34678889999999999999 678888899999999999999999998888887766544
No 39
>PF05700 BCAS2: Breast carcinoma amplified sequence 2 (BCAS2); InterPro: IPR008409 This family consists of several eukaryotic sequences of unknown function. The mammalian members of this family are annotated as breast carcinoma amplified sequence 2 (BCAS2) proteins []. BCAS2 is a putative spliceosome associated protein [].
Probab=29.20 E-value=2.4e+02 Score=20.90 Aligned_cols=48 Identities=8% Similarity=0.200 Sum_probs=37.2
Q ss_pred ChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhh
Q psy312 40 DFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEEEYYTS 87 (90)
Q Consensus 40 DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~eYYsS 87 (90)
.+..+...........++..+++++.=..--.+++..|..||..+..-
T Consensus 140 ~Le~~~~~le~~l~~~k~~ie~vN~~RK~~Q~~~~~~L~~Le~~W~~~ 187 (221)
T PF05700_consen 140 QLEAMLKRLEKELAKLKKEIEEVNRERKRRQEEAGEELRYLEQRWKEL 187 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 345666777777788888888888777777788899999999888754
No 40
>PRK02506 dihydroorotate dehydrogenase 1A; Reviewed
Probab=28.97 E-value=97 Score=24.06 Aligned_cols=46 Identities=17% Similarity=0.330 Sum_probs=35.9
Q ss_pred hHHHHHHHHHhHHHHHHhHhhHH--------HHHHHHHHHHHhcChhhHHHHHH
Q psy312 4 CELDLYEMHVRAGNIVRAGESLL--------KLVSDIKQYLILNDFPSVNEAIT 49 (90)
Q Consensus 4 ~~qe~fem~vRAa~mVrAaesLL--------kLvseLKq~LIL~DF~~lne~i~ 49 (90)
+.+|++||-.--|+.|+-|-.++ ++..+|++++-=.+|.++++.+-
T Consensus 252 s~~da~e~i~aGA~~Vqv~ta~~~~gp~~~~~i~~~L~~~l~~~g~~si~e~~G 305 (310)
T PRK02506 252 TGRDAFEHILCGASMVQVGTALHKEGPAVFERLTKELKAIMAEKGYQSLEDFRG 305 (310)
T ss_pred CHHHHHHHHHcCCCHHhhhHHHHHhChHHHHHHHHHHHHHHHHhCCCCHHHHhC
Confidence 45778888777777777777665 47888999999999999998765
No 41
>PF02185 HR1: Hr1 repeat; InterPro: IPR000861 The HR1 repeat was first described as a three times repeated homology region of the N-terminal non-catalytic part of protein kinase PRK1(PKN) []. The first two of these repeats were later shown to bind the small G protein rho [, ] known to activate PKN in its GTP-bound form. Similar rho-binding domains also occur in a number of other protein kinases and in the rho-binding proteins rhophilin and rhotekin. Recently, the structure of the N-terminal HR1 repeat complexed with RhoA has been determined by X-ray crystallography []. It forms an antiparallel coiled-coil fold termed an ACC finger. This entry includes domains found within rho-associated protein kinases.; GO: 0007165 signal transduction, 0005622 intracellular; PDB: 1CXZ_B 3O0Z_C 2RMK_B 1URF_A.
Probab=28.88 E-value=1.4e+02 Score=18.06 Aligned_cols=43 Identities=23% Similarity=0.315 Sum_probs=25.3
Q ss_pred HHHHhHhhHHHHH-HHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHH
Q psy312 17 NIVRAGESLLKLV-SDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAA 75 (90)
Q Consensus 17 ~mVrAaesLLkLv-seLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~ 75 (90)
.|..+||.++++. ++=|. ....+.....++.+++.-|+.++..
T Consensus 15 ki~~Gae~m~~~~~t~~~~----------------~~~~~~~~l~~s~~kI~~L~~~L~~ 58 (70)
T PF02185_consen 15 KIKEGAENMLQAYSTDKKK----------------VLSEAESQLRESNQKIELLREQLEK 58 (70)
T ss_dssp HHHHHHHHHHHHHCCHHCH-----------------HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHccCcHH----------------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566777777763 22222 2445566667777777777776654
No 42
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=28.34 E-value=1.8e+02 Score=19.29 Aligned_cols=36 Identities=28% Similarity=0.414 Sum_probs=20.3
Q ss_pred HHHHHHHHHhcChh-----hHHHHHHHhHHHHHHHHHHHHH
Q psy312 29 VSDIKQYLILNDFP-----SVNEAITQNSKLFRTKQTECDQ 64 (90)
Q Consensus 29 vseLKq~LIL~DF~-----~lne~i~~~~~~~~~~~~~~d~ 64 (90)
+.|+|+++-+.+.+ .+.+.+..+...++++..+...
T Consensus 60 L~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T cd04784 60 LDEIRTLLQLQDDPEASCAEVNALIDEHLAHVRARIAELQA 100 (127)
T ss_pred HHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56888888765533 3344455555555555555433
No 43
>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=27.73 E-value=1.7e+02 Score=18.82 Aligned_cols=11 Identities=9% Similarity=0.304 Sum_probs=7.1
Q ss_pred HHHHHHHHHhc
Q psy312 29 VSDIKQYLILN 39 (90)
Q Consensus 29 vseLKq~LIL~ 39 (90)
+.|+|+++=+.
T Consensus 58 L~eI~~~l~~~ 68 (107)
T cd04777 58 LIEIQKIFSYK 68 (107)
T ss_pred HHHHHHHHHhc
Confidence 46777777553
No 44
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=27.69 E-value=2e+02 Score=19.40 Aligned_cols=42 Identities=19% Similarity=0.280 Sum_probs=23.5
Q ss_pred HHHHHHHHHhcCh-----hhHHHHHHHhHHHHHHHHHHHHHHHHhHH
Q psy312 29 VSDIKQYLILNDF-----PSVNEAITQNSKLFRTKQTECDQKLMNLR 70 (90)
Q Consensus 29 vseLKq~LIL~DF-----~~lne~i~~~~~~~~~~~~~~d~~l~~lr 70 (90)
+.++|+++=+.+= +.+.+.+..+...++++..+.......|.
T Consensus 60 L~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~ 106 (127)
T TIGR02047 60 LAEIRQLLRYQDKPEKSCSDVNALLDEHISHVRARIIKLQALIEQLV 106 (127)
T ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5788888765432 23445555555555555555554444433
No 45
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=27.26 E-value=2e+02 Score=19.24 Aligned_cols=43 Identities=23% Similarity=0.369 Sum_probs=22.2
Q ss_pred HHHHHHHHHhcChhh--------HHHHHHHhHHHHHHHHHHHHHHHHhHHH
Q psy312 29 VSDIKQYLILNDFPS--------VNEAITQNSKLFRTKQTECDQKLMNLRD 71 (90)
Q Consensus 29 vseLKq~LIL~DF~~--------lne~i~~~~~~~~~~~~~~d~~l~~lrd 71 (90)
++++|.++-+.+.+. .-+.+..+...++++..+.+..+..|.+
T Consensus 58 L~~I~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~L~~ 108 (118)
T cd04776 58 LEEIRELLDLYDPPGGNRKQLEKMLEKIEKRRAELEQQRRDIDAALAELDA 108 (118)
T ss_pred HHHHHHHHHhhccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478888887766532 1123444444444444444444444333
No 46
>PF11945 WASH_WAHD: WAHD domain of WASH complex; InterPro: IPR021854 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. This entry represents the WASH subunit of the WASH complex. WASH genes duplicated to multiple chromosomal ends during primate evolution, with highest copy number reached in humans, whose WASH repertoires probably vary extensively among individuals []. It is therefore difficult to determine which gene is functional or not. The telomeric region of chromosome 9p is paralogous to the pericentromeric regions of chromosome 9 as well as to 2q. Paralogous regions contain 7 transcriptional units. Duplicated WASH genes are also present in the Xq/Yq pseudoautosomal region, as well as on chromosome 1 and 15. The chromosome 16 copy seems to be a pseudogene.
Probab=27.04 E-value=3.2e+02 Score=21.68 Aligned_cols=44 Identities=23% Similarity=0.268 Sum_probs=20.8
Q ss_pred HHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHH
Q psy312 18 IVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDM 73 (90)
Q Consensus 18 mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel 73 (90)
|+.|-+-|-+.+.++ |..|+++ ++..+++.+..+.++......+
T Consensus 23 i~~aL~~L~~v~~di--------F~rI~~R----v~~~~~~l~~i~~Ri~~~qaKi 66 (297)
T PF11945_consen 23 IADALEYLDKVSNDI--------FSRISAR----VERNRERLQAIQQRIEVAQAKI 66 (297)
T ss_pred HHHHHHHHHHHHHHH--------HHHHHHH----HHHHHHHHHHHHHHHHHHHHHH
Confidence 344444455555554 4444444 4444444444444444444433
No 47
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). 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=27.00 E-value=1.9e+02 Score=18.99 Aligned_cols=39 Identities=5% Similarity=0.054 Sum_probs=19.8
Q ss_pred HHHHHHHHHhcChh--------hHHHHHHHhHHHHHHHHHHHHHHHH
Q psy312 29 VSDIKQYLILNDFP--------SVNEAITQNSKLFRTKQTECDQKLM 67 (90)
Q Consensus 29 vseLKq~LIL~DF~--------~lne~i~~~~~~~~~~~~~~d~~l~ 67 (90)
+.++|+++-+.+.. .+-+.+..+...++.+..++.....
T Consensus 59 l~eI~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~ 105 (112)
T cd01282 59 LEEIREFLPCLRGGEPTFRPCPDLLAVLRRELARIDRQIADLTRSRD 105 (112)
T ss_pred HHHHHHHHHHhhCCCccCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788877665442 3334444444444444444444433
No 48
>PF11690 DUF3287: Protein of unknown function (DUF3287); InterPro: IPR021704 This eukaryotic family of proteins has no known function.
Probab=26.37 E-value=1.6e+02 Score=20.42 Aligned_cols=37 Identities=11% Similarity=0.277 Sum_probs=28.2
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q psy312 46 EAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEEEY 84 (90)
Q Consensus 46 e~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~eY 84 (90)
+.+..+.+.+..+...+..++..| -++..+.-||++=
T Consensus 45 ~kV~~qH~~~~~e~r~L~kKi~~l--~veRkmr~Les~p 81 (109)
T PF11690_consen 45 DKVVDQHQRYCDERRKLRKKIQDL--RVERKMRALESHP 81 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHhccCCh
Confidence 456777788888888888888877 6677788887653
No 49
>PF02561 FliS: Flagellar protein FliS; InterPro: IPR003713 The fliD operon of several bacteria consists of three flagellar genes, fliD, fliS, and fliT, and is transcribed in this order []. In Bacillus subtilis the operon encoding the flagellar proteins FliD, FliS, and FliT is sigma D-dependent [].; GO: 0009296 flagellum assembly, 0009288 bacterial-type flagellum; PDB: 1VH6_A 3IQC_B 3K1I_B 1ORJ_B 1ORY_A.
Probab=26.29 E-value=1.5e+02 Score=19.73 Aligned_cols=73 Identities=18% Similarity=0.305 Sum_probs=44.1
Q ss_pred HHHHH-HHHHhHHH----HHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q psy312 5 ELDLY-EMHVRAGN----IVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYD 79 (90)
Q Consensus 5 ~qe~f-em~vRAa~----mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~e 79 (90)
...+| +..|.+++ ++-=-|.+++-+..-+...-=+||+.-+.++.....-+.....-+|.. -+-|++..|..
T Consensus 4 ~~~~Y~~~~v~tasp~~Li~~Lyd~ai~~l~~a~~a~~~~~~~~~~~~l~ka~~Ii~~L~~~Ld~e---~g~eia~~L~~ 80 (122)
T PF02561_consen 4 AYQAYRQNAVATASPHQLILMLYDGAIEFLKQAKEAIEQGDIEEKNEALQKAQDIITELQSSLDFE---KGGEIADNLFR 80 (122)
T ss_dssp CGGGCSGTTGGG-HHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHTCCTT---TTHHHHHHHHH
T ss_pred HHHHHHHHhHhcCCHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhhcCCC---CCcHHHHHHHH
Confidence 33444 23455444 566677777777777887777888888877777766666544433331 12456666655
Q ss_pred H
Q psy312 80 L 80 (90)
Q Consensus 80 L 80 (90)
|
T Consensus 81 l 81 (122)
T PF02561_consen 81 L 81 (122)
T ss_dssp H
T ss_pred H
Confidence 4
No 50
>PRK07565 dihydroorotate dehydrogenase 2; Reviewed
Probab=25.95 E-value=61 Score=25.19 Aligned_cols=46 Identities=11% Similarity=0.252 Sum_probs=32.6
Q ss_pred HHHHHHHHHhHHHHHHhHhhH--------HHHHHHHHHHHHhcChhhHHHHHHH
Q psy312 5 ELDLYEMHVRAGNIVRAGESL--------LKLVSDIKQYLILNDFPSVNEAITQ 50 (90)
Q Consensus 5 ~qe~fem~vRAa~mVrAaesL--------LkLvseLKq~LIL~DF~~lne~i~~ 50 (90)
..|+.++-.--+++|+-|-.+ -+|+.+|++++--.+|.++.+.+-.
T Consensus 251 ~~Da~e~l~aGA~~V~v~t~~~~~g~~~~~~i~~~L~~~l~~~g~~~i~e~~g~ 304 (334)
T PRK07565 251 AEDVIKMLLAGADVVMIASALLRHGPDYIGTILRGLEDWMERHGYESLQQFRGS 304 (334)
T ss_pred HHHHHHHHHcCCCceeeehHHhhhCcHHHHHHHHHHHHHHHHcCCCCHHHHhcc
Confidence 455666555444455444444 4599999999999999999998763
No 51
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=25.66 E-value=2.1e+02 Score=18.96 Aligned_cols=43 Identities=16% Similarity=0.262 Sum_probs=33.3
Q ss_pred ChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q psy312 40 DFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEE 82 (90)
Q Consensus 40 DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~ 82 (90)
+++...+.++.+.+.+.+..++....+..+++++......+..
T Consensus 84 ~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~~~~~~~~l~~ 126 (129)
T cd00584 84 DLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEAELQE 126 (129)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455667788888888888888888888888888777666654
No 52
>KOG3499|consensus
Probab=25.48 E-value=51 Score=21.22 Aligned_cols=11 Identities=27% Similarity=0.739 Sum_probs=9.0
Q ss_pred HHHHHHHHHHh
Q psy312 28 LVSDIKQYLIL 38 (90)
Q Consensus 28 LvseLKq~LIL 38 (90)
=|+|+|+||.+
T Consensus 4 ~i~eiK~FL~~ 14 (69)
T KOG3499|consen 4 QITEIKDFLLT 14 (69)
T ss_pred hHHHHHHHHHH
Confidence 47899999875
No 53
>COG2841 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.12 E-value=1.9e+02 Score=18.81 Aligned_cols=53 Identities=15% Similarity=0.300 Sum_probs=37.3
Q ss_pred HHHHHHHHH-----HHhcChhhHHHHHHHhHH----HHHHHHHHHHHHHHhHHHHHHHHHHH
Q psy312 27 KLVSDIKQY-----LILNDFPSVNEAITQNSK----LFRTKQTECDQKLMNLRDDMAADLYD 79 (90)
Q Consensus 27 kLvseLKq~-----LIL~DF~~lne~i~~~~~----~~~~~~~~~d~~l~~lrdel~~~L~e 79 (90)
-++|.||+. =||-+-.+|+..|..... -.........++=..|.||++..|..
T Consensus 7 ~~is~Lk~~dahF~rLfd~hn~LDd~I~~~E~n~~~~s~~ev~~LKKqkL~LKDEi~~~L~~ 68 (72)
T COG2841 7 DLISKLKANDAHFARLFDKHNELDDRIKRAEGNRQPGSDAEVSNLKKQKLQLKDEIASILQK 68 (72)
T ss_pred HHHHHHhccchHHHHHHHHHhHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 466777762 466667777777766554 34456677778888899999998863
No 54
>PF01627 Hpt: Hpt domain; InterPro: IPR008207 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents a domain present at the N terminus in proteins which undergo autophosphorylation. The group includes, the gliding motility regulatory protein from Myxococcus xanthus and a number of bacterial chemotaxis proteins.; GO: 0004871 signal transducer activity, 0000160 two-component signal transduction system (phosphorelay); PDB: 3KYJ_A 3KYI_A 3IQT_A 1Y6D_A 2LD6_A 1TQG_A 2R25_A 1OXB_A 1QSP_B 1C03_B ....
Probab=24.77 E-value=1.5e+02 Score=17.20 Aligned_cols=61 Identities=21% Similarity=0.184 Sum_probs=39.9
Q ss_pred hHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q psy312 21 AGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLE 81 (90)
Q Consensus 21 AaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE 81 (90)
-.+.+.+.+|.||-..---+++.+.+.-..=...++......-..+..+-+++...+..|+
T Consensus 28 d~~~l~~~~H~lkG~a~~~g~~~l~~~~~~lE~~~~~~~~~~~~~~~~~~~~l~~~l~~l~ 88 (90)
T PF01627_consen 28 DWEELRRLAHRLKGSAGNLGAPRLAELAEQLEQALKSGDKPEAEELEQLLDELEAMLEQLR 88 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTHHHHSHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHhhhHHhcCHHHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHHHHh
Confidence 4578899999999999999998887766554444444333332344555555555555554
No 55
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=24.75 E-value=2.5e+02 Score=19.67 Aligned_cols=33 Identities=15% Similarity=0.300 Sum_probs=22.1
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q psy312 46 EAITQNSKLFRTKQTECDQKLMNLRDDMAADLY 78 (90)
Q Consensus 46 e~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~ 78 (90)
+.+..+++.++++.+..+.++..|+.++-..+.
T Consensus 80 E~Le~ri~tLekQe~~l~e~l~eLq~~i~~~l~ 112 (119)
T COG1382 80 ETLELRIKTLEKQEEKLQERLEELQSEIQKALG 112 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 445566667777777777777777777666554
No 56
>smart00761 HDAC_interact Histone deacetylase (HDAC) interacting. This domain is found on transcriptional regulators. It forms interactions with histone deacetylases.
Probab=24.74 E-value=1.6e+02 Score=20.07 Aligned_cols=31 Identities=16% Similarity=0.310 Sum_probs=25.0
Q ss_pred hhHHHHHHHHHhHHHHHHhHhhHHHHHHHHH
Q psy312 3 QCELDLYEMHVRAGNIVRAGESLLKLVSDIK 33 (90)
Q Consensus 3 q~~qe~fem~vRAa~mVrAaesLLkLvseLK 33 (90)
.|+-|.||+.+.-..+.++..-|-.|...|.
T Consensus 63 r~EDeR~E~D~~ie~~~~ti~~le~l~~~~~ 93 (102)
T smart00761 63 RCEDERFELDMVIESNSSTIKLLEEILNKIE 93 (102)
T ss_pred HhhhhhhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5788999999999998888877777766554
No 57
>PF11598 COMP: Cartilage oligomeric matrix protein; InterPro: IPR024665 Thrombospondins are adhesive glycoproteins that mediate cell-to-cell and cell-to-matrix interactions. Cartilage oligomeric matrix protein may play a role in the structural integrity of cartilage via its interaction with other extracellular matrix proteins such as collagen and fibronectin [, ]. Thrombospondin 3 and 4 and cartilage oligomeric matrix proteins contain a five-stranded coiled-coil domain represented by this entry. This domain has a binding site between two internal rings formed by Leu37 and Thr40 [].; PDB: 1MZ9_D 1FBM_A 1VDF_E.
Probab=24.67 E-value=1.6e+02 Score=17.33 Aligned_cols=20 Identities=10% Similarity=0.388 Sum_probs=11.4
Q ss_pred HHHHHhHhhHHHHHHHHHHH
Q psy312 16 GNIVRAGESLLKLVSDIKQY 35 (90)
Q Consensus 16 a~mVrAaesLLkLvseLKq~ 35 (90)
..++..--.|.+++.|||+-
T Consensus 4 ~~l~~ql~~l~~~l~elk~~ 23 (45)
T PF11598_consen 4 SQLIKQLSELNQMLQELKEL 23 (45)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34555555666666666654
No 58
>PRK12692 flgG flagellar basal body rod protein FlgG; Reviewed
Probab=24.62 E-value=1.1e+02 Score=23.47 Aligned_cols=26 Identities=19% Similarity=0.284 Sum_probs=20.5
Q ss_pred HHHHHHHHHhHHHHHHhHhhHHHHHHHHH
Q psy312 5 ELDLYEMHVRAGNIVRAGESLLKLVSDIK 33 (90)
Q Consensus 5 ~qe~fem~vRAa~mVrAaesLLkLvseLK 33 (90)
.|-+|||..|+ ++.++.+.+.+.+||
T Consensus 236 ~~R~ye~~~k~---i~~~~~~~~~~~~~~ 261 (262)
T PRK12692 236 AQRAFEMNSKV---IQAADEMAGTVSKGI 261 (262)
T ss_pred HHHHHHHHHHH---HHHHHHHHHHHHhhc
Confidence 57788888765 556899999998887
No 59
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=24.32 E-value=2.3e+02 Score=21.12 Aligned_cols=40 Identities=15% Similarity=0.300 Sum_probs=31.1
Q ss_pred hHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHH
Q psy312 24 SLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQ 64 (90)
Q Consensus 24 sLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~ 64 (90)
.+.+++..|++|+ =.|.|+.-+.+..|...++....+.|-
T Consensus 106 ~m~~m~~~L~~~v-~~d~Pf~~~eR~~Rl~~L~~~l~~~dv 145 (251)
T PF11932_consen 106 LMEQMIDELEQFV-ELDLPFLLEERQERLARLRAMLDDADV 145 (251)
T ss_pred HHHHHHHHHHHHH-hcCCCCChHHHHHHHHHHHHhhhccCC
Confidence 4556888887764 469999999999999888887766543
No 60
>PF06791 TMP_2: Prophage tail length tape measure protein; InterPro: IPR009628 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpH, tail tape measure protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a conserved region located towards the N-terminal end of prophage tail length tape measure protein (TMP). TMP is important for assembly of phage tails and involved in tail length determination. Mutated forms TMP cause tail fibres to be shortened [].
Probab=24.01 E-value=2.8e+02 Score=20.44 Aligned_cols=46 Identities=22% Similarity=0.312 Sum_probs=38.9
Q ss_pred cChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q psy312 39 NDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEEEY 84 (90)
Q Consensus 39 ~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~eY 84 (90)
..|..+.+....-.....+..++.-+.+.++.+|-...+.+|-+.|
T Consensus 152 ~~~~~v~~aa~~~a~~tG~~~~~~~~~~~~l~~dp~ka~~~Ln~q~ 197 (210)
T PF06791_consen 152 EQLEQVAQAAADMAKATGQSVDEAAKEFAKLADDPVKAAEELNEQY 197 (210)
T ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence 3677777777777777888899999999999999999999998765
No 61
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=23.61 E-value=2.2e+02 Score=18.49 Aligned_cols=45 Identities=4% Similarity=0.099 Sum_probs=37.1
Q ss_pred HHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q psy312 35 YLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYD 79 (90)
Q Consensus 35 ~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~e 79 (90)
.+|.-|-+.+...++.+.+.+......++.++..+..++..-=..
T Consensus 55 vfv~~~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~~elk~~ 99 (105)
T cd00632 55 VLVKQEKEEARTELKERLETIELRIKRLERQEEDLQEKLKELQEK 99 (105)
T ss_pred HHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678889999999999999999999999999988777776654333
No 62
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal 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=23.61 E-value=2.2e+02 Score=18.63 Aligned_cols=40 Identities=18% Similarity=0.213 Sum_probs=21.2
Q ss_pred HHHHHHHHHhcCh-----hhHHHHHHHhHHHHHHHHHHHHHHHHh
Q psy312 29 VSDIKQYLILNDF-----PSVNEAITQNSKLFRTKQTECDQKLMN 68 (90)
Q Consensus 29 vseLKq~LIL~DF-----~~lne~i~~~~~~~~~~~~~~d~~l~~ 68 (90)
+.|+|.++=..+. +.+-+.+..+...++++..+..+....
T Consensus 60 l~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~ 104 (123)
T cd04770 60 LAEIRELLSLRDDGAAPCAEVRALLEEKLAEVEAKIAELQALRAE 104 (123)
T ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677877755443 234444555555555555554444433
No 63
>PF15136 UPF0449: Uncharacterised protein family UPF0449
Probab=22.80 E-value=2.6e+02 Score=19.05 Aligned_cols=32 Identities=25% Similarity=0.310 Sum_probs=19.5
Q ss_pred hhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHH
Q psy312 41 FPSVNEAITQNSKLFRTKQTECDQKLMNLRDD 72 (90)
Q Consensus 41 F~~lne~i~~~~~~~~~~~~~~d~~l~~lrde 72 (90)
|-.+|+.+.+....++++.+++...=..|..+
T Consensus 62 Yv~~NerLqqa~~~Lkkk~e~L~~age~Le~~ 93 (97)
T PF15136_consen 62 YVAMNERLQQARDQLKKKCEELRQAGEELERD 93 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44677777777777777766665544444333
No 64
>PF15272 BBP1_C: Spindle pole body component BBP1, C-terminal
Probab=22.52 E-value=3.3e+02 Score=20.66 Aligned_cols=55 Identities=16% Similarity=0.380 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q psy312 26 LKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEE 82 (90)
Q Consensus 26 LkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~ 82 (90)
++|+..|.+.= -+.+.|++-+..+-+....+......+...||.|+-..|..=..
T Consensus 8 ~~lld~l~~Nn--r~L~~L~~dl~~~~~~~~~~e~~~~~KY~~lR~ElI~ELkqsKk 62 (196)
T PF15272_consen 8 LELLDQLDQNN--RALSDLNQDLRERDERYELQETSYKEKYQQLRQELINELKQSKK 62 (196)
T ss_pred HHHHHHHHHhH--HHHHHHHHHHHHhhhHHHhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444321 12456777888888888888899999999999999998876543
No 65
>TIGR00511 ribulose_e2b2 ribose-1,5-bisphosphate isomerase, e2b2 family. The delineation of this family was based originally, in part, on a discussion and neighbor-joining phylogenetic study by Kyrpides and Woese of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. Recently, Sato, et al. assigned the function ribulose-1,5 bisphosphate isomerase.
Probab=22.41 E-value=3.8e+02 Score=20.89 Aligned_cols=49 Identities=14% Similarity=0.270 Sum_probs=33.3
Q ss_pred HHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHH
Q psy312 18 IVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDM 73 (90)
Q Consensus 18 mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel 73 (90)
|-.|.+.+++.++ -.||..+-+.+-...+.|.++....++++.....+.
T Consensus 64 l~nai~~~~~~i~-------~~~~~~~k~~l~~~~~~~~~e~~~a~~~I~~~a~~~ 112 (301)
T TIGR00511 64 LPNAVRYVLKYMS-------GEDVETLRETVIERADAFINQSDKAQERIGEIGAKR 112 (301)
T ss_pred HHHHHHHHHHHhc-------cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345555555442 267888888888888888888888888776655443
No 66
>PF10960 DUF2762: Protein of unknown function (DUF2762); InterPro: IPR024405 BhlA is a SP-beta prophage-derived protein found in Bacillus subtilis [, ] and other Bacilli. A related protein, UviB, has also been described in Clostridia, where it is believed to be involved in bacteriocin secretion or immunity [, ].
Probab=22.15 E-value=2.2e+02 Score=18.07 Aligned_cols=56 Identities=21% Similarity=0.256 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q psy312 25 LLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEE 82 (90)
Q Consensus 25 LLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~ 82 (90)
+++++..==-|.+| |-+|==.+-..++....++++-..++..+-+.+...+..+++
T Consensus 5 i~k~~~sQG~fA~L--Fv~Ll~yvlK~~~~re~~~~~RE~kyq~~I~~lte~~~~~~~ 60 (71)
T PF10960_consen 5 IIKLALSQGIFAVL--FVWLLFYVLKENKKREEKQEEREEKYQEQIEKLTEKLNVIEE 60 (71)
T ss_pred HHHHHHHcCcHHHH--HHHHHHHHHHHhHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444444445555 556555566666655666666666666666666666655554
No 67
>PF00611 FCH: Fes/CIP4, and EFC/F-BAR homology domain; InterPro: IPR001060 The FCH domain is a short conserved region of around 60 amino acids first described as a region of homology between FER and CIP4 proteins []. Many proteins containing an FCH domain are involved in the regulation of cytoskeletal rearrangements, vesicular transport and endocytosis. In the CIP4 protein the FCH domain binds to microtubules []. The FCH domain is always found N-terminally and is followed by a coiled-coil region. Proteins containing an FCH domain can be divided in 3 classes []: A subfamily of protein kinases usually associated with an SH2 domain: Fps/fes (Fujimani poultry sarcoma/feline sarcoma) proto-oncogenes. They are non-receptor protein-tyrosine kinases preferentially expressed in myeloid lineage. The viral oncogene has an unregulated kinase activity which abrogates the need for cytokines and influences differentiation of haematopoietic progenitor cells. Fes related protein (fer). It is an ubiquitously expressed homologue of Fes. Adaptor proteins usually associated with a C-terminal SH3 domain: Schizosaccharomyces pombe CDC15 protein. It mediates cytoskeletal rearrangements required for cytokinesis. It is essential for viability. CD2 cytoplasmic domain binding protein. Mammalian Cdc42-interacting protein 4 (CIP4). It may act as a link between Cdc42 signaling and regulation of the actin cytoskeleton. Mammalian PACSIN proteins. A family of cytoplasmic phosphoproteins playing a role in vesicle formation and transport. A subfamily of Rho-GAP proteins: Mammalian RhoGAP4 proteins. They may down-regulate Rho-like GTPases in hematopoietic cells. Yeast hypothetical protein YBR260C. Caenorhabditis elegans hypothetical protein ZK669.1. ; PDB: 2EFK_A 2EFL_A 2X3W_A 2X3X_C 2X3V_C 3I2W_A 3ABH_B 3Q0K_B 3HAJ_A 3ACO_B ....
Probab=21.95 E-value=1.9e+02 Score=17.29 Aligned_cols=20 Identities=20% Similarity=0.313 Sum_probs=11.6
Q ss_pred cChhhHHHHHHHhHHHHHHH
Q psy312 39 NDFPSVNEAITQNSKLFRTK 58 (90)
Q Consensus 39 ~DF~~lne~i~~~~~~~~~~ 58 (90)
+.|+.|.+.++.....+...
T Consensus 9 ~g~~~l~~~~~~~~~~~~~l 28 (91)
T PF00611_consen 9 DGFEVLFKRLKQGIKLLEEL 28 (91)
T ss_dssp CTTHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHH
Confidence 45666666666665544433
No 68
>PF07350 DUF1479: Protein of unknown function (DUF1479); InterPro: IPR010856 This family consists of several hypothetical Enterobacterial proteins, of around 420 residues in length. Members of this family are often known as YbiU. The function of this family is unknown.; PDB: 2CSG_A 2DBI_A 2DBN_A.
Probab=21.89 E-value=2.1e+02 Score=23.95 Aligned_cols=37 Identities=14% Similarity=0.107 Sum_probs=27.9
Q ss_pred HHHHHHHHHH--hcChhhHHHHHHHhHHHHHHHHHHHHH
Q psy312 28 LVSDIKQYLI--LNDFPSVNEAITQNSKLFRTKQTECDQ 64 (90)
Q Consensus 28 LvseLKq~LI--L~DF~~lne~i~~~~~~~~~~~~~~d~ 64 (90)
=..+||+-|| ..+...+.+....-...++...++..+
T Consensus 6 rf~~lK~~L~~~~~~~~~v~~sw~rll~~l~~~~~~i~~ 44 (416)
T PF07350_consen 6 RFAELKRSLIAKPGNEEAVFASWERLLEALEREIEEIAA 44 (416)
T ss_dssp HHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3678999999 999888888888777777776666543
No 69
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=21.84 E-value=2.9e+02 Score=19.26 Aligned_cols=42 Identities=19% Similarity=0.172 Sum_probs=22.8
Q ss_pred HHHHHHHHHhcChh---hHHHHHHHhHHHHHHHHHHHHHHHHhHH
Q psy312 29 VSDIKQYLILNDFP---SVNEAITQNSKLFRTKQTECDQKLMNLR 70 (90)
Q Consensus 29 vseLKq~LIL~DF~---~lne~i~~~~~~~~~~~~~~d~~l~~lr 70 (90)
+.++|+++=+.|-+ ..-+-+.++...++++..+..+....|.
T Consensus 67 L~eI~~ll~~~~~~~~~~~~~ll~~k~~~l~~~i~~L~~~~~~L~ 111 (144)
T PRK13752 67 LDEIAELLRLEDGTHCEEASSLAEHKLKDVREKMADLARMEAVLS 111 (144)
T ss_pred HHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788877655542 2344445555555555555544444443
No 70
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=21.69 E-value=4.1e+02 Score=20.94 Aligned_cols=41 Identities=29% Similarity=0.490 Sum_probs=25.3
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhh
Q psy312 46 EAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEEEYYTS 87 (90)
Q Consensus 46 e~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~eYYsS 87 (90)
+...++...+++..++.++.+..+..+... |.+-|.+|+..
T Consensus 60 ~~l~~eL~~LE~e~~~l~~el~~le~e~~~-l~~eE~~~~~~ 100 (314)
T PF04111_consen 60 EELLQELEELEKEREELDQELEELEEELEE-LDEEEEEYWRE 100 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH
Confidence 344455566666666777776666665544 66667777643
No 71
>PRK08334 translation initiation factor IF-2B subunit beta; Validated
Probab=21.65 E-value=4.5e+02 Score=21.49 Aligned_cols=53 Identities=15% Similarity=0.277 Sum_probs=37.9
Q ss_pred HHHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHH
Q psy312 17 NIVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDM 73 (90)
Q Consensus 17 ~mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel 73 (90)
|+-.|++-+++.+..- +- .||+.+.+.+-++...+.++-.++++++....-++
T Consensus 105 nL~~a~~~~~~~~~~~---~~-~~~~~~~~~l~~~a~~i~~~d~~~~~~Ig~~g~~l 157 (356)
T PRK08334 105 NLFWALNRIKKLVEEH---LE-DPLDEIKRLIVEEAQKIADEDVEANLRMGHYGAEV 157 (356)
T ss_pred hHHHHHHHHHHHHHhh---cc-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4455556655555422 11 68999999999999999998888888887666554
No 72
>PF03410 Peptidase_M44: Protein G1; InterPro: IPR005072 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 metallopeptidases belong to MEROPS peptidase family M44 (clan ME). The active site residues for members of this family and family M16 occur in the motif HXXEHProtein. The type example is the vaccinia virus-type metalloendopeptidase G1 from vaccinia virus, it is a metalloendopeptidase expressed by many Poxviridae which appears to play a role in the maturation of viral proteins.; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0019067 viral assembly, maturation, egress, and release
Probab=21.51 E-value=64 Score=28.23 Aligned_cols=15 Identities=33% Similarity=0.762 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHh
Q psy312 71 DDMAADLYDLEEEYY 85 (90)
Q Consensus 71 del~~~L~eLE~eYY 85 (90)
..+..-.+|||.|||
T Consensus 102 ~~i~~hikELENEYY 116 (590)
T PF03410_consen 102 SKIKNHIKELENEYY 116 (590)
T ss_pred hHHHHHHHHHhhhhh
Confidence 456677899999999
No 73
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=21.10 E-value=3e+02 Score=19.27 Aligned_cols=64 Identities=17% Similarity=0.198 Sum_probs=39.6
Q ss_pred HhHHHHHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q psy312 13 VRAGNIVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLE 81 (90)
Q Consensus 13 vRAa~mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE 81 (90)
|-=.||-.|+.++-|=+..+=..| +..-.++.+|+..+..+.+++......+++|+...--+++
T Consensus 36 vTrr~m~~A~~~v~kql~~vs~~l-----~~tKkhLsqRId~vd~klDe~~ei~~~i~~eV~~v~~dv~ 99 (126)
T PF07889_consen 36 VTRRSMSDAVASVSKQLEQVSESL-----SSTKKHLSQRIDRVDDKLDEQKEISKQIKDEVTEVREDVS 99 (126)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhHH
Confidence 444578899998877665554433 4455566666666666666666666666666654444433
No 74
>KOG0977|consensus
Probab=20.98 E-value=4e+02 Score=23.26 Aligned_cols=49 Identities=14% Similarity=0.232 Sum_probs=40.6
Q ss_pred HHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Q psy312 35 YLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEEE 83 (90)
Q Consensus 35 ~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~e 83 (90)
+-+|++...=...+..+.+.++....++.+...+|++++...-.+|+.|
T Consensus 147 ~~~l~~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~r~~ld~E 195 (546)
T KOG0977|consen 147 LSRLSELEAEINTLKRRIKALEDELKRLKAENSRLREELARARKQLDDE 195 (546)
T ss_pred hhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence 3456666666677888889999999999999999999999998888876
No 75
>PF05600 DUF773: Protein of unknown function (DUF773); InterPro: IPR008491 This family contains several eukaryotic sequences which are thought to be CDK5 activator-binding proteins, however, the function of this family is unknown.
Probab=20.76 E-value=2.7e+02 Score=23.58 Aligned_cols=36 Identities=11% Similarity=0.177 Sum_probs=22.6
Q ss_pred HHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhhc
Q psy312 49 TQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEEEYYTSV 88 (90)
Q Consensus 49 ~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE~eYYsS~ 88 (90)
..++..+.++..+|+++.. |+-........+|++++
T Consensus 130 kKqi~k~~q~~~d~~kk~~----e~~~~~~~~~~~~~~~c 165 (507)
T PF05600_consen 130 KKQIAKCQQQLEDLDKKEE----ELQRSAAEARERYKKAC 165 (507)
T ss_pred HHHHHHHHHHHHHHHhHHH----HHHHHHHHHHHHHHHHH
Confidence 4556666666777777655 55566666666666553
No 76
>KOG2196|consensus
Probab=20.60 E-value=4.4e+02 Score=20.92 Aligned_cols=64 Identities=16% Similarity=0.158 Sum_probs=42.7
Q ss_pred HHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q psy312 18 IVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLE 81 (90)
Q Consensus 18 mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~~~~~d~~l~~lrdel~~~L~eLE 81 (90)
|.+--..|=.++..|-.-+-+-+-.-+..+.|.+..+--...++.|.+|.+|..|+...+..|-
T Consensus 139 I~sqQ~ELE~~L~~lE~k~~~~~g~~~~~~~D~eR~qty~~a~nidsqLk~l~~dL~~ii~~lN 202 (254)
T KOG2196|consen 139 ILSQQQELEDLLDPLETKLELQSGHTYLSRADVEREQTYKMAENIDSQLKRLSEDLKQIIKSLN 202 (254)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccchhhhhhhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 3334444555555554444333333346677777777788999999999999999988877663
No 77
>TIGR02425 decarb_PcaC 4-carboxymuconolactone decarboxylase. Members of this family are 4-carboxymuconolactone decarboxylase, which catalyzes the third step in the catabolism of protocatechuate (and therefore the fourth step in the catabolism of para-hydroxybenzoate, of 3-hydroxybenzoate, of vanillate, etc.). Most members of this family are encoded within protocatechuate catabolism operons. This protein is sometimes found as a fusion protein with other enzymes of the pathway, as in Rhodococcus opacus, Streptomyces avermitilis, and Caulobacter crescentus.
Probab=20.34 E-value=2.9e+02 Score=18.78 Aligned_cols=51 Identities=20% Similarity=0.233 Sum_probs=41.4
Q ss_pred HHHHHHHHHhHHHHHHhHhhHHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHH
Q psy312 5 ELDLYEMHVRAGNIVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRT 57 (90)
Q Consensus 5 ~qe~fem~vRAa~mVrAaesLLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~ 57 (90)
..+.+..|++++ +++|=+--.|..=|.|.....+||....++..-.+.|.+
T Consensus 71 ~~~~l~~h~~~A--l~~G~T~~ei~Evl~q~~~y~G~P~a~~al~~~~~v~~e 121 (123)
T TIGR02425 71 RDEELAMHVRAT--ANTGVTEDDIKEVLLHVAIYAGVPAANHAFALAKEALAE 121 (123)
T ss_pred CHHHHHHHHHHH--HHcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHh
Confidence 356788888766 577877788888899999999999999998887777654
No 78
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; 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 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=20.34 E-value=2.6e+02 Score=18.17 Aligned_cols=43 Identities=23% Similarity=0.311 Sum_probs=22.4
Q ss_pred HHHHHHHHHhcCh-----hhHHHHHHHhHHHHHHHHHHHHHHHHhHHH
Q psy312 29 VSDIKQYLILNDF-----PSVNEAITQNSKLFRTKQTECDQKLMNLRD 71 (90)
Q Consensus 29 vseLKq~LIL~DF-----~~lne~i~~~~~~~~~~~~~~d~~l~~lrd 71 (90)
+.|+|+++-..+. +...+.+..+...++++..+..+.+..|..
T Consensus 60 L~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~ 107 (113)
T cd01109 60 IKDIKEYAELRREGDSTIPERLELLEEHREELEEQIAELQETLAYLDY 107 (113)
T ss_pred HHHHHHHHHHHccCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3577776654321 233444555555555555555555554443
No 79
>COG1564 THI80 Thiamine pyrophosphokinase [Coenzyme metabolism]
Probab=20.29 E-value=19 Score=27.42 Aligned_cols=36 Identities=25% Similarity=0.275 Sum_probs=28.3
Q ss_pred HHHHHHhcChhhHHHHHHHhHHHHHH------HHHHHHHHHH
Q psy312 32 IKQYLILNDFPSVNEAITQNSKLFRT------KQTECDQKLM 67 (90)
Q Consensus 32 LKq~LIL~DF~~lne~i~~~~~~~~~------~~~~~d~~l~ 67 (90)
++-.++++||-|+.+...+..++... .++.||-.++
T Consensus 42 l~P~~~vGDfDSv~~e~~~~~~~~~~~~~f~~eKd~TD~elA 83 (212)
T COG1564 42 LVPDLAVGDFDSVSEELLAYYKEKTVTIKFPAEKDSTDLELA 83 (212)
T ss_pred CCccEEEecccccCHHHHHHHhhcCcceecChhhccchHHHH
Confidence 78889999999999999887776655 6666665543
No 80
>TIGR01220 Pmev_kin_Gr_pos phosphomevalonate kinase, ERG8-type, Gram-positive branch. This enzyme is part of the mevalonate pathway, one of two alternative pathways for the biosynthesis of IPP. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found - the animal type and this ERG8 type. This model represents the low GC Gram-positive organism forms of the ERG8 type of phosphomevalonate kinase.
Probab=20.05 E-value=4.1e+02 Score=20.97 Aligned_cols=34 Identities=15% Similarity=0.114 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHhHHHHHHH
Q psy312 25 LLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTK 58 (90)
Q Consensus 25 LLkLvseLKq~LIL~DF~~lne~i~~~~~~~~~~ 58 (90)
+=.++.++++.|.=+||..+-+.++.+...+++.
T Consensus 254 ~~~i~~~~~~al~~~d~~~lg~~~~~~~~lL~~l 287 (358)
T TIGR01220 254 STDCVESAITAFETGDITSLQKEIRRNRQELARL 287 (358)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHh
Confidence 3377889999999999999999998888887765
Done!