Query 032730
Match_columns 135
No_of_seqs 116 out of 129
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 05:13:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032730.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032730hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3046 Transcription factor, 100.0 1.3E-39 2.9E-44 247.7 10.7 110 26-135 4-114 (147)
2 PF09748 Med10: Transcription 100.0 3.6E-37 7.8E-42 230.1 10.4 94 42-135 4-106 (128)
3 PF05008 V-SNARE: Vesicle tran 78.7 7.3 0.00016 25.8 5.2 55 30-84 21-75 (79)
4 KOG1666 V-SNARE [Intracellular 70.3 15 0.00033 30.4 5.9 57 28-84 30-86 (220)
5 PF11315 Med30: Mediator compl 67.5 57 0.0012 25.4 8.8 43 92-134 80-136 (150)
6 PF14712 Snapin_Pallidin: Snap 65.0 38 0.00082 23.0 6.4 37 63-102 28-64 (92)
7 PF08535 KorB: KorB domain; I 60.5 36 0.00078 23.3 5.6 55 64-123 5-59 (93)
8 PF05430 Methyltransf_30: S-ad 56.1 6 0.00013 29.3 1.1 18 104-121 62-79 (124)
9 PF03433 EspA: EspA-like secre 54.2 4.2 9.1E-05 32.8 0.0 89 34-133 37-140 (188)
10 PRK09432 metF 5,10-methylenete 52.3 25 0.00054 29.5 4.3 43 78-120 216-266 (296)
11 PF04129 Vps52: Vps52 / Sac2 f 51.4 1.2E+02 0.0026 27.3 8.8 33 90-122 81-113 (508)
12 KOG3936 Nitroreductases [Energ 46.8 46 0.001 24.2 4.4 37 65-101 58-94 (100)
13 PF10232 Med8: Mediator of RNA 46.5 89 0.0019 25.4 6.6 53 27-85 11-63 (226)
14 PF08745 UPF0278: UPF0278 fami 44.2 7.5 0.00016 31.8 0.0 78 24-104 6-100 (205)
15 KOG3990 Uncharacterized conser 43.9 1.7E+02 0.0037 25.2 8.0 51 12-62 206-260 (305)
16 PF02669 KdpC: K+-transporting 41.6 1.2E+02 0.0025 24.5 6.4 61 66-129 92-155 (188)
17 TIGR02878 spore_ypjB sporulati 40.5 1.4E+02 0.0031 24.9 6.9 54 67-123 122-182 (233)
18 TIGR02684 dnstrm_HI1420 probab 40.1 1.2E+02 0.0025 21.2 5.6 49 64-115 29-78 (89)
19 PF14202 TnpW: Transposon-enco 40.0 24 0.00051 21.2 1.7 21 57-77 15-35 (37)
20 PRK15364 pathogenicity island 39.5 39 0.00085 27.5 3.4 42 67-111 76-123 (196)
21 PF01017 STAT_alpha: STAT prot 37.9 1.2E+02 0.0027 23.5 5.9 52 28-79 118-179 (182)
22 PF14181 YqfQ: YqfQ-like prote 37.7 75 0.0016 25.0 4.7 47 35-86 53-99 (161)
23 KOG1961 Vacuolar sorting prote 37.7 1.4E+02 0.003 28.6 7.0 38 68-105 115-157 (683)
24 PF09577 Spore_YpjB: Sporulati 36.7 2.1E+02 0.0045 23.6 7.4 54 65-121 119-179 (232)
25 KOG0484 Transcription factor P 36.2 27 0.00058 26.3 1.9 14 103-116 38-51 (125)
26 PF01220 DHquinase_II: Dehydro 35.4 57 0.0012 25.1 3.6 30 49-78 37-66 (140)
27 PLN03094 Substrate binding sub 35.3 75 0.0016 28.0 4.8 49 38-86 290-343 (370)
28 PRK14139 heat shock protein Gr 32.9 1.3E+02 0.0028 24.0 5.4 34 19-52 20-53 (185)
29 PF13413 HTH_25: Helix-turn-he 32.6 97 0.0021 20.1 3.9 31 90-120 19-53 (62)
30 KOG0564 5,10-methylenetetrahyd 31.1 2.4E+02 0.0052 26.5 7.4 83 28-120 181-268 (590)
31 PRK04358 hypothetical protein; 31.1 94 0.002 25.7 4.4 76 25-103 11-103 (217)
32 cd00537 MTHFR Methylenetetrahy 31.0 87 0.0019 25.3 4.3 40 78-117 200-240 (274)
33 PF06657 Cep57_MT_bd: Centroso 30.8 1.8E+02 0.0039 19.9 6.3 54 24-80 3-67 (79)
34 PF05130 FlgN: FlgN protein; 29.9 1.3E+02 0.0027 20.8 4.5 92 31-124 5-106 (143)
35 PRK10132 hypothetical protein; 29.7 2.2E+02 0.0048 20.7 6.0 50 31-80 9-58 (108)
36 TIGR00677 fadh2_euk methylenet 29.6 87 0.0019 26.1 4.1 35 82-116 205-240 (281)
37 TIGR00676 fadh2 5,10-methylene 28.7 1.2E+02 0.0027 24.7 4.8 34 87-120 206-240 (272)
38 PF02219 MTHFR: Methylenetetra 28.6 64 0.0014 26.5 3.1 40 80-119 214-254 (287)
39 COG1344 FlgL Flagellin and rel 27.9 1.4E+02 0.003 25.5 5.1 49 39-87 79-129 (360)
40 PRK08026 flagellin; Validated 27.7 1.3E+02 0.0027 27.9 5.1 49 40-88 82-132 (529)
41 cd00466 DHQase_II Dehydroquina 27.5 91 0.002 24.1 3.6 27 49-75 36-62 (140)
42 cd08812 CARD_RIG-I_like Caspas 27.5 61 0.0013 22.4 2.4 35 92-132 19-53 (88)
43 PF13324 GCIP: Grap2 and cycli 27.4 3.1E+02 0.0067 22.4 6.9 15 66-80 255-269 (275)
44 COG4121 Uncharacterized conser 27.4 27 0.00058 29.2 0.7 28 104-132 180-207 (252)
45 TIGR00681 kdpC K+-transporting 27.3 2.8E+02 0.006 22.4 6.4 64 64-130 89-155 (187)
46 TIGR03875 RNA_lig_partner RNA 27.2 1.2E+02 0.0027 24.8 4.5 73 28-103 10-99 (206)
47 PF06831 H2TH: Formamidopyrimi 27.0 89 0.0019 21.7 3.2 49 5-55 33-86 (92)
48 PRK00315 potassium-transportin 26.4 3E+02 0.0065 22.3 6.5 63 65-130 92-157 (193)
49 PF12554 MOZART1: Mitotic-spin 26.2 1.1E+02 0.0023 19.5 3.2 32 81-112 7-42 (48)
50 PRK12584 flagellin A; Reviewed 26.1 1.4E+02 0.0031 27.2 5.1 48 39-86 81-130 (510)
51 PF03334 PhaG_MnhG_YufB: Na+/H 25.7 32 0.0007 23.6 0.8 9 105-113 18-26 (81)
52 PLN02540 methylenetetrahydrofo 25.6 76 0.0017 29.5 3.3 30 80-109 211-240 (565)
53 PRK13588 flagellin B; Provisio 25.5 1.5E+02 0.0031 27.3 5.1 49 38-86 80-130 (514)
54 PF00210 Ferritin: Ferritin-li 25.3 2.3E+02 0.005 19.4 5.9 55 30-84 79-134 (142)
55 PRK10667 Hha toxicity attenuat 24.9 82 0.0018 23.9 2.8 27 20-50 36-62 (122)
56 PRK06771 hypothetical protein; 24.8 1.7E+02 0.0036 21.2 4.3 37 71-107 31-69 (93)
57 PF10757 YbaJ: Biofilm formati 24.8 80 0.0017 24.0 2.7 27 20-50 36-62 (122)
58 PF08849 DUF1819: Putative inn 24.8 83 0.0018 24.3 3.0 61 43-103 121-183 (189)
59 PRK05395 3-dehydroquinate dehy 24.5 1.1E+02 0.0023 23.8 3.5 28 49-76 38-65 (146)
60 COG3076 Uncharacterized protei 24.5 1.3E+02 0.0027 23.0 3.7 38 96-133 13-52 (135)
61 PRK06819 flagellin; Validated 24.2 1.8E+02 0.004 25.6 5.3 49 38-86 80-130 (376)
62 PRK12806 flagellin; Provisiona 24.1 1.7E+02 0.0037 26.6 5.2 47 40-86 82-130 (475)
63 PRK14001 potassium-transportin 23.9 3.7E+02 0.0081 21.7 6.6 63 65-129 91-156 (189)
64 PF11116 DUF2624: Protein of u 23.6 1.7E+02 0.0038 20.7 4.2 54 66-121 6-62 (85)
65 PRK08645 bifunctional homocyst 23.6 1.2E+02 0.0026 28.0 4.2 44 80-123 531-575 (612)
66 COG4800 Predicted transcriptio 23.6 2.1E+02 0.0047 22.6 5.0 57 64-123 13-71 (170)
67 COG1182 AcpD Acyl carrier prot 23.4 85 0.0018 25.6 2.9 39 65-103 71-112 (202)
68 TIGR01088 aroQ 3-dehydroquinat 23.3 1.2E+02 0.0026 23.5 3.5 27 49-75 36-62 (141)
69 PF11458 Mistic: Membrane-inte 23.1 2.8E+02 0.0061 19.6 5.1 53 30-82 5-75 (84)
70 PHA01748 hypothetical protein 22.6 1.5E+02 0.0032 19.2 3.4 34 90-123 6-44 (60)
71 PF02981 FokI_N: Restriction e 22.5 1.8E+02 0.0039 22.7 4.4 37 49-85 20-59 (145)
72 PRK12805 flagellin; Provisiona 22.2 2.3E+02 0.005 23.4 5.3 50 37-86 77-128 (287)
73 PRK13015 3-dehydroquinate dehy 21.8 1.4E+02 0.003 23.2 3.6 29 49-77 38-66 (146)
74 PF08407 Chitin_synth_1N: Chit 21.7 54 0.0012 22.8 1.3 22 90-111 19-40 (79)
75 PRK12803 flagellin; Provisiona 21.5 2.3E+02 0.005 24.5 5.3 50 38-87 78-129 (335)
76 PRK13999 potassium-transportin 21.5 3.7E+02 0.008 21.9 6.2 67 58-130 97-166 (201)
77 PF04912 Dynamitin: Dynamitin 21.3 1.7E+02 0.0038 25.2 4.5 37 50-86 248-284 (388)
78 PRK08359 transcription factor; 21.2 2.8E+02 0.0061 22.0 5.4 29 91-119 108-137 (176)
79 PRK14002 potassium-transportin 21.1 4.3E+02 0.0094 21.3 6.4 65 64-130 86-153 (186)
80 PF01261 AP_endonuc_2: Xylose 21.0 2.5E+02 0.0054 20.3 4.8 54 36-89 66-124 (213)
81 PF00435 Spectrin: Spectrin re 21.0 2.3E+02 0.005 17.9 6.4 46 41-86 51-96 (105)
82 PRK12802 flagellin; Provisiona 20.9 2.6E+02 0.0056 22.9 5.3 49 38-86 80-130 (282)
83 PRK13890 conjugal transfer pro 20.8 3E+02 0.0064 20.0 5.1 26 93-118 30-56 (120)
84 PF12169 DNA_pol3_gamma3: DNA 20.7 99 0.0021 22.1 2.5 21 100-120 40-60 (143)
85 PF05250 UPF0193: Uncharacteri 20.3 4.7E+02 0.01 21.4 6.6 54 29-87 149-202 (212)
86 PF00137 ATP-synt_C: ATP synth 20.2 1.5E+02 0.0031 19.3 3.0 25 104-128 33-57 (66)
87 PRK12807 flagellin; Provisiona 20.2 2.8E+02 0.0062 22.8 5.4 47 38-84 78-126 (287)
No 1
>KOG3046 consensus Transcription factor, subunit of SRB subcomplex of RNA polymerase II [Transcription]
Probab=100.00 E-value=1.3e-39 Score=247.71 Aligned_cols=110 Identities=49% Similarity=0.702 Sum_probs=106.3
Q ss_pred ccccCChHHHHHHHHHHHHHHHHHHHHhhhhccccCCCchhHHHHHHHHHHHHHHHHHhhhhhcC-CCCcHHHHHhhhcC
Q 032730 26 TVAADDPKQNLNQVINSVQKTLGLLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVKLSEKCN-IQVPTEVLNLIDDG 104 (135)
Q Consensus 26 ~~~~~~~~~~L~~~iesl~~~l~~L~ql~i~Vs~f~~~sq~~L~~kin~LV~~L~~L~~~a~~~~-i~IP~EVl~yID~G 104 (135)
++..++..+.|.++.++|+++++.+||++++|++|+|.||+.|.++|++||..|++|++++++++ ++||+||++|||||
T Consensus 4 ~~~~~q~~ekl~~l~~~le~~~e~~~~Lgl~vs~F~~tsq~~L~qrl~tLv~~L~~l~~~s~k~n~i~IPleVl~yIddG 83 (147)
T KOG3046|consen 4 STNNDQMQEKLAQLENSLEKFLENFRQLGLIVSNFQPTSQDALNQRLNTLVRGLQDLDKLSSKLNDIQIPLEVLEYIDDG 83 (147)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhcCCCCcHHHHHHHHHHHHHHhhhhHHHHHhhccccCcHHHHHHHhcC
Confidence 45678899999999999999999999999999999999999999999999999999999999886 99999999999999
Q ss_pred CCchHHHHHHHHHHHHhhhhhhhhHHHhhcC
Q 032730 105 KNPDEFTRDVINSCIAKNQVTKGKTDAFKVL 135 (135)
Q Consensus 105 rNPDiyTre~vE~~~~~Nq~~kGK~~a~~~l 135 (135)
||||+|||+|+|+|+++||++|||++|||+|
T Consensus 84 rNPd~ytke~le~~~~kNq~vkGK~~~~K~f 114 (147)
T KOG3046|consen 84 RNPDLYTKEFLEKCLAKNQYVKGKIDAFKKF 114 (147)
T ss_pred CCccHHHHHHHHHHHHhhhHHhhhHHHHHHH
Confidence 9999999999999999999999999999986
No 2
>PF09748 Med10: Transcription factor subunit Med10 of Mediator complex; InterPro: IPR019145 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med10 is one of the protein subunits of the Mediator complex, tethered to Med14 (Rgr1) protein. Med10 specifically mediates basal-level HIS4 transcription via Gcn4. In addition, there is a putative requirement for Med10 in Bas2-mediated transcription []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=100.00 E-value=3.6e-37 Score=230.11 Aligned_cols=94 Identities=40% Similarity=0.632 Sum_probs=88.2
Q ss_pred HHHHHHHHHHHhhhhccccC-CCchhHHHHHHHHHHHHHHHHHhhhhh--------cCCCCcHHHHHhhhcCCCchHHHH
Q 032730 42 SVQKTLGLLHQLYLTVSSFN-AASQLPLLQRLNSLVSELDNMVKLSEK--------CNIQVPTEVLNLIDDGKNPDEFTR 112 (135)
Q Consensus 42 sl~~~l~~L~ql~i~Vs~f~-~~sq~~L~~kin~LV~~L~~L~~~a~~--------~~i~IP~EVl~yID~GrNPDiyTr 112 (135)
+|++++++|+|++++|++|+ |+|++.|.+||+.|+++|++|++++.. ++++||+|||+|||+|||||+|||
T Consensus 4 ~l~~~i~~l~el~~~v~d~~~~~s~~~L~~ki~~lv~~L~~l~~~~~~~~~~~~~~~~~~IP~evl~yID~GrNPDiyTr 83 (128)
T PF09748_consen 4 QLEDVIQSLYELGVIVSDFQGPPSQEALNQKINQLVTSLQELDKLAQQTNDPDSPLQDIQIPLEVLEYIDDGRNPDIYTR 83 (128)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHHHHHHHHHHHhcccCCCCcccccCCCCHHHHHHHhCCCCchHHHH
Confidence 34445557999999999999 999999999999999999999999987 789999999999999999999999
Q ss_pred HHHHHHHHhhhhhhhhHHHhhcC
Q 032730 113 DVINSCIAKNQVTKGKTDAFKVL 135 (135)
Q Consensus 113 e~vE~~~~~Nq~~kGK~~a~~~l 135 (135)
||||+|+++||++|||++||++|
T Consensus 84 e~vE~~~~~Nq~~kGK~~a~~~f 106 (128)
T PF09748_consen 84 EFVELVRRENQYVKGKMEAFKSF 106 (128)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHH
Confidence 99999999999999999999986
No 3
>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.
Probab=78.73 E-value=7.3 Score=25.81 Aligned_cols=55 Identities=24% Similarity=0.319 Sum_probs=46.3
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHhhhhccccCCCchhHHHHHHHHHHHHHHHHHh
Q 032730 30 DDPKQNLNQVINSVQKTLGLLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVK 84 (135)
Q Consensus 30 ~~~~~~L~~~iesl~~~l~~L~ql~i~Vs~f~~~sq~~L~~kin~LV~~L~~L~~ 84 (135)
++.+..|..+=..|.+.-+.|.||.+-|.+..++....+..||..+=..|..+.+
T Consensus 21 ~~r~~~i~~~e~~l~ea~~~l~qMe~E~~~~p~s~r~~~~~kl~~yr~~l~~lk~ 75 (79)
T PF05008_consen 21 EQRKSLIREIERDLDEAEELLKQMELEVRSLPPSERNQYKSKLRSYRSELKKLKK 75 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6777777777778888888999999999999777888999999999999988764
No 4
>KOG1666 consensus V-SNARE [Intracellular trafficking, secretion, and vesicular transport]
Probab=70.33 E-value=15 Score=30.37 Aligned_cols=57 Identities=21% Similarity=0.323 Sum_probs=51.0
Q ss_pred ccCChHHHHHHHHHHHHHHHHHHHHhhhhccccCCCchhHHHHHHHHHHHHHHHHHh
Q 032730 28 AADDPKQNLNQVINSVQKTLGLLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVK 84 (135)
Q Consensus 28 ~~~~~~~~L~~~iesl~~~l~~L~ql~i~Vs~f~~~sq~~L~~kin~LV~~L~~L~~ 84 (135)
+.++.++.|.++=.++++.=++|.||.+-|..-.|+....+..||.++=+.|.+++.
T Consensus 30 ~~~ekk~~l~~i~~~leEa~ell~qMdlEvr~lp~~~Rs~~~~KlR~yksdl~~l~~ 86 (220)
T KOG1666|consen 30 PGSEKKQLLSEIDSKLEEANELLDQMDLEVRELPPNFRSSYLSKLREYKSDLKKLKR 86 (220)
T ss_pred CchHHHHHHHHHHHhHHHHHHHHHHHHHHHHhCCchhhhHHHHHHHHHHHHHHHHHH
Confidence 456777788888888888888999999999999999999999999999999998875
No 5
>PF11315 Med30: Mediator complex subunit 30; InterPro: IPR021019 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med30 is a metazoan-specific subunit of Mediator [], having no homologues in yeasts.
Probab=67.53 E-value=57 Score=25.39 Aligned_cols=43 Identities=23% Similarity=0.369 Sum_probs=32.6
Q ss_pred CCcHH-HHHhhhcCCCchHHH-------------HHHHHHHHHhhhhhhhhHHHhhc
Q 032730 92 QVPTE-VLNLIDDGKNPDEFT-------------RDVINSCIAKNQVTKGKTDAFKV 134 (135)
Q Consensus 92 ~IP~E-Vl~yID~GrNPDiyT-------------re~vE~~~~~Nq~~kGK~~a~~~ 134 (135)
..|+| +|-|+|...+...-+ +|.+|++..+|+.+|--|+-++.
T Consensus 80 ~~~iEsLIP~~~~~~~k~e~~~~s~~~~~~~~er~el~e~v~~KN~qLk~iid~lR~ 136 (150)
T PF11315_consen 80 PTPIESLIPYKEEPRNKEEERDSSEEYRQLLEERKELIEQVKQKNQQLKEIIDQLRN 136 (150)
T ss_pred CCCHHHhccccCCccccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34554 678999988766442 57899999999999988887653
No 6
>PF14712 Snapin_Pallidin: Snapin/Pallidin
Probab=65.00 E-value=38 Score=23.00 Aligned_cols=37 Identities=22% Similarity=0.319 Sum_probs=25.6
Q ss_pred CchhHHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHHhhh
Q 032730 63 ASQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLID 102 (135)
Q Consensus 63 ~sq~~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~yID 102 (135)
.||..|...|..+...|+.+....... =|+++..|+.
T Consensus 28 ~sQ~~L~~~i~~~~~~L~~~~~~~~~~---~~~~~~~y~~ 64 (92)
T PF14712_consen 28 QSQEELLQQIDRLNEKLKELNEVEQIN---EPFDLDPYVK 64 (92)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhh---hHHHhhHHHH
Confidence 477799999999999998887643211 1555555654
No 7
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=60.48 E-value=36 Score=23.32 Aligned_cols=55 Identities=24% Similarity=0.276 Sum_probs=29.3
Q ss_pred chhHHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHHhhhcCCCchHHHHHHHHHHHHhhh
Q 032730 64 SQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGKNPDEFTRDVINSCIAKNQ 123 (135)
Q Consensus 64 sq~~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~yID~GrNPDiyTre~vE~~~~~Nq 123 (135)
+|..+..+|..--+...+.-++. ..|.+|.+.|++|+-.|+.+..-+.+..+++.
T Consensus 5 tq~eIA~~lGks~s~Vs~~l~Ll-----~lP~~i~~~v~~g~~~~~~a~~~L~~~~~~~~ 59 (93)
T PF08535_consen 5 TQEEIAKRLGKSRSWVSNHLALL-----DLPEEIKELVRSGRISDIRALYELRKLAEKNP 59 (93)
T ss_dssp -HHHHHHHTT--HHHHHHHHGGG-----S--HHHHHHHHTTS---HHHHHHHHHHHHH-H
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH-----cCCHHHHHHHHcCCCchHHHHHHHHHHHHhCH
Confidence 34455566643333333332222 37999999999999999988877776666654
No 8
>PF05430 Methyltransf_30: S-adenosyl-L-methionine-dependent methyltransferase; InterPro: IPR008471 This entry contains several uncharacterised bacterial proteins with no known function.; GO: 0016645 oxidoreductase activity, acting on the CH-NH group of donors, 0055114 oxidation-reduction process; PDB: 2E58_D 3SGL_A 3PVC_A 3AWI_D 3PS9_A 2QY6_A.
Probab=56.14 E-value=6 Score=29.30 Aligned_cols=18 Identities=17% Similarity=0.407 Sum_probs=15.7
Q ss_pred CCCchHHHHHHHHHHHHh
Q 032730 104 GKNPDEFTRDVINSCIAK 121 (135)
Q Consensus 104 GrNPDiyTre~vE~~~~~ 121 (135)
.+||++||.|++..+.+-
T Consensus 62 ~~nPelWs~e~~~~l~~~ 79 (124)
T PF05430_consen 62 AKNPELWSEELFKKLARL 79 (124)
T ss_dssp TTSGGGSSHHHHHHHHHH
T ss_pred cCCcccCCHHHHHHHHHH
Confidence 799999999999987653
No 9
>PF03433 EspA: EspA-like secreted protein ; InterPro: IPR005095 EspA is the prototypical member of this family. EspA, together with EspB, EspD and Tir are exported by a type III secretion system. These proteins are essential for attaching and effacing lesion formation. EspA is a structural protein and a major component of a large, transiently expressed, filamentous surface organelle which forms a direct link between the bacterium and the host cell [, ].; PDB: 1XOU_A.
Probab=54.16 E-value=4.2 Score=32.84 Aligned_cols=89 Identities=22% Similarity=0.412 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccccC---------CCchhHHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHHhhhc-
Q 032730 34 QNLNQVINSVQKTLGLLHQLYLTVSSFN---------AASQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDD- 103 (135)
Q Consensus 34 ~~L~~~iesl~~~l~~L~ql~i~Vs~f~---------~~sq~~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~yID~- 103 (135)
.-|..=|--|++|+-.|.+|. -.-|. ...| -+.++++++|-.+.+=+. +...++|.|||+|+++
T Consensus 37 ~~~s~gisvL~~fm~lls~La--~akf~~m~~~~~~ar~aQ-~maN~vDevIA~~~k~~d---k~k~~lp~dVi~Ym~~n 110 (188)
T PF03433_consen 37 NKLSGGISVLYMFMNLLSELA--NAKFAQMQKKAERARDAQ-DMANRVDEVIAEVAKSDD---KAKAPLPDDVIDYMRDN 110 (188)
T ss_dssp HHHHHHHHHHHHHHHHHHT-------------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHhccCCCc---cccccCCHHHHHHHHHc
Confidence 345554555555555554433 23342 1223 377777777766654433 3455799999999965
Q ss_pred -----CCCchHHHHHHHHHHHHhhhhhhhhHHHhh
Q 032730 104 -----GKNPDEFTRDVINSCIAKNQVTKGKTDAFK 133 (135)
Q Consensus 104 -----GrNPDiyTre~vE~~~~~Nq~~kGK~~a~~ 133 (135)
|++=+-|-++.=. -+.-+|+..|.|
T Consensus 111 gI~VdG~si~~Yl~~n~~-----~~LdkG~LqaVK 140 (188)
T PF03433_consen 111 GIKVDGKSIDDYLKKNGS-----GGLDKGQLQAVK 140 (188)
T ss_dssp -----------------------------------
T ss_pred CCeecCeeccchhhhhhh-----ccCCchhHHHHH
Confidence 6777777666543 344445544443
No 10
>PRK09432 metF 5,10-methylenetetrahydrofolate reductase; Provisional
Probab=52.31 E-value=25 Score=29.53 Aligned_cols=43 Identities=12% Similarity=0.338 Sum_probs=30.0
Q ss_pred HHHHHHhhhhhcCCCCcHHHHHhhhcCCC-ch-------HHHHHHHHHHHH
Q 032730 78 ELDNMVKLSEKCNIQVPTEVLNLIDDGKN-PD-------EFTRDVINSCIA 120 (135)
Q Consensus 78 ~L~~L~~~a~~~~i~IP~EVl~yID~GrN-PD-------iyTre~vE~~~~ 120 (135)
+++++..++..|.+.||.++++.++..++ |+ -|+.|+++....
T Consensus 216 s~~~~~~~~~~~Gv~vP~~l~~~l~~~~d~~~~~~~~Gi~~a~e~i~~L~~ 266 (296)
T PRK09432 216 NFKQLKKFADMTNVRIPAWMAKMFDGLDDDAETRKLVGASIAMDMVKILSR 266 (296)
T ss_pred CHHHHHHHHHccCCCCCHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34555566667899999999999999754 44 256666665543
No 11
>PF04129 Vps52: Vps52 / Sac2 family ; InterPro: IPR007258 Vps52 complexes with Vps53 and Vps54 to form a multi-subunit complex involved in regulating membrane trafficking events [].
Probab=51.44 E-value=1.2e+02 Score=27.33 Aligned_cols=33 Identities=15% Similarity=0.397 Sum_probs=22.4
Q ss_pred CCCCcHHHHHhhhcCCCchHHHHHHHHHHHHhh
Q 032730 90 NIQVPTEVLNLIDDGKNPDEFTRDVINSCIAKN 122 (135)
Q Consensus 90 ~i~IP~EVl~yID~GrNPDiyTre~vE~~~~~N 122 (135)
++-||+++++-|-+|.==+-|-++.++...+..
T Consensus 81 ~i~ipP~lI~~I~~~~v~e~~~~~~~~~~~k~~ 113 (508)
T PF04129_consen 81 DIVIPPDLIRSICEGPVNEQYIEELLELLKKKI 113 (508)
T ss_pred HHcCCHHHHHhHhcCCCCHHHHHHHHHHHHHHH
Confidence 788999999999888433346665555444433
No 12
>KOG3936 consensus Nitroreductases [Energy production and conversion]
Probab=46.84 E-value=46 Score=24.15 Aligned_cols=37 Identities=22% Similarity=0.226 Sum_probs=27.3
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHHhh
Q 032730 65 QLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLI 101 (135)
Q Consensus 65 q~~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~yI 101 (135)
.+.+..+-+.+-+.|..=..+....+-+||++||+-+
T Consensus 58 dd~~lknSQ~FYEelk~RRScR~fSn~dVPleVI~Nl 94 (100)
T KOG3936|consen 58 DDEMLKNSQEFYEELKKRRSCRFFSNEDVPLEVIDNL 94 (100)
T ss_pred hHHHHHhHHHHHHHHHhhhhhhhhccccCcHHHHHHH
Confidence 3455556667777777767777778999999999754
No 13
>PF10232 Med8: Mediator of RNA polymerase II transcription complex subunit 8; InterPro: IPR019364 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Arc32, or Med8, is one of the subunits of the Mediator complex of RNA polymerase II. The region conserved contains two alpha helices putatively necessary for binding to other subunits within the core of the Mediator complex. The N terminus of Med8 binds to the essential core Head part of Mediator and the C terminus hinges to Med18 on the non-essential part of the Head that also includes Med20 []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3C0T_B 3RJ1_J 2HZS_I.
Probab=46.53 E-value=89 Score=25.39 Aligned_cols=53 Identities=25% Similarity=0.238 Sum_probs=36.5
Q ss_pred cccCChHHHHHHHHHHHHHHHHHHHHhhhhccccCCCchhHHHHHHHHHHHHHHHHHhh
Q 032730 27 VAADDPKQNLNQVINSVQKTLGLLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVKL 85 (135)
Q Consensus 27 ~~~~~~~~~L~~~iesl~~~l~~L~ql~i~Vs~f~~~sq~~L~~kin~LV~~L~~L~~~ 85 (135)
.+.|..++.|.++..||.+++..|. ..+...+-..|..+.+-|.++|..|.+.
T Consensus 11 ~aLe~ir~Rl~qL~~SL~~l~~~L~------~~~~lp~W~slq~qf~il~~qL~sL~~~ 63 (226)
T PF10232_consen 11 KALEAIRQRLAQLKHSLQSLIDKLE------QSQPLPPWPSLQDQFAILSSQLSSLSKT 63 (226)
T ss_dssp TTTSTTTHHHHHHHHHHHHHHHHHT-------T-SS---HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH------ccCCCCCcHHHHHHHHHHHHHHHHHHHH
Confidence 4788999999999999998776666 2334455566777777777777777653
No 14
>PF08745 UPF0278: UPF0278 family; InterPro: IPR022785 This entry contains proteins of the UPF0278 family and proteins containing PIN domains. Members of the UPF0278 family are uncharacterised and about 200 amino acids in length.; PDB: 2LCQ_A.
Probab=44.17 E-value=7.5 Score=31.81 Aligned_cols=78 Identities=18% Similarity=0.422 Sum_probs=0.0
Q ss_pred ccccccCChHHH--HHHHHHHHHHHHHHHHH--hhhhccccCCCchhHHHHHHHHHHH-------HHHHHH-----hhhh
Q 032730 24 TTTVAADDPKQN--LNQVINSVQKTLGLLHQ--LYLTVSSFNAASQLPLLQRLNSLVS-------ELDNMV-----KLSE 87 (135)
Q Consensus 24 ~~~~~~~~~~~~--L~~~iesl~~~l~~L~q--l~i~Vs~f~~~sq~~L~~kin~LV~-------~L~~L~-----~~a~ 87 (135)
+++-+-.+++++ .+++.+.+..+|+.+.+ +...+|-|-|+| +-..+..++. -+.+++ +...
T Consensus 6 TS~fTdp~vr~~fG~~~l~ea~~~~l~Lia~arl~l~is~YmPpS---Vy~El~~fl~~~~~~~e~~~k~~twvv~KsP~ 82 (205)
T PF08745_consen 6 TSAFTDPEVREQFGDEDLCEAVEKFLDLIARARLKLGISCYMPPS---VYKELKNFLERNGCDEEVISKLDTWVVKKSPD 82 (205)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccc---cccccccccccccccccccccccccccccccc
Confidence 333344455554 34666677777777776 566778888865 3344433333 222222 2334
Q ss_pred hcCCCCcHHHH-HhhhcC
Q 032730 88 KCNIQVPTEVL-NLIDDG 104 (135)
Q Consensus 88 ~~~i~IP~EVl-~yID~G 104 (135)
.+++.||-+++ +||++=
T Consensus 83 ryev~IPA~i~yEyI~em 100 (205)
T PF08745_consen 83 RYEVKIPAEIFYEYIEEM 100 (205)
T ss_dssp ------------------
T ss_pred cccccccccccccccccc
Confidence 57999999998 788763
No 15
>KOG3990 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.92 E-value=1.7e+02 Score=25.21 Aligned_cols=51 Identities=24% Similarity=0.125 Sum_probs=27.3
Q ss_pred CCCCCccCCCccccccccCChHHHHHHHHHHHHHHHHHHHHh----hhhccccCC
Q 032730 12 GGNGMVSNQANDTTTVAADDPKQNLNQVINSVQKTLGLLHQL----YLTVSSFNA 62 (135)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~L~~~iesl~~~l~~L~ql----~i~Vs~f~~ 62 (135)
|+||...+..-|.-..---...++|++-|.+|++.|-.=+|+ .-.+++..+
T Consensus 206 ~~NG~~f~P~~D~~~~dh~V~i~~lkeeia~Lkk~L~qkdq~ileKdkqisnLKa 260 (305)
T KOG3990|consen 206 NENGDGFPPFGDRDPGDHMVKIQKLKEEIARLKKLLHQKDQLILEKDKQISNLKA 260 (305)
T ss_pred CCCCCcCCCCCCCCCcchHHHHHHHHHHHHHHHHHHhhhHHHHHhhhhhhhccCc
Confidence 456644333223322222345788999999988865533332 344555544
No 16
>PF02669 KdpC: K+-transporting ATPase, c chain; InterPro: IPR003820 Kdp, the high affinity ATP-driven K+-transport system of Escherichia coli, is a complex of the membrane-bound subunits KdpA, KdpB, KdpC and the small peptide KdpF. KdpC forms strong interactions with the KdpA subunit, serving to assemble and stabilise the Kdp complex []. It has been suggested that KdpC could be one of the connecting links between the energy providing subunit KdpB and the K+- transporting subunit KdpA []. The K+ transport system actively transports K+ ions via ATP hydrolysis.; GO: 0008556 potassium-transporting ATPase activity, 0006813 potassium ion transport, 0016020 membrane
Probab=41.65 E-value=1.2e+02 Score=24.51 Aligned_cols=61 Identities=11% Similarity=0.163 Sum_probs=37.8
Q ss_pred hHHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHHhhhcCCCchH---HHHHHHHHHHHhhhhhhhhH
Q 032730 66 LPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGKNPDE---FTRDVINSCIAKNQVTKGKT 129 (135)
Q Consensus 66 ~~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~yID~GrNPDi---yTre~vE~~~~~Nq~~kGK~ 129 (135)
..|.+++.+-+..+..-+ .....+||.|++..==-|=+||| +-+=++.|+.+.......++
T Consensus 92 ~~l~~~v~~~~~~~~~~~---~~~~~~vP~dlvtaSgSGLDP~IS~~aA~~Qv~RVA~argl~~~~v 155 (188)
T PF02669_consen 92 PELRERVEERIAALRKEN---PVAPSPVPADLVTASGSGLDPHISPAAALIQVPRVAKARGLSEEEV 155 (188)
T ss_pred hHHHHHHHHHHHHHHhhc---ccCCCCCCHHHHhcccccCCCCcCHHHHHHHHHHHHHHhCcCHHHH
Confidence 347777776666654433 12345789888888778888887 45556666666544433333
No 17
>TIGR02878 spore_ypjB sporulation protein YpjB. Members of this protein, YpjB, family are restricted to a subset of endospore-forming bacteria, including Bacillus species but not CLostridium or some others. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon, where sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect. This protein family is not, however, a part of the endospore formation minimal gene set.
Probab=40.45 E-value=1.4e+02 Score=24.91 Aligned_cols=54 Identities=13% Similarity=0.189 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHH-------hhhcCCCchHHHHHHHHHHHHhhh
Q 032730 67 PLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLN-------LIDDGKNPDEFTRDVINSCIAKNQ 123 (135)
Q Consensus 67 ~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~-------yID~GrNPDiyTre~vE~~~~~Nq 123 (135)
.+.+++|++++...-+. +...|.+|++-++ |||+.||-.+=..+..+.....+.
T Consensus 122 ~f~~~ln~Fl~~Y~~I~---PSl~Idl~~~~~q~v~~~i~~l~~~r~~~~~~~~~~~~L~~~~~ 182 (233)
T TIGR02878 122 AFQEKLNEFLSLYDLIY---PSLTIDVPEDQVQRVDSHLSYLENFRFQQRSEDEKEEQLSLMRG 182 (233)
T ss_pred HHHHHHHHHHHHhhhcc---cceeeecCHHHHHHHHHHHHHHHhhhhhccChHHHHHHHHHHHH
Confidence 34444444444443332 1246889998775 888899887777776666655444
No 18
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=40.06 E-value=1.2e+02 Score=21.23 Aligned_cols=49 Identities=22% Similarity=0.186 Sum_probs=34.1
Q ss_pred chhHHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHHhhhcCC-CchHHHHHHH
Q 032730 64 SQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGK-NPDEFTRDVI 115 (135)
Q Consensus 64 sq~~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~yID~Gr-NPDiyTre~v 115 (135)
....+..+|.++.... .++.++..+. |+..-|..|+.|+ ||.+-|-.-|
T Consensus 29 ~~~~~~~~l~~~r~~~-glSqLAe~~G--Is~stLs~iE~g~~~Ps~~tL~kI 78 (89)
T TIGR02684 29 DPAYIAHALGYIARAR-GMTQLARKTG--LSRESLYKALSGKGNPTFDTILKV 78 (89)
T ss_pred CHHHHHHHHHHHHHHC-ChHHHHHHHC--CCHHHHHHHHcCCCCCCHHHHHHH
Confidence 3445777777776654 5665555444 7999999999995 9988765443
No 19
>PF14202 TnpW: Transposon-encoded protein TnpW
Probab=40.03 E-value=24 Score=21.17 Aligned_cols=21 Identities=14% Similarity=0.343 Sum_probs=18.1
Q ss_pred ccccCCCchhHHHHHHHHHHH
Q 032730 57 VSSFNAASQLPLLQRLNSLVS 77 (135)
Q Consensus 57 Vs~f~~~sq~~L~~kin~LV~ 77 (135)
-..|.+.+.+.+.+||..|+.
T Consensus 15 ~~~F~~~s~et~~DKi~rli~ 35 (37)
T PF14202_consen 15 EVHFSETSKETMQDKIKRLIR 35 (37)
T ss_pred EEEECCCccccHHHHHHHHHh
Confidence 346789999999999999985
No 20
>PRK15364 pathogenicity island 2 effector protein SseB; Provisional
Probab=39.45 E-value=39 Score=27.48 Aligned_cols=42 Identities=17% Similarity=0.399 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHHhhhc------CCCchHHH
Q 032730 67 PLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDD------GKNPDEFT 111 (135)
Q Consensus 67 ~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~yID~------GrNPDiyT 111 (135)
-+.+++.+.|-.+++= -.+...++|.|||+||.+ |..=|-|-
T Consensus 76 ~mAN~VDevIA~v~k~---ddK~k~~LPddVI~YmrdNgI~VdG~sid~Yl 123 (196)
T PRK15364 76 EKSNEMDEVIAKAAKG---DAKTKEEVPEDVIKYMRDNGILIDGMTIDDYM 123 (196)
T ss_pred HHHHHHHHHHHHHhcC---CCcccccCCHHHHHHHHHcCceecccchHHHH
Confidence 3666666666555442 223456899999999954 45544444
No 21
>PF01017 STAT_alpha: STAT protein, all-alpha domain; InterPro: IPR013800 The STAT protein (Signal Transducers and Activators of Transcription) family contains transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors, hence they act as signal transducers in the cytoplasm and transcription activators in the nucleus []. Binding of these factors to cell-surface receptors leads to receptor autophosphorylation at a tyrosine, the phosphotyrosine being recognised by the STAT SH2 domain, which mediates the recruitment of STAT proteins from the cytosol and their association with the activated receptor. The STAT proteins are then activated by phosphorylation via members of the JAK family of protein kinases, causing them to dimerise and translocated to the nucleus, where they bind to specific promoter sequences in target genes. In mammals, STATs comprise a family of seven structurally and functionally related proteins: Stat1, Stat2, Stat3, Stat4, Stat5a and Stat5b, Stat6. STAT proteins play a critical role in regulating innate and acquired host immune responses. Dysregulation of at least two STAT signalling cascades (i.e. Stat3 and Stat5) is associated with cellular transformation. Signalling through the JAK/STAT pathway is initiated when a cytokine binds to its corresponding receptor. This leads to conformational changes in the cytoplasmic portion of the receptor, initiating activation of receptor associated members of the JAK family of kinases. The JAKs, in turn, mediate phosphorylation at the specific receptor tyrosine residues, which then serve as docking sites for STATs and other signalling molecules. Once recruited to the receptor, STATs also become phosphorylated by JAKs, on a single tyrosine residue. Activated STATs dissociate from the receptor, dimerise, translocate to the nucleus and bind to members of the GAS (gamma activated site) family of enhancers. The seven STAT proteins identified in mammals range in size from 750 and 850 amino acids. The chromosomal distribution of these STATs, as well as the identification of STATs in more primitive eukaryotes, suggest that this family arose from a single primordial gene. STATs share structurally and functionally conserved domains including: an N-terminal domain that strengthens interactions between STAT dimers on adjacent DNA-binding sites; a coiled-coil STAT domain that is implicated in protein-protein interactions; a DNA-binding domain with an immunoglobulin-like fold similar to p53 tumour suppressor protein; an EF-hand-like linker domain connecting the DNA-binding and SH2 domains; an SH2 domain (IPR000980 from INTERPRO) that acts as a phosphorylation-dependent switch to control receptor recognition and DNA-binding; and a C-terminal transactivation domain []. The crystal structure of the N terminus of Stat4 reveals a dimer. The interface of this dimer is formed by a ring-shaped element consisting of five short helices. Several studies suggest that this N-terminal dimerisation promotes cooperativity of binding to tandem GAS elements and with the transcriptional coactivator CBP/p300. This entry represents the all-alpha helical domain, which consists of four long helices arranged in a bundle with a left-handed twist (coiled-coil), which in turn forms a right-handed superhelix.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0004871 signal transducer activity, 0006355 regulation of transcription, DNA-dependent, 0007165 signal transduction, 0005634 nucleus; PDB: 1YVL_A 1BF5_A 3CWG_B 1BG1_A 1Y1U_B.
Probab=37.92 E-value=1.2e+02 Score=23.47 Aligned_cols=52 Identities=19% Similarity=0.259 Sum_probs=28.4
Q ss_pred ccCChHHHHHHHHHHHHHHHHHHHHhhhhc----c--ccCCCc----hhHHHHHHHHHHHHH
Q 032730 28 AADDPKQNLNQVINSVQKTLGLLHQLYLTV----S--SFNAAS----QLPLLQRLNSLVSEL 79 (135)
Q Consensus 28 ~~~~~~~~L~~~iesl~~~l~~L~ql~i~V----s--~f~~~s----q~~L~~kin~LV~~L 79 (135)
..++..++|..--++|.+.+|.++|--.-+ . .|.++. ...|.+++..|.+.|
T Consensus 118 P~~~~LD~LQ~wfe~LAe~l~qlrqqlk~l~~l~~k~~~~~d~~~~~~~~L~~~v~~ll~~L 179 (182)
T PF01017_consen 118 PFDSSLDQLQNWFESLAEILWQLRQQLKKLEELQQKLTYENDPIPDQLPQLNERVTELLKNL 179 (182)
T ss_dssp S----THHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS--TT-THHHHHHHHHHHHHHHHHHH
T ss_pred CChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCchhhhHHHHHHHHHHHHHHH
Confidence 346677888888888888888777722211 1 233322 346667776666655
No 22
>PF14181 YqfQ: YqfQ-like protein
Probab=37.70 E-value=75 Score=24.98 Aligned_cols=47 Identities=21% Similarity=0.367 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhccccCCCchhHHHHHHHHHHHHHHHHHhhh
Q 032730 35 NLNQVINSVQKTLGLLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVKLS 86 (135)
Q Consensus 35 ~L~~~iesl~~~l~~L~ql~i~Vs~f~~~sq~~L~~kin~LV~~L~~L~~~a 86 (135)
.|...|+..+++|+.+-|++=.|.-|.| |.+.|=.++.-++.|....
T Consensus 53 ~l~~mL~N~QKvl~vaQqv~PmIQQYGP-----LVrNLPam~kiyr~l~s~~ 99 (161)
T PF14181_consen 53 SLSGMLNNVQKVLGVAQQVGPMIQQYGP-----LVRNLPAMWKIYRGLKSSD 99 (161)
T ss_pred cHHHHHHHHHHHHHHHHHhhHHHHHHhH-----HHHhhHHHHHHHHccCCCC
Confidence 4788888889999888888887877765 8888888888888776554
No 23
>KOG1961 consensus Vacuolar sorting protein VPS52/suppressor of actin Sac2 [Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=37.66 E-value=1.4e+02 Score=28.59 Aligned_cols=38 Identities=34% Similarity=0.514 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHH----hhhhhc-CCCCcHHHHHhhhcCC
Q 032730 68 LLQRLNSLVSELDNMV----KLSEKC-NIQVPTEVLNLIDDGK 105 (135)
Q Consensus 68 L~~kin~LV~~L~~L~----~~a~~~-~i~IP~EVl~yID~Gr 105 (135)
|..|=+.+-..|.+.. ++++.. ++-||+++|.-|=+|.
T Consensus 115 lqekS~~m~~~L~Nrq~v~s~Ls~fVdd~iVpp~lI~~I~~g~ 157 (683)
T KOG1961|consen 115 LQEKSNDMQLRLENRQAVESKLSQFVDDLIVPPELIKTIVDGD 157 (683)
T ss_pred HHHHhhHHHHHHHhHHHHHHHHHHHhccccCCHHHHHHHHcCC
Confidence 4444444444444433 233344 7899999999998874
No 24
>PF09577 Spore_YpjB: Sporulation protein YpjB (SpoYpjB); InterPro: IPR014231 Proteins in thie entry, typified by YpjB, are restricted to a subset of the endospore-forming bacteria which includes Bacillus species, but not species. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon []. Sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect, but this gene is not, however, a part of the endospore formation minimal gene set.
Probab=36.71 E-value=2.1e+02 Score=23.65 Aligned_cols=54 Identities=13% Similarity=0.130 Sum_probs=32.1
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHH-------hhhcCCCchHHHHHHHHHHHHh
Q 032730 65 QLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLN-------LIDDGKNPDEFTRDVINSCIAK 121 (135)
Q Consensus 65 q~~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~-------yID~GrNPDiyTre~vE~~~~~ 121 (135)
...+.+.+|++.+++.-+.-. ..|++|++-++ |||.+++...=..+..+....-
T Consensus 119 ~~~f~~~~n~f~~~y~~I~Ps---l~I~~~~~~v~~v~s~i~yl~~~~~~~~~~~~~~~~l~~l 179 (232)
T PF09577_consen 119 KEAFRASLNEFLSHYELIRPS---LTIDRPPEQVQRVDSHISYLERLRFQQLDQKEVQEALEQL 179 (232)
T ss_pred HHHHHHHHHHHHHHHHHhcch---hhccCCHHHHHHHHHHHHHHHHhhhcccChHHHHHHHHHH
Confidence 345555555555555544322 46889988665 8888888665555554444333
No 25
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=36.22 E-value=27 Score=26.32 Aligned_cols=14 Identities=36% Similarity=0.648 Sum_probs=10.9
Q ss_pred cCCCchHHHHHHHH
Q 032730 103 DGKNPDEFTRDVIN 116 (135)
Q Consensus 103 ~GrNPDiyTre~vE 116 (135)
.-+=|||||||-+-
T Consensus 38 ETHYPDIYTREEiA 51 (125)
T KOG0484|consen 38 ETHYPDIYTREEIA 51 (125)
T ss_pred hhcCCcchhHHHHH
Confidence 45679999999764
No 26
>PF01220 DHquinase_II: Dehydroquinase class II; InterPro: IPR001874 3-dehydroquinate dehydratase (4.2.1.10 from EC), or dehydroquinase, catalyzes the conversion of 3-dehydroquinate into 3-dehydroshikimate. It is the third step in the shikimate pathway for the biosynthesis of aromatic amino acids from chorismate. Two classes of dehydroquinases exist, known as types I and II. Class-II enzymes are homododecameric enzymes of about 17 kDa. They are found in some bacteria such as actinomycetales [, ] and some fungi where they act in a catabolic pathway that allows the use of quinic acid as a carbon source.; GO: 0003855 3-dehydroquinate dehydratase activity; PDB: 3N8K_J 3N7A_I 3N87_F 3N8N_H 3N86_N 1H0S_A 3N59_J 1H05_A 1H0R_A 2Y71_A ....
Probab=35.41 E-value=57 Score=25.15 Aligned_cols=30 Identities=13% Similarity=0.183 Sum_probs=24.2
Q ss_pred HHHHhhhhccccCCCchhHHHHHHHHHHHH
Q 032730 49 LLHQLYLTVSSFNAASQLPLLQRLNSLVSE 78 (135)
Q Consensus 49 ~L~ql~i~Vs~f~~~sq~~L~~kin~LV~~ 78 (135)
...++++.|.-||.++...|.++|++-...
T Consensus 37 ~a~~~g~~v~~~QSN~EGelid~I~~a~~~ 66 (140)
T PF01220_consen 37 TAAELGVEVEFFQSNHEGELIDWIHEARDD 66 (140)
T ss_dssp HHHHTTEEEEEEE-SSHHHHHHHHHHHTCT
T ss_pred HHHHCCCeEEEEecCCHHHHHHHHHHHHhh
Confidence 466789999999999999999999876443
No 27
>PLN03094 Substrate binding subunit of ER-derived-lipid transporter; Provisional
Probab=35.32 E-value=75 Score=27.97 Aligned_cols=49 Identities=14% Similarity=0.189 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHhhhhcccc-----CCCchhHHHHHHHHHHHHHHHHHhhh
Q 032730 38 QVINSVQKTLGLLHQLYLTVSSF-----NAASQLPLLQRLNSLVSELDNMVKLS 86 (135)
Q Consensus 38 ~~iesl~~~l~~L~ql~i~Vs~f-----~~~sq~~L~~kin~LV~~L~~L~~~a 86 (135)
+++..++.+...|.+-.-.+..| +|+....|-+-+.++...++++++..
T Consensus 290 ~lL~Nle~lt~~LA~as~~l~~l~~~l~~p~~~~~L~qtl~sl~~t~~ni~~vs 343 (370)
T PLN03094 290 GLLKEVEKLTRVAAEASEDLRRLNSSILTPENTELLRQSIYTLTKTLKHIESIS 343 (370)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444444444444432222222 34444555555555655555555544
No 28
>PRK14139 heat shock protein GrpE; Provisional
Probab=32.87 E-value=1.3e+02 Score=23.97 Aligned_cols=34 Identities=21% Similarity=0.269 Sum_probs=22.0
Q ss_pred CCCccccccccCChHHHHHHHHHHHHHHHHHHHH
Q 032730 19 NQANDTTTVAADDPKQNLNQVINSVQKTLGLLHQ 52 (135)
Q Consensus 19 ~~~~~~~~~~~~~~~~~L~~~iesl~~~l~~L~q 52 (135)
.+.-.+++|++++....|+.-|+.+++-+..+.+
T Consensus 20 ~~~~~~~~~~~~~e~~~l~~~l~~le~e~~elkd 53 (185)
T PRK14139 20 AQAAAAAAAAAEDAAPALEAELAEAEAKAAELQD 53 (185)
T ss_pred cccccccccccchhHHHHHHHHHHHHHHHHHHHH
Confidence 3444555556777777787777777766665554
No 29
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=32.57 E-value=97 Score=20.06 Aligned_cols=31 Identities=13% Similarity=0.342 Sum_probs=22.1
Q ss_pred CCCCcHHHHHhhhcCC----CchHHHHHHHHHHHH
Q 032730 90 NIQVPTEVLNLIDDGK----NPDEFTRDVINSCIA 120 (135)
Q Consensus 90 ~i~IP~EVl~yID~Gr----NPDiyTre~vE~~~~ 120 (135)
...||...|+.||+|. .+..|.|-||....+
T Consensus 19 ~t~I~~~~l~aiE~~~~~~lp~~~y~rg~lr~Ya~ 53 (62)
T PF13413_consen 19 ETKISVSYLEAIENGDFDSLPSPVYARGYLRKYAR 53 (62)
T ss_dssp HCS--HHHHHHHHCT-GCCSSSHHHHHHHHHHHHH
T ss_pred HhCCCHHHHHHHHCcChhhCCcHHHHHHHHHHHHH
Confidence 4579999999999973 346899999876543
No 30
>KOG0564 consensus 5,10-methylenetetrahydrofolate reductase [Amino acid transport and metabolism]
Probab=31.09 E-value=2.4e+02 Score=26.53 Aligned_cols=83 Identities=13% Similarity=0.240 Sum_probs=54.4
Q ss_pred ccCChHHHHHHHHHHHHHHHHHHHHhhhhccccCCCchhHHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHHhhhcCCCc
Q 032730 28 AADDPKQNLNQVINSVQKTLGLLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGKNP 107 (135)
Q Consensus 28 ~~~~~~~~L~~~iesl~~~l~~L~ql~i~Vs~f~~~sq~~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~yID~GrNP 107 (135)
++|=+..||==-.+.|.+|+.++|++++.+--|-. -- =|+....+.+++..|.+.||.++.+.+|.-|.=
T Consensus 181 GaDFIiTQlFYd~e~flkfv~~cR~~gi~~PIvPG--IM--------PI~~Y~sf~R~~kls~~~IP~~~~~~L~piKdd 250 (590)
T KOG0564|consen 181 GADFIITQLFYDVETFLKFVKDCRAAGINVPIVPG--IM--------PIQSYRSFLRIAKLSGVSIPQHLMDRLEPIKDD 250 (590)
T ss_pred cchhhhhhhhcCHHHHHHHHHHHHHhCCCCCcccc--cc--------cchhHHHHHHHHHHhCCCCCHHHHHhcccCCCc
Confidence 44444444444456778888899998885533321 00 134456667777889999999999999987777
Q ss_pred hHHHHH-----HHHHHHH
Q 032730 108 DEFTRD-----VINSCIA 120 (135)
Q Consensus 108 DiyTre-----~vE~~~~ 120 (135)
|.--|+ .||.|++
T Consensus 251 DeaVr~~Gvel~vemc~k 268 (590)
T KOG0564|consen 251 DEAVRNYGVELIVEMCRK 268 (590)
T ss_pred HHHHHHHhHHHHHHHHHH
Confidence 765554 3555554
No 31
>PRK04358 hypothetical protein; Provisional
Probab=31.07 E-value=94 Score=25.70 Aligned_cols=76 Identities=21% Similarity=0.473 Sum_probs=42.4
Q ss_pred cccccCChHHHH--HHHHHHHHHHHHHHHH--hhhhccccCCCchhHHHHHHHHHHHH-------HHHHH-----hhhhh
Q 032730 25 TTVAADDPKQNL--NQVINSVQKTLGLLHQ--LYLTVSSFNAASQLPLLQRLNSLVSE-------LDNMV-----KLSEK 88 (135)
Q Consensus 25 ~~~~~~~~~~~L--~~~iesl~~~l~~L~q--l~i~Vs~f~~~sq~~L~~kin~LV~~-------L~~L~-----~~a~~ 88 (135)
++-+-.++++++ +++.+.+..+|+++.+ +...+|-|-|+| +-..+..++.. +.+++ +....
T Consensus 11 S~fT~p~vr~~fg~e~l~ea~~~~l~Lia~arl~l~is~YmPpS---Vy~El~~f~~~~~~~~e~~~kl~twi~~KsP~r 87 (217)
T PRK04358 11 SAFTDPDVREQFGVEDLEEAVEKFLDLIARARLKLGISCYMPPS---VYKELRGFLERNGCSPEVIAKLDTWIVKKSPNR 87 (217)
T ss_pred cccCCHHHHHHcCCCCHHHHHHHHHHHHHHhhhccCceEEcCHH---HHHHHHHHHHhcCCCHHHHhhheeEEEEcCCCc
Confidence 333444455533 3555666677777666 445778888865 44444433321 11121 12234
Q ss_pred cCCCCcHHHH-Hhhhc
Q 032730 89 CNIQVPTEVL-NLIDD 103 (135)
Q Consensus 89 ~~i~IP~EVl-~yID~ 103 (135)
+++.||-+++ +||++
T Consensus 88 y~v~IPA~i~ye~I~~ 103 (217)
T PRK04358 88 YEIKIPAEIFYEYIED 103 (217)
T ss_pred eeeeccHHHHHHHHHH
Confidence 6889999988 67764
No 32
>cd00537 MTHFR Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase to convert homocysteine to methionine. The enzymatic mechanism is a ping-pong bi-bi mechanism, in which NAD(P)+ release precedes the binding of methylenetetrahydrofolate and the acceptor is free FAD. The family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from prokaryotes and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The bacterial enzyme is a homotetramer and NADH is the preferred reductant while the eukaryotic enzyme is a homodimer and NADPH is the preferred reductant. In humans, there are several clinically significant mutations in MTHFR that result in hyperhomocysteinemia, which is a risk factor for the development of cardiovascular disease.
Probab=31.01 E-value=87 Score=25.33 Aligned_cols=40 Identities=10% Similarity=0.367 Sum_probs=26.6
Q ss_pred HHHHHHhhhhhcCCCCcHHHHHhhhc-CCCchHHHHHHHHH
Q 032730 78 ELDNMVKLSEKCNIQVPTEVLNLIDD-GKNPDEFTRDVINS 117 (135)
Q Consensus 78 ~L~~L~~~a~~~~i~IP~EVl~yID~-GrNPDiyTre~vE~ 117 (135)
+++.+..+...+.+.||.++++.++. +.+|+..-+.-++.
T Consensus 200 s~~~l~~~~~~~Gv~vP~~~~~~l~~~~~~~~~~~~~g~~~ 240 (274)
T cd00537 200 SYKQAKRFAKLCGVEIPDWLLERLEKLKDDAEAVRAEGIEI 240 (274)
T ss_pred CHHHHHHHHHhhCCCCCHHHHHHHHhcCCCHHHHHHHHHHH
Confidence 44566666667899999999999984 35554433333333
No 33
>PF06657 Cep57_MT_bd: Centrosome microtubule-binding domain of Cep57; InterPro: IPR010597 This entry is thought to represent a centrosomal protein of 57 kDa (Cep57-related protein). It is required for spindle microtubule attachment to both kinetochores and centrosomes and functions to tether minus-ends of spindle microtubules to centrosomes. It may act by forming ring-like structures around microtubules, or by serving as a cross-linker or scaffold at the attachment site [].
Probab=30.83 E-value=1.8e+02 Score=19.94 Aligned_cols=54 Identities=20% Similarity=0.430 Sum_probs=31.5
Q ss_pred ccccccCChHHHHHHHHHHHHHHHHHHHHhhhhcccc-------CC----CchhHHHHHHHHHHHHHH
Q 032730 24 TTTVAADDPKQNLNQVINSVQKTLGLLHQLYLTVSSF-------NA----ASQLPLLQRLNSLVSELD 80 (135)
Q Consensus 24 ~~~~~~~~~~~~L~~~iesl~~~l~~L~ql~i~Vs~f-------~~----~sq~~L~~kin~LV~~L~ 80 (135)
++......+...|..+|..|+.=++ ++...-..+ ++ ..+..|...|..||..|.
T Consensus 3 ~t~r~s~~p~~~Ls~vl~~LqDE~~---hm~~e~~~L~~~~~~~d~s~~~~~R~~L~~~l~~lv~~mE 67 (79)
T PF06657_consen 3 PTSRPSQSPGEALSEVLKALQDEFG---HMKMEHQELQDEYKQMDPSLGRRKRRDLEQELEELVKRME 67 (79)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcccccChHHHHHHHHHHHHHHHHHH
Confidence 4445666677777777777766333 322211111 23 335678888888887774
No 34
>PF05130 FlgN: FlgN protein; InterPro: IPR007809 Flagella synthesis protein FlgN is an export chaperone involved in flagellar synthesis []. This entry represents a FlgN-like domain, consisting of a 4 long helices bundle, where the last helix is shorter than the three others.; GO: 0009296 flagellum assembly, 0019861 flagellum; PDB: 2FUP_A 3OPC_A.
Probab=29.85 E-value=1.3e+02 Score=20.85 Aligned_cols=92 Identities=17% Similarity=0.200 Sum_probs=53.9
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHhhhhccccCCCchhHHHHHHHHHHHHHHHHHhhhhh----cCCC-CcHHHHHhhhcCC
Q 032730 31 DPKQNLNQVINSVQKTLGLLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVKLSEK----CNIQ-VPTEVLNLIDDGK 105 (135)
Q Consensus 31 ~~~~~L~~~iesl~~~l~~L~ql~i~Vs~f~~~sq~~L~~kin~LV~~L~~L~~~a~~----~~i~-IP~EVl~yID~Gr 105 (135)
+...-|+..++-+.+.+..+.+-.-++..-++..-..+..+.+.++..+..+.+.... .... -+.-+=.+++ .
T Consensus 5 ~L~~~L~~~~~~~~~L~~ll~~e~~~l~~~d~~~l~~~~~~k~~l~~~l~~le~~r~~~~~~~~~~~~~~~l~~~~~--~ 82 (143)
T PF05130_consen 5 ELIELLEEQIELLQELLELLEEEREALISGDIDELEELVEEKQELLEELRELEKQRQQLLAKLGAEPEEATLSELIE--E 82 (143)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHC--C
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCccccccHHHHHh--c
Confidence 3445555555555555555555555555557777788899999999999888765432 1212 2223334455 5
Q ss_pred CchHHH-----HHHHHHHHHhhhh
Q 032730 106 NPDEFT-----RDVINSCIAKNQV 124 (135)
Q Consensus 106 NPDiyT-----re~vE~~~~~Nq~ 124 (135)
.|++.. ++.++.|...|+.
T Consensus 83 ~~~l~~~~~~l~~~~~~~~~~n~~ 106 (143)
T PF05130_consen 83 REELQALWRELRELLEELQELNER 106 (143)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHH
Confidence 555532 4456666666653
No 35
>PRK10132 hypothetical protein; Provisional
Probab=29.70 E-value=2.2e+02 Score=20.71 Aligned_cols=50 Identities=14% Similarity=0.153 Sum_probs=26.7
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHhhhhccccCCCchhHHHHHHHHHHHHHH
Q 032730 31 DPKQNLNQVINSVQKTLGLLHQLYLTVSSFNAASQLPLLQRLNSLVSELD 80 (135)
Q Consensus 31 ~~~~~L~~~iesl~~~l~~L~ql~i~Vs~f~~~sq~~L~~kin~LV~~L~ 80 (135)
+++.|.+++...|...+.++-++--..++..-+.-..|-.|+.......+
T Consensus 9 ~~~~q~e~L~~Dl~~L~~~le~ll~~~~~~~~~~~~~lR~r~~~~L~~ar 58 (108)
T PRK10132 9 DVDDGVQDIQNDVNQLADSLESVLKSWGSDAKGEAEAARRKAQALLKETR 58 (108)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 44555555555555555555554333333333334567777777666655
No 36
>TIGR00677 fadh2_euk methylenetetrahydrofolate reductase, eukaryotic type. This protein is an FAD-containing flavoprotein.
Probab=29.62 E-value=87 Score=26.05 Aligned_cols=35 Identities=11% Similarity=0.283 Sum_probs=22.5
Q ss_pred HHhhhhhcCCCCcHHHHHhhhcCCCc-hHHHHHHHH
Q 032730 82 MVKLSEKCNIQVPTEVLNLIDDGKNP-DEFTRDVIN 116 (135)
Q Consensus 82 L~~~a~~~~i~IP~EVl~yID~GrNP-DiyTre~vE 116 (135)
+......+.+.||.++++.++..++. +..-+.-++
T Consensus 205 ~~~~~~~~Gi~vP~~l~~~l~~~~~~~~~~~~~gi~ 240 (281)
T TIGR00677 205 FLRRAKWSKTKIPQEIMSRLEPIKDDDEAVRDYGIE 240 (281)
T ss_pred HHHHHhcCCCCCCHHHHHHHHhccCCHHHHHHHHHH
Confidence 33334457899999999999887544 533333333
No 37
>TIGR00676 fadh2 5,10-methylenetetrahydrofolate reductase, prokaryotic form. This protein is an FAD-containing flavoprotein.
Probab=28.70 E-value=1.2e+02 Score=24.75 Aligned_cols=34 Identities=15% Similarity=0.338 Sum_probs=22.8
Q ss_pred hhcCCCCcHHHHHhhhcCCCc-hHHHHHHHHHHHH
Q 032730 87 EKCNIQVPTEVLNLIDDGKNP-DEFTRDVINSCIA 120 (135)
Q Consensus 87 ~~~~i~IP~EVl~yID~GrNP-DiyTre~vE~~~~ 120 (135)
..+.+.||.++++-++..+++ +-.-+.-++.|..
T Consensus 206 ~~~Gv~vP~~~~~~l~~~~~~~~~~~~~gi~~~~~ 240 (272)
T TIGR00676 206 ERCGAEIPAWLVKRLEKYDDDPEEVRAVGIEYATD 240 (272)
T ss_pred hccCCCCCHHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 357899999999999987665 4333334444433
No 38
>PF02219 MTHFR: Methylenetetrahydrofolate reductase; InterPro: IPR003171 This family includes the 5,10-methylenetetrahydrofolate reductase 1.7.99.5 from EC from bacteria and methylenetetrahydrofolate reductase 1.5.1.20 from EC from eukaryotes. The structure for this domain is known [] to be a TIM barrel.; GO: 0004489 methylenetetrahydrofolate reductase (NADPH) activity, 0006555 methionine metabolic process, 0055114 oxidation-reduction process; PDB: 3IJD_B 1B5T_B 3FSU_C 1ZPT_C 2FMO_B 3FST_C 2FMN_C 1ZP3_A 1ZP4_B 1ZRQ_B ....
Probab=28.62 E-value=64 Score=26.51 Aligned_cols=40 Identities=18% Similarity=0.479 Sum_probs=25.1
Q ss_pred HHHHhhhhhcCCCCcHHHHHhhhcCCC-chHHHHHHHHHHH
Q 032730 80 DNMVKLSEKCNIQVPTEVLNLIDDGKN-PDEFTRDVINSCI 119 (135)
Q Consensus 80 ~~L~~~a~~~~i~IP~EVl~yID~GrN-PDiyTre~vE~~~ 119 (135)
+.+..+...+.+.||.++++-++..++ |+...+--++.+.
T Consensus 214 ~~~~~~~~~~Gv~iP~~~~~~l~~~~~~~~~~~~~gi~~a~ 254 (287)
T PF02219_consen 214 KSARFLAKLCGVDIPDELIERLEEAKDDPEAVREIGIEIAV 254 (287)
T ss_dssp HHHHHHHHHHT-EEEHHHHHHHHTTTT-HHHHHHHHHHHHH
T ss_pred HHHHHHHhccCccCCHHHHHHHHHhcCCHHHHHHHhHHHHH
Confidence 344444556799999999999997665 4444444444443
No 39
>COG1344 FlgL Flagellin and related hook-associated proteins [Cell motility and secretion]
Probab=27.87 E-value=1.4e+02 Score=25.47 Aligned_cols=49 Identities=18% Similarity=0.415 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHHhhhhccc--cCCCchhHHHHHHHHHHHHHHHHHhhhh
Q 032730 39 VINSVQKTLGLLHQLYLTVSS--FNAASQLPLLQRLNSLVSELDNMVKLSE 87 (135)
Q Consensus 39 ~iesl~~~l~~L~ql~i~Vs~--f~~~sq~~L~~kin~LV~~L~~L~~~a~ 87 (135)
-++++.++|+.++++-+...+ +.+..+..+...|+.|.++|.++-..+.
T Consensus 79 aL~~~~~~lqrirelavqaan~t~s~~dr~~iq~Ei~~l~~el~~iantt~ 129 (360)
T COG1344 79 ALSEISKILQRIKELAVQAANGTLSDADRAAIQKEIEQLLDELDNIANTTS 129 (360)
T ss_pred HHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 344555666678887777776 7788889999999999999999987763
No 40
>PRK08026 flagellin; Validated
Probab=27.72 E-value=1.3e+02 Score=27.90 Aligned_cols=49 Identities=10% Similarity=0.220 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHhhhhccc--cCCCchhHHHHHHHHHHHHHHHHHhhhhh
Q 032730 40 INSVQKTLGLLHQLYLTVSS--FNAASQLPLLQRLNSLVSELDNMVKLSEK 88 (135)
Q Consensus 40 iesl~~~l~~L~ql~i~Vs~--f~~~sq~~L~~kin~LV~~L~~L~~~a~~ 88 (135)
++++.+.|..++++.+...+ +.++.+..+...|+.|.++|..+.....+
T Consensus 82 L~~i~d~LqRmrELaVqAaNGT~S~~DR~aiq~Ei~qL~~eI~~ia~~T~f 132 (529)
T PRK08026 82 LSEINNNLQRVRELTVQAATGTNSQSDLDSIQDEIKSRLDEIDRVSGQTQF 132 (529)
T ss_pred HHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 44455556667777776644 56677889999999999999988775543
No 41
>cd00466 DHQase_II Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway and the catabolic quinate pathway. There are two types of DHQases, which are distinct from each other in amino acid sequence and three-dimensional structure. Type I enzymes usually catalyze the biosynthetic reaction using a syn elimination mechanism. In contrast, type II enzymes, found in the quinate pathway of fungi and in the shikimate pathway of many bacteria, are dodecameric enzymes that employ an anti elimination reaction mechanism.
Probab=27.53 E-value=91 Score=24.06 Aligned_cols=27 Identities=19% Similarity=0.254 Sum_probs=23.3
Q ss_pred HHHHhhhhccccCCCchhHHHHHHHHH
Q 032730 49 LLHQLYLTVSSFNAASQLPLLQRLNSL 75 (135)
Q Consensus 49 ~L~ql~i~Vs~f~~~sq~~L~~kin~L 75 (135)
...++++.|.-||.++...|.++|++-
T Consensus 36 ~a~~~g~~v~~~QSN~Egelid~I~~a 62 (140)
T cd00466 36 LAAELGVEVEFFQSNHEGELIDWIHEA 62 (140)
T ss_pred HHHHcCCEEEEEeeCcHHHHHHHHHHh
Confidence 455789999999999999999999875
No 42
>cd08812 CARD_RIG-I_like Caspase activation and recruitment domains found in RIG-I-like DEAD box helicases. Caspase activation and recruitment domains (CARDs) found in Retinoic acid Inducible Gene I (RIG-I)-like DEAD box helicases. These helicases, including MDA5 and RIG-I, contain two N-terminal CARD domains and a C-terminal DEAD box RNA helicase domain. They are cytoplasmic RNA helicases that play an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, RIG-I and MDA5 have been shown to recognize different sets of viruses. MDA5 and RIG-I associate with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mec
Probab=27.50 E-value=61 Score=22.45 Aligned_cols=35 Identities=20% Similarity=0.371 Sum_probs=21.8
Q ss_pred CCcHHHHHhhhcCCCchHHHHHHHHHHHHhhhhhhhhHHHh
Q 032730 92 QVPTEVLNLIDDGKNPDEFTRDVINSCIAKNQVTKGKTDAF 132 (135)
Q Consensus 92 ~IP~EVl~yID~GrNPDiyTre~vE~~~~~Nq~~kGK~~a~ 132 (135)
-.|.+|+.|+-. .+|.+..|..+++ ...+|.+.+-
T Consensus 19 l~p~~il~~l~~-----~L~~~~~e~I~a~-~~~~g~~~aa 53 (88)
T cd08812 19 IIPRDILDHLPE-----CLTDEDKEQILAE-ERNKGNIAAA 53 (88)
T ss_pred cCHHHHHHHHHH-----HcCHHHHHHHHHH-HhccChHHHH
Confidence 467777777755 7777777776664 3334555443
No 43
>PF13324 GCIP: Grap2 and cyclin-D-interacting; PDB: 3AY5_A.
Probab=27.39 E-value=3.1e+02 Score=22.39 Aligned_cols=15 Identities=20% Similarity=0.018 Sum_probs=5.9
Q ss_pred hHHHHHHHHHHHHHH
Q 032730 66 LPLLQRLNSLVSELD 80 (135)
Q Consensus 66 ~~L~~kin~LV~~L~ 80 (135)
..|...+..|.+.+.
T Consensus 255 ~~v~~~~~~L~~~l~ 269 (275)
T PF13324_consen 255 DEVRAAAAKLSSVLK 269 (275)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 333333333333333
No 44
>COG4121 Uncharacterized conserved protein [Function unknown]
Probab=27.35 E-value=27 Score=29.24 Aligned_cols=28 Identities=18% Similarity=0.279 Sum_probs=20.7
Q ss_pred CCCchHHHHHHHHHHHHhhhhhhhhHHHh
Q 032730 104 GKNPDEFTRDVINSCIAKNQVTKGKTDAF 132 (135)
Q Consensus 104 GrNPDiyTre~vE~~~~~Nq~~kGK~~a~ 132 (135)
.||||.||-|++....+. -+-+|+.-+|
T Consensus 180 ~kNP~mW~~e~l~~~a~~-~~~~~~l~t~ 207 (252)
T COG4121 180 VKNPEMWEDELLNLMARI-PYRDPTLATF 207 (252)
T ss_pred cCChhhccHHHHHHHHhh-cCCCCceech
Confidence 599999999999877765 4555554444
No 45
>TIGR00681 kdpC K+-transporting ATPase, C subunit. This chain has a single predicted transmembrane region near the amino end. It is part of a K+-transport ATPase that contains two other membrane-bound subunits, KdpA and KdpB, and a small subunit KdpF. KdpA is the K+-translocating subunit, KdpB the ATP-hydrolyzing subunit. During assembly of the complex, KdpA and KdpC bind to each other. This interaction is thought to stabilize the complex [PubMed:9858692]. Data indicates that KdpC might connect the KdpA, the K+-transporting subunit, to KdpB, the ATP-hydrolyzing (energy providing) subunit [PubMed:9858692].
Probab=27.26 E-value=2.8e+02 Score=22.39 Aligned_cols=64 Identities=16% Similarity=0.215 Sum_probs=42.2
Q ss_pred chhHHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHHhhhcCCCchH---HHHHHHHHHHHhhhhhhhhHH
Q 032730 64 SQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGKNPDE---FTRDVINSCIAKNQVTKGKTD 130 (135)
Q Consensus 64 sq~~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~yID~GrNPDi---yTre~vE~~~~~Nq~~kGK~~ 130 (135)
|-..|.+++.+-+..+..-+. ...-+||.|++..==-|=.||| +-+-++.++.+.......++.
T Consensus 89 snp~l~~~v~~r~~~~~~~~~---~~~~~vP~DlvTaSgSGLDPhISp~aA~~Qv~RVA~argl~~~~v~ 155 (187)
T TIGR00681 89 SNPDLLSRIAARVEAQRLENL---DAAVQVPVDLVTSSGSGLDPHISPAAAQAQFPRVAKARNISPQQLQ 155 (187)
T ss_pred CCHHHHHHHHHHHHHHHHhCC---CCCCCCCHHHHhcccccCCCCCCHHHHHHHHHHHHHHhCcCHHHHH
Confidence 335577777777766654321 1235799999998888889987 555667777766655444443
No 46
>TIGR03875 RNA_lig_partner RNA ligase partner, MJ_0950 family. This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown.
Probab=27.22 E-value=1.2e+02 Score=24.81 Aligned_cols=73 Identities=18% Similarity=0.450 Sum_probs=40.5
Q ss_pred ccCChHHHHH--HHHHHHHHHHHHHHH--hhhhccccCCCchhHHHHHHHHHHHH-------HHHHH-----hhhhhcCC
Q 032730 28 AADDPKQNLN--QVINSVQKTLGLLHQ--LYLTVSSFNAASQLPLLQRLNSLVSE-------LDNMV-----KLSEKCNI 91 (135)
Q Consensus 28 ~~~~~~~~L~--~~iesl~~~l~~L~q--l~i~Vs~f~~~sq~~L~~kin~LV~~-------L~~L~-----~~a~~~~i 91 (135)
+-.++++++. ++.+.+.+++..+.+ +...+|-|-|+| +-..+..++.. +.+++ +....+++
T Consensus 10 Tdp~vr~~fg~~~l~ea~~~~l~Lia~arl~l~iscYmPps---Vy~El~~fl~~~~~~~e~~~kl~twv~~KsP~rye~ 86 (206)
T TIGR03875 10 TDPELREQLGDEDLCEAVRTFLDLIARARLKLGIECYMPPS---VYKELRRFLERNGCDPETLAKLDTWVVKKSPNRYEV 86 (206)
T ss_pred CCHHHHHHcCCCCHHHHHHHHHHHHHHhhhccCceeecCHH---HHHHHHHHHHhcCCCHHHHHhheeEEEEcCCCeeee
Confidence 4444444442 444566667776665 456777788855 44444333321 11222 12234688
Q ss_pred CCcHHHH-Hhhhc
Q 032730 92 QVPTEVL-NLIDD 103 (135)
Q Consensus 92 ~IP~EVl-~yID~ 103 (135)
.||-+++ +||++
T Consensus 87 ~IPA~i~ye~I~e 99 (206)
T TIGR03875 87 KIPAEIFYEYIEE 99 (206)
T ss_pred eccHHHHHHHHHH
Confidence 9999988 67764
No 47
>PF06831 H2TH: Formamidopyrimidine-DNA glycosylase H2TH domain; InterPro: IPR015886 This entry represents a helix-2turn-helix DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ]. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (3.2.2 from EC, 4.2.99.18 from EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine []. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger []. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger []. This entry represents the central domain containing the DNA-binding helix-two turn-helix domain [].; GO: 0003684 damaged DNA binding, 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0008270 zinc ion binding, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, 0006289 nucleotide-excision repair; PDB: 3GQ3_A 3JR5_A 3SAT_A 3GPX_A 2F5Q_A 3SBJ_A 3U6S_A 3SAU_A 3SAR_A 2F5P_A ....
Probab=26.97 E-value=89 Score=21.70 Aligned_cols=49 Identities=10% Similarity=0.067 Sum_probs=29.8
Q ss_pred CCCCcccCCCC-----CccCCCccccccccCChHHHHHHHHHHHHHHHHHHHHhhh
Q 032730 5 VGGSRASGGNG-----MVSNQANDTTTVAADDPKQNLNQVINSVQKTLGLLHQLYL 55 (135)
Q Consensus 5 ~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~L~~~iesl~~~l~~L~ql~i 55 (135)
|.-.+|+| |- -....+.|.+. +.+=.+.+++.+.+++.+++....+++.
T Consensus 33 Q~~iaGiG-Niy~~EiLf~a~i~P~~~-~~~L~~~~~~~l~~~~~~vl~~ai~~gg 86 (92)
T PF06831_consen 33 QSVIAGIG-NIYADEILFRAGIHPERP-ASSLSEEELRRLHEAIKRVLREAIEVGG 86 (92)
T ss_dssp TTTSTT---HHHHHHHHHHTTB-TTSB-GGGSHHHHHHHHHHHHHHHHHHHHHTT-
T ss_pred CCccccCc-HHHHHHHHHHcCCCccCc-cccCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 34557776 54 12234555444 5667788899999999988887776554
No 48
>PRK00315 potassium-transporting ATPase subunit C; Reviewed
Probab=26.36 E-value=3e+02 Score=22.28 Aligned_cols=63 Identities=16% Similarity=0.158 Sum_probs=41.6
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHHhhhcCCCchH---HHHHHHHHHHHhhhhhhhhHH
Q 032730 65 QLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGKNPDE---FTRDVINSCIAKNQVTKGKTD 130 (135)
Q Consensus 65 q~~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~yID~GrNPDi---yTre~vE~~~~~Nq~~kGK~~ 130 (135)
-..|.+++.+-+..+..-+.. ..-+||.|++..==-|=.|+| +-+=++.|+.+.......++.
T Consensus 92 np~l~~~v~~r~~~~~~~~~~---~~~~vP~DlvTaSgSGLDPhIS~~aA~~Qv~RVA~argl~~~~v~ 157 (193)
T PRK00315 92 NPALDDAIKARVAALRAANPG---ASSPVPVDLVTASGSGLDPHISPAAAAYQIPRVAAARQLPVEQVA 157 (193)
T ss_pred CHHHHHHHHHHHHHHHHhCCC---CCCCCCHHHHhccccCCCCCCCHHHHHHHHHHHHHHhCcCHHHHH
Confidence 345777777777766553321 235799999988888888887 555667777766655444443
No 49
>PF12554 MOZART1: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR022214 This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 105 amino acids in length. There is a single completely conserved residue L that may be functionally important.
Probab=26.25 E-value=1.1e+02 Score=19.51 Aligned_cols=32 Identities=25% Similarity=0.462 Sum_probs=19.6
Q ss_pred HHHhhhhhcCCCCcHHHH----HhhhcCCCchHHHH
Q 032730 81 NMVKLSEKCNIQVPTEVL----NLIDDGKNPDEFTR 112 (135)
Q Consensus 81 ~L~~~a~~~~i~IP~EVl----~yID~GrNPDiyTr 112 (135)
-++.++..-+..+..|-+ +.+|.|-||+-...
T Consensus 7 ~l~eiS~lLntgLd~etL~ici~L~e~GVnPeaLA~ 42 (48)
T PF12554_consen 7 VLHEISDLLNTGLDRETLSICIELCENGVNPEALAA 42 (48)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHCCCCHHHHHH
Confidence 344444444555566554 57899999986543
No 50
>PRK12584 flagellin A; Reviewed
Probab=26.07 E-value=1.4e+02 Score=27.21 Aligned_cols=48 Identities=15% Similarity=0.185 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHhhhhcc--ccCCCchhHHHHHHHHHHHHHHHHHhhh
Q 032730 39 VINSVQKTLGLLHQLYLTVS--SFNAASQLPLLQRLNSLVSELDNMVKLS 86 (135)
Q Consensus 39 ~iesl~~~l~~L~ql~i~Vs--~f~~~sq~~L~~kin~LV~~L~~L~~~a 86 (135)
-++.+.+.|..++++-+... .+.++.+..+...|+.|.++|..+-...
T Consensus 81 aL~~i~~~Lqr~relavqaangt~s~~dR~ai~~Ei~~L~~ei~~ian~t 130 (510)
T PRK12584 81 AMDEQLKILDTIKVKATQAAQDGQTTESRKAIQSDIVRLIQGLDNIGNTT 130 (510)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 34555566667888777764 3567788999999999999999998754
No 51
>PF03334 PhaG_MnhG_YufB: Na+/H+ antiporter subunit; InterPro: IPR005133 This is a family of small, transmembrane proteins believed to be components of Na+/H+ and K+/H+ antiporters. Members, including proteins designated MnhG from Staphylococcus aureus and PhaG from Rhizobium meliloti (Sinorhizobium meliloti), show some similarity to chain L of the NADH dehydrogenase I, which also translocates protons. ; GO: 0005451 monovalent cation:hydrogen antiporter activity, 0015672 monovalent inorganic cation transport, 0015992 proton transport
Probab=25.68 E-value=32 Score=23.58 Aligned_cols=9 Identities=44% Similarity=0.604 Sum_probs=7.7
Q ss_pred CCchHHHHH
Q 032730 105 KNPDEFTRD 113 (135)
Q Consensus 105 rNPDiyTre 113 (135)
|-||.|||=
T Consensus 18 R~pd~y~Rl 26 (81)
T PF03334_consen 18 RFPDFYTRL 26 (81)
T ss_pred hCCcHHHHh
Confidence 789999984
No 52
>PLN02540 methylenetetrahydrofolate reductase
Probab=25.57 E-value=76 Score=29.53 Aligned_cols=30 Identities=20% Similarity=0.542 Sum_probs=23.7
Q ss_pred HHHHhhhhhcCCCCcHHHHHhhhcCCCchH
Q 032730 80 DNMVKLSEKCNIQVPTEVLNLIDDGKNPDE 109 (135)
Q Consensus 80 ~~L~~~a~~~~i~IP~EVl~yID~GrNPDi 109 (135)
+.+.+++..|.+.||.++++.++..++.|.
T Consensus 211 k~l~r~~~l~Gi~IP~~i~~rLe~~kddde 240 (565)
T PLN02540 211 KGFLRMTGFCKTKIPAEITAALEPIKDNDE 240 (565)
T ss_pred HHHHHHHhccCCcCCHHHHHHHHhcCCCHH
Confidence 444555567899999999999999887754
No 53
>PRK13588 flagellin B; Provisional
Probab=25.45 E-value=1.5e+02 Score=27.34 Aligned_cols=49 Identities=18% Similarity=0.278 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHHHhhhhccc--cCCCchhHHHHHHHHHHHHHHHHHhhh
Q 032730 38 QVINSVQKTLGLLHQLYLTVSS--FNAASQLPLLQRLNSLVSELDNMVKLS 86 (135)
Q Consensus 38 ~~iesl~~~l~~L~ql~i~Vs~--f~~~sq~~L~~kin~LV~~L~~L~~~a 86 (135)
.-++++.+.|..++++.+...+ +.+..+..+...++.|.++|..+-...
T Consensus 80 ~aL~~i~~iLqrireLavqAaNgt~s~~dR~aiq~Ei~qL~~eI~~iantt 130 (514)
T PRK13588 80 KAMDEQIKILDTIKTKAVQAAQDGQTLESRRALQSDIQRLLEELDNIANTT 130 (514)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3444555566677787777644 567788999999999999999998765
No 54
>PF00210 Ferritin: Ferritin-like domain; InterPro: IPR008331 Ferritin is one of the major non-haem iron storage proteins in animals, plants, and microorganisms []. It consists of a mineral core of hydrated ferric oxide, and a multi-subunit protein shell that encloses the former and assures its solubility in an aqueous environment. In animals the protein is mainly cytoplasmic and there are generally two or more genes that encode closely related subunits - in mammals there are two subunits which are known as H(eavy) and L(ight). In plants ferritin is found in the chloroplast []. This entry represents the main structural domain of ferritin. The domain is also found in other ferritin-like proteins such as members of the DNA protection during starvation (DPS) family and bacterioferritins.; GO: 0008199 ferric iron binding, 0006879 cellular iron ion homeostasis; PDB: 1N1Q_C 4DYU_E 2YJJ_D 2YJK_B 2VXX_B 3FVB_A 2WLU_A 2XGW_A 2WLA_A 1Z4A_D ....
Probab=25.26 E-value=2.3e+02 Score=19.36 Aligned_cols=55 Identities=11% Similarity=0.094 Sum_probs=40.8
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHhhhhcccc-CCCchhHHHHHHHHHHHHHHHHHh
Q 032730 30 DDPKQNLNQVINSVQKTLGLLHQLYLTVSSF-NAASQLPLLQRLNSLVSELDNMVK 84 (135)
Q Consensus 30 ~~~~~~L~~~iesl~~~l~~L~ql~i~Vs~f-~~~sq~~L~~kin~LV~~L~~L~~ 84 (135)
.++.+.|+..++.-..+...++++.-.+..- ++.+...+..-+.+....+..|.+
T Consensus 79 ~~~~~~l~~~l~~e~~~~~~~~~l~~~a~~~~D~~t~~~~~~~l~~~~~~~~~l~~ 134 (142)
T PF00210_consen 79 TDPREALEAALEDEKEIIEEYRELIKLAEKEGDPETADFLDEFLEEEEKHIWMLQA 134 (142)
T ss_dssp SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5899999999998888888888887777655 566666676666666666655554
No 55
>PRK10667 Hha toxicity attenuator; Provisional
Probab=24.88 E-value=82 Score=23.88 Aligned_cols=27 Identities=22% Similarity=0.224 Sum_probs=20.8
Q ss_pred CCccccccccCChHHHHHHHHHHHHHHHHHH
Q 032730 20 QANDTTTVAADDPKQNLNQVINSVQKTLGLL 50 (135)
Q Consensus 20 ~~~~~~~~~~~~~~~~L~~~iesl~~~l~~L 50 (135)
-+||.+| ++--||+.+||+|-.|++..
T Consensus 36 WvNDptS----~~nlqLNeLIEHIa~f~~~f 62 (122)
T PRK10667 36 WVNDPTS----AVNLQLNELIEHIATFALNF 62 (122)
T ss_pred CcCCCch----HhhhhHHHHHHHHHHHHHHh
Confidence 5787766 46789999999988876643
No 56
>PRK06771 hypothetical protein; Provisional
Probab=24.85 E-value=1.7e+02 Score=21.25 Aligned_cols=37 Identities=22% Similarity=0.329 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHhhhhhcCC--CCcHHHHHhhhcCCCc
Q 032730 71 RLNSLVSELDNMVKLSEKCNI--QVPTEVLNLIDDGKNP 107 (135)
Q Consensus 71 kin~LV~~L~~L~~~a~~~~i--~IP~EVl~yID~GrNP 107 (135)
++..+=..|+.+.+.-.-.+. .+|.||.+.+.+|++=
T Consensus 31 ~~k~ie~~L~~I~~~~Gi~~~~~~~~~e~~~Li~~Gkki 69 (93)
T PRK06771 31 RLKRMEDRLQLITKEMGIVDREPPVNKELRQLMEEGQTV 69 (93)
T ss_pred HHHHHHHHHHHHHHHcCCCCCcccccHHHHHHHHcCCch
Confidence 444444444455444433333 7889999999999863
No 57
>PF10757 YbaJ: Biofilm formation regulator YbaJ; InterPro: IPR019693 YbaJ regulates biofilm formation. It also has an important role in the regulation of motility in the biofilm. YbaJ functions in increasing conjugation, aggregation and decreasing the motility, resulting in an increase of biofilm [].
Probab=24.79 E-value=80 Score=23.96 Aligned_cols=27 Identities=22% Similarity=0.272 Sum_probs=20.8
Q ss_pred CCccccccccCChHHHHHHHHHHHHHHHHHH
Q 032730 20 QANDTTTVAADDPKQNLNQVINSVQKTLGLL 50 (135)
Q Consensus 20 ~~~~~~~~~~~~~~~~L~~~iesl~~~l~~L 50 (135)
-+||.+| ++--||+.+||+|-.|++..
T Consensus 36 WvNDptS----~~nlqLNeLIEHIA~F~~~f 62 (122)
T PF10757_consen 36 WVNDPTS----AVNLQLNELIEHIAAFIWNF 62 (122)
T ss_pred CcCCCch----hhhhhHHHHHHHHHHHHHhh
Confidence 5787766 46679999999988876643
No 58
>PF08849 DUF1819: Putative inner membrane protein (DUF1819); InterPro: IPR014948 These proteins are functionally uncharacterised. Several are annotated as putative inner membrane proteins. ; PDB: 3BHW_A.
Probab=24.75 E-value=83 Score=24.35 Aligned_cols=61 Identities=11% Similarity=0.013 Sum_probs=32.7
Q ss_pred HHHHHHHHHHhhhhccccCCCchhHHHHHHHHHHHHHHHHHhhh--hhcCCCCcHHHHHhhhc
Q 032730 43 VQKTLGLLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVKLS--EKCNIQVPTEVLNLIDD 103 (135)
Q Consensus 43 l~~~l~~L~ql~i~Vs~f~~~sq~~L~~kin~LV~~L~~L~~~a--~~~~i~IP~EVl~yID~ 103 (135)
+..|+....+-+-.+..+.+++..-|.+.+-.+.....=|+... ....+.++++|.+|+..
T Consensus 121 ~~~F~~~k~~~~~~i~~WSdsT~~Kl~~~~~~~L~eaGlL~~~~~~~i~~~~l~~~~~~~l~~ 183 (189)
T PF08849_consen 121 WDAFFEEKAEQDPEIASWSDSTIKKLRQVLFRILREAGLLEGSRSKKIQPPLLSPEVREYLKR 183 (189)
T ss_dssp HHHHHHHHHHH-TTS----HHHHHHHHHHHHHHHHHTTSBS-TTT-BB------HHHHHHHHH
T ss_pred HHHHHHHHHhcCCcccccCHHHHHHHHHHHHHHHHHcCCccCCCCCeeecCcCCHHHHHHHHH
Confidence 44555556666666667777777777777776666666564422 33478899999999977
No 59
>PRK05395 3-dehydroquinate dehydratase; Provisional
Probab=24.55 E-value=1.1e+02 Score=23.83 Aligned_cols=28 Identities=14% Similarity=0.196 Sum_probs=23.8
Q ss_pred HHHHhhhhccccCCCchhHHHHHHHHHH
Q 032730 49 LLHQLYLTVSSFNAASQLPLLQRLNSLV 76 (135)
Q Consensus 49 ~L~ql~i~Vs~f~~~sq~~L~~kin~LV 76 (135)
...++++.|.-||.++...|.++|++-.
T Consensus 38 ~a~~~g~~v~~~QSN~EGelId~I~~a~ 65 (146)
T PRK05395 38 EAAELGVELEFFQSNHEGELIDRIHEAR 65 (146)
T ss_pred HHHHcCCEEEEEeeCcHHHHHHHHHhcc
Confidence 3557899999999999999999998753
No 60
>COG3076 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.48 E-value=1.3e+02 Score=22.99 Aligned_cols=38 Identities=29% Similarity=0.473 Sum_probs=23.5
Q ss_pred HHHH-hhhcCCCch-HHHHHHHHHHHHhhhhhhhhHHHhh
Q 032730 96 EVLN-LIDDGKNPD-EFTRDVINSCIAKNQVTKGKTDAFK 133 (135)
Q Consensus 96 EVl~-yID~GrNPD-iyTre~vE~~~~~Nq~~kGK~~a~~ 133 (135)
++|+ .+++|..|| +||.|.=-.+-.=-..-|.-++|||
T Consensus 13 ~IIe~LL~DGSdPdALY~IEHHl~~~dFd~LEK~AveAFK 52 (135)
T COG3076 13 LIIEELLEDGSDPDALYTIEHHLSADDFETLEKAAVEAFK 52 (135)
T ss_pred HHHHHHHhcCCCcchhhhhhhhhhhhHHHHHHHHHHHHHh
Confidence 4443 568999998 6887654433333344455567776
No 61
>PRK06819 flagellin; Validated
Probab=24.24 E-value=1.8e+02 Score=25.58 Aligned_cols=49 Identities=10% Similarity=0.245 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHhhhhccc--cCCCchhHHHHHHHHHHHHHHHHHhhh
Q 032730 38 QVINSVQKTLGLLHQLYLTVSS--FNAASQLPLLQRLNSLVSELDNMVKLS 86 (135)
Q Consensus 38 ~~iesl~~~l~~L~ql~i~Vs~--f~~~sq~~L~~kin~LV~~L~~L~~~a 86 (135)
.-++++.+.|..++++.+...+ +.+..+..+...++.|.+++..+-...
T Consensus 80 ~aL~~i~~iLqR~reLavqAaNgT~s~~dR~ai~~Ei~qL~~qI~~ian~t 130 (376)
T PRK06819 80 GALNEINNNLQRVRELTVQAQNGSNSSSDLDSIQDEISQRLAEIDRVSDQT 130 (376)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 3344555556668887777643 667778899999999999999987654
No 62
>PRK12806 flagellin; Provisional
Probab=24.07 E-value=1.7e+02 Score=26.57 Aligned_cols=47 Identities=15% Similarity=0.306 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHhhhhccc--cCCCchhHHHHHHHHHHHHHHHHHhhh
Q 032730 40 INSVQKTLGLLHQLYLTVSS--FNAASQLPLLQRLNSLVSELDNMVKLS 86 (135)
Q Consensus 40 iesl~~~l~~L~ql~i~Vs~--f~~~sq~~L~~kin~LV~~L~~L~~~a 86 (135)
++++.+.|..++++.+...+ +.+..+..+...++.|.++|..+-...
T Consensus 82 L~~i~~iLqr~reLavqaaNgt~s~~dR~ai~~Ei~~L~~~i~~ian~t 130 (475)
T PRK12806 82 MQETTNILQRMRELSVQAANSTNNSSDRASIQSEISQLKSELERIAQNT 130 (475)
T ss_pred HHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 44455556667777776644 567788899999999999999988644
No 63
>PRK14001 potassium-transporting ATPase subunit C; Provisional
Probab=23.88 E-value=3.7e+02 Score=21.66 Aligned_cols=63 Identities=11% Similarity=0.110 Sum_probs=40.6
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHHhhhcCCCchH---HHHHHHHHHHHhhhhhhhhH
Q 032730 65 QLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGKNPDE---FTRDVINSCIAKNQVTKGKT 129 (135)
Q Consensus 65 q~~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~yID~GrNPDi---yTre~vE~~~~~Nq~~kGK~ 129 (135)
-..|.+++.+-+..+..-+. ....-+||.|++..==-|=.||| +-+-++.++.+.......++
T Consensus 91 np~l~~~v~~r~~~~~~~~~--~~~~~~vP~DlvTaSgSGLDPhIS~~aA~~Qv~RVA~argl~~~~v 156 (189)
T PRK14001 91 NEKLLAAVAERVTAYRKENN--LPADTLVPVDAVTGSGSGLDPAISVVNAKLQAPRVAQARNISIRQV 156 (189)
T ss_pred CHHHHHHHHHHHHHHHHhCC--CccCCCCCHHHHhcccccCCCCCCHHHHHHHHHHHHHHhCcCHHHH
Confidence 35577777777766655331 11235799999988888889987 45556666666655444443
No 64
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=23.61 E-value=1.7e+02 Score=20.72 Aligned_cols=54 Identities=22% Similarity=0.329 Sum_probs=34.4
Q ss_pred hHHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHHhh---hcCCCchHHHHHHHHHHHHh
Q 032730 66 LPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLI---DDGKNPDEFTRDVINSCIAK 121 (135)
Q Consensus 66 ~~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~yI---D~GrNPDiyTre~vE~~~~~ 121 (135)
.-+++||+.+.- .+|-+.+..++++|-.+=.+-| =.|+|.|+|-.+-.-+..++
T Consensus 6 qiVn~Kln~iT~--~eLlkyskqy~i~it~~QA~~I~~~lr~k~inIfn~~~r~~llke 62 (85)
T PF11116_consen 6 QIVNQKLNNITA--KELLKYSKQYNISITKKQAEQIANILRGKNINIFNEQERKKLLKE 62 (85)
T ss_pred HHHHHHHhcCCH--HHHHHHHHHhCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHH
Confidence 456777777642 3555556667777765544333 45899999987766555544
No 65
>PRK08645 bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein; Reviewed
Probab=23.60 E-value=1.2e+02 Score=27.96 Aligned_cols=44 Identities=14% Similarity=0.157 Sum_probs=30.0
Q ss_pred HHHHhhhhhc-CCCCcHHHHHhhhcCCCchHHHHHHHHHHHHhhh
Q 032730 80 DNMVKLSEKC-NIQVPTEVLNLIDDGKNPDEFTRDVINSCIAKNQ 123 (135)
Q Consensus 80 ~~L~~~a~~~-~i~IP~EVl~yID~GrNPDiyTre~vE~~~~~Nq 123 (135)
+++..++..+ .+.||.++++.++..++||-+-..-++.|.+.=+
T Consensus 531 k~~~~~~~~~~Gv~vP~~l~~~l~~~~d~~~~~~~gv~~a~e~i~ 575 (612)
T PRK08645 531 RNAEFLHNEVPGITLPEEIRERMRAVEDKEEAREEGVAIARELID 575 (612)
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHhcCCchHHHHHHHHHHHHHHH
Confidence 3444444334 8999999999999999887655555555554443
No 66
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=23.55 E-value=2.1e+02 Score=22.58 Aligned_cols=57 Identities=23% Similarity=0.252 Sum_probs=37.5
Q ss_pred chhHHHHHHHHHHHHHHHHH--hhhhhcCCCCcHHHHHhhhcCCCchHHHHHHHHHHHHhhh
Q 032730 64 SQLPLLQRLNSLVSELDNMV--KLSEKCNIQVPTEVLNLIDDGKNPDEFTRDVINSCIAKNQ 123 (135)
Q Consensus 64 sq~~L~~kin~LV~~L~~L~--~~a~~~~i~IP~EVl~yID~GrNPDiyTre~vE~~~~~Nq 123 (135)
|++.+..-++.++.+|. |+ +.+. --.||+.-+=-|=+|+.|-.-|--.+.++.|+-+
T Consensus 13 s~E~F~~~l~~~l~Elg-lt~~eFak--~anIP~StLYKil~G~dpr~~tl~~I~ktir~~e 71 (170)
T COG4800 13 SGEDFGSCLQKLLDELG-LTPSEFAK--RANIPLSTLYKILKGSDPRYDTLTRIFKTIRSYE 71 (170)
T ss_pred chhHHHHHHHHHHHHcC-CCHHHHHH--HcCCCHHHHHHHHhCCCccHHHHHHHHHHHHHHH
Confidence 44555555555555532 22 1222 2358999999999999999988888888876544
No 67
>COG1182 AcpD Acyl carrier protein phosphodiesterase [Lipid metabolism]
Probab=23.37 E-value=85 Score=25.60 Aligned_cols=39 Identities=23% Similarity=0.352 Sum_probs=32.0
Q ss_pred hhHHHHHHHHHHHHHHHHHhh---hhhcCCCCcHHHHHhhhc
Q 032730 65 QLPLLQRLNSLVSELDNMVKL---SEKCNIQVPTEVLNLIDD 103 (135)
Q Consensus 65 q~~L~~kin~LV~~L~~L~~~---a~~~~i~IP~EVl~yID~ 103 (135)
+.....+.+.|+++|..-|+. .+..|..||..+-.|||.
T Consensus 71 ~~~~~~~sd~l~~ef~aAD~vVi~~PM~Nf~iPa~LK~yiD~ 112 (202)
T COG1182 71 EKEALARSDKLLEEFLAADKVVIAAPMYNFNIPAQLKAYIDH 112 (202)
T ss_pred HHHHHHHHHHHHHHHHhcCeEEEEecccccCCCHHHHHHHHH
Confidence 456778888999999888773 356799999999999986
No 68
>TIGR01088 aroQ 3-dehydroquinate dehydratase, type II. This model specifies the type II enzyme. The type I enzyme, often found as part of a multifunctional protein, is described by TIGR01093.
Probab=23.30 E-value=1.2e+02 Score=23.47 Aligned_cols=27 Identities=19% Similarity=0.340 Sum_probs=23.3
Q ss_pred HHHHhhhhccccCCCchhHHHHHHHHH
Q 032730 49 LLHQLYLTVSSFNAASQLPLLQRLNSL 75 (135)
Q Consensus 49 ~L~ql~i~Vs~f~~~sq~~L~~kin~L 75 (135)
...++++.|.-||.++...|.++|++-
T Consensus 36 ~a~~~g~~v~~~QSN~EGelId~i~~a 62 (141)
T TIGR01088 36 FAAQLNVELEFFQSNSEGQLIDKIHEA 62 (141)
T ss_pred HHHHcCCEEEEEeeCcHHHHHHHHHhc
Confidence 455789999999999999999999874
No 69
>PF11458 Mistic: Membrane-integrating protein Mistic; InterPro: IPR021078 Mistic is an integral membrane protein that folds autonomously into the membrane []. It is conserved in the Bacilli bacteria. The protein forms a helical bundle with a polar lipid-facing surface. Mistic can be used for high-level production of other membrane proteins in their native conformations [].
Probab=23.12 E-value=2.8e+02 Score=19.64 Aligned_cols=53 Identities=23% Similarity=0.390 Sum_probs=33.5
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHhhhhcc------ccCC------------CchhHHHHHHHHHHHHHHHH
Q 032730 30 DDPKQNLNQVINSVQKTLGLLHQLYLTVS------SFNA------------ASQLPLLQRLNSLVSELDNM 82 (135)
Q Consensus 30 ~~~~~~L~~~iesl~~~l~~L~ql~i~Vs------~f~~------------~sq~~L~~kin~LV~~L~~L 82 (135)
+.-++||..-|..+-+-|..+.|++---. .|.. -.++.+++|+|.+|.++-.+
T Consensus 5 ~~EkeQLS~AID~mnEGLD~fI~lYNeSe~DepLiql~detael~~~A~~~yG~e~~n~klN~iIkqiLs~ 75 (84)
T PF11458_consen 5 DQEKEQLSTAIDRMNEGLDTFIQLYNESEKDEPLIQLEDETAELIRQAREKYGQEKLNEKLNAIIKQILSI 75 (84)
T ss_pred hHHHHHHHHHHHHHHhhHHHHHHHHcccccccchhhcchhHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcc
Confidence 34567788877777777776666542111 1111 24678899999999887654
No 70
>PHA01748 hypothetical protein
Probab=22.60 E-value=1.5e+02 Score=19.23 Aligned_cols=34 Identities=24% Similarity=0.458 Sum_probs=23.8
Q ss_pred CCCCcHHHHHhhhc-----CCCchHHHHHHHHHHHHhhh
Q 032730 90 NIQVPTEVLNLIDD-----GKNPDEFTRDVINSCIAKNQ 123 (135)
Q Consensus 90 ~i~IP~EVl~yID~-----GrNPDiyTre~vE~~~~~Nq 123 (135)
.+.+|.|+++.+|. |.|---.=|+.|+....+..
T Consensus 6 SvrLp~el~~eld~~a~~~g~~RSE~Ir~Ai~~~~~~~~ 44 (60)
T PHA01748 6 TFKIEEDLLELLDRYAIKHGLNRSEAIRKAIEKMVKDEL 44 (60)
T ss_pred EEECCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 56789999988877 77766666666665555443
No 71
>PF02981 FokI_N: Restriction endonuclease FokI, recognition domain; InterPro: IPR004234 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. Thie entry represents the type IIS restriction endonuclease FokI (3.1.21.4 from EC), which is a member of an unusual class of bipartite restriction enzymes that recognise a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence []. FokI contains amino- and carboxy-terminal domains corresponding to the DNA-recognition and cleavage functions (IPR004233 from INTERPRO), respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP []. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 1FOK_A 2FOK_B.
Probab=22.48 E-value=1.8e+02 Score=22.68 Aligned_cols=37 Identities=24% Similarity=0.178 Sum_probs=22.8
Q ss_pred HHHHhhhhccccCCCc---hhHHHHHHHHHHHHHHHHHhh
Q 032730 49 LLHQLYLTVSSFNAAS---QLPLLQRLNSLVSELDNMVKL 85 (135)
Q Consensus 49 ~L~ql~i~Vs~f~~~s---q~~L~~kin~LV~~L~~L~~~ 85 (135)
++..|--+|+-|.+.| ++...++|.+||....-=.++
T Consensus 20 ~f~~LkkVvsiF~~~Ski~~~L~~~~i~~lv~~~~~~~~L 59 (145)
T PF02981_consen 20 DFENLKKVVSIFDPNSKIYKELKETKIPRLVYDEDLQKEL 59 (145)
T ss_dssp -HHHHHHHHHTT-TTSHHHHHHHHTHHHHH--SHHHHHHH
T ss_pred HHHHhhceeeeecCCCHHHHHHHHhhHHHHHhhhhHHHHH
Confidence 3555667888899988 466788888888776543333
No 72
>PRK12805 flagellin; Provisional
Probab=22.18 E-value=2.3e+02 Score=23.38 Aligned_cols=50 Identities=22% Similarity=0.373 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHHHHhhhhc--cccCCCchhHHHHHHHHHHHHHHHHHhhh
Q 032730 37 NQVINSVQKTLGLLHQLYLTV--SSFNAASQLPLLQRLNSLVSELDNMVKLS 86 (135)
Q Consensus 37 ~~~iesl~~~l~~L~ql~i~V--s~f~~~sq~~L~~kin~LV~~L~~L~~~a 86 (135)
+.-++++...|..++++-+.. ..+.++.+..+...++.|.+++..+-..+
T Consensus 77 e~~L~~i~~~l~r~rel~v~a~ngt~s~~dr~ai~~Ei~~l~~~i~~~an~~ 128 (287)
T PRK12805 77 DSALSSMSSILQRMRQLAVQSSNGSFSDEDRKQYTAEFGSLIKELDHVADTT 128 (287)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 334555555566677777666 34566778899999999999999887654
No 73
>PRK13015 3-dehydroquinate dehydratase; Reviewed
Probab=21.79 E-value=1.4e+02 Score=23.25 Aligned_cols=29 Identities=14% Similarity=0.059 Sum_probs=24.2
Q ss_pred HHHHhhhhccccCCCchhHHHHHHHHHHH
Q 032730 49 LLHQLYLTVSSFNAASQLPLLQRLNSLVS 77 (135)
Q Consensus 49 ~L~ql~i~Vs~f~~~sq~~L~~kin~LV~ 77 (135)
...++++.+.-||.++...|.++|++-..
T Consensus 38 ~a~~~g~~~~~~QSN~EGelId~i~~a~~ 66 (146)
T PRK13015 38 AAEALGLEVEFRQSNHEGELIDWIHEARG 66 (146)
T ss_pred HHHHcCCEEEEEeeCcHHHHHHHHHHhhh
Confidence 35578899999999999999999987643
No 74
>PF08407 Chitin_synth_1N: Chitin synthase N-terminal; InterPro: IPR013616 This is the N-terminal domain of Chitin synthase (IPR004834 from INTERPRO). ; GO: 0004100 chitin synthase activity
Probab=21.73 E-value=54 Score=22.81 Aligned_cols=22 Identities=36% Similarity=0.705 Sum_probs=19.3
Q ss_pred CCCCcHHHHHhhhcCCCchHHH
Q 032730 90 NIQVPTEVLNLIDDGKNPDEFT 111 (135)
Q Consensus 90 ~i~IP~EVl~yID~GrNPDiyT 111 (135)
|.+||..+++.+-.+++++.||
T Consensus 19 D~PVP~~ll~~~~~~~~~~Eft 40 (79)
T PF08407_consen 19 DCPVPSALLNSLPRGRDEREFT 40 (79)
T ss_pred ECcCCHHHHhhCCCCCCCcchh
Confidence 7899999999998888887776
No 75
>PRK12803 flagellin; Provisional
Probab=21.55 E-value=2.3e+02 Score=24.46 Aligned_cols=50 Identities=16% Similarity=0.317 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHhhhhc--cccCCCchhHHHHHHHHHHHHHHHHHhhhh
Q 032730 38 QVINSVQKTLGLLHQLYLTV--SSFNAASQLPLLQRLNSLVSELDNMVKLSE 87 (135)
Q Consensus 38 ~~iesl~~~l~~L~ql~i~V--s~f~~~sq~~L~~kin~LV~~L~~L~~~a~ 87 (135)
.-++++...|..++++.+.. ..+.+..+..+...++.|.++|..+-....
T Consensus 78 ~aL~~i~~~LqrirELavqA~Ngt~s~~dR~ai~~Ei~qL~~~i~~ian~t~ 129 (335)
T PRK12803 78 GNLNEVEKVLVRMKELAVQSGNGTYSDADRGSIQIEIEQLTDEINRIADQAQ 129 (335)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 34445555566677777766 345667788999999999999999887543
No 76
>PRK13999 potassium-transporting ATPase subunit C; Provisional
Probab=21.47 E-value=3.7e+02 Score=21.94 Aligned_cols=67 Identities=16% Similarity=0.189 Sum_probs=42.8
Q ss_pred cccCCCchhHHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHHhhhcCCCchH---HHHHHHHHHHHhhhhhhhhHH
Q 032730 58 SSFNAASQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGKNPDE---FTRDVINSCIAKNQVTKGKTD 130 (135)
Q Consensus 58 s~f~~~sq~~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~yID~GrNPDi---yTre~vE~~~~~Nq~~kGK~~ 130 (135)
|++.|.+ ..|.+++.+-+..+..-+.. -+||.|++..==-|=.|+| +-+-++.++.+.......++.
T Consensus 97 SNlgpsn-p~L~~~v~~r~~~~~~~~~~-----~~vP~DlvTaSgSGLDPhISp~aA~~Qv~RVA~argls~~~v~ 166 (201)
T PRK13999 97 SNLGPTS-KALADRVKEDVDALKAENPG-----APVPVDLVTTSGSGLDPDISPEAALFQVPRVAKARGLPEDRLR 166 (201)
T ss_pred cCCCCCC-HHHHHHHHHHHHHHHHhCCC-----CCCCHHHHhcccccCCCCCCHHHHHHHHHHHHHHhCcCHHHHH
Confidence 3344433 45777777777666553311 3799999888888888887 556677777776655444443
No 77
>PF04912 Dynamitin: Dynamitin ; InterPro: IPR006996 Dynamitin is a subunit of the microtubule-dependent motor complex, it is also implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS) []. It is also thought to modulate cytoplasmic dynein binding to an organelle, and plays a role in prometaphase chromosome alignment and spindle organisation during mitosis. Dynamitin is also involved in anchoring microtubules to centrosomes and may play a role in synapse formation during brain development []. ; GO: 0007017 microtubule-based process, 0005869 dynactin complex
Probab=21.28 E-value=1.7e+02 Score=25.17 Aligned_cols=37 Identities=30% Similarity=0.397 Sum_probs=25.6
Q ss_pred HHHhhhhccccCCCchhHHHHHHHHHHHHHHHHHhhh
Q 032730 50 LHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVKLS 86 (135)
Q Consensus 50 L~ql~i~Vs~f~~~sq~~L~~kin~LV~~L~~L~~~a 86 (135)
|..|.-.++-.++..-+.+..|+..|...+.++.+.+
T Consensus 248 l~~L~~~lslL~~~~Ld~i~~rl~~L~~~~~~l~~~~ 284 (388)
T PF04912_consen 248 LNELERQLSLLDPAKLDSIERRLKSLLSELEELAEKR 284 (388)
T ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3445555555666667788888888888888777654
No 78
>PRK08359 transcription factor; Validated
Probab=21.23 E-value=2.8e+02 Score=21.97 Aligned_cols=29 Identities=14% Similarity=0.204 Sum_probs=18.6
Q ss_pred CCCcHHHHHhhhcC-CCchHHHHHHHHHHH
Q 032730 91 IQVPTEVLNLIDDG-KNPDEFTRDVINSCI 119 (135)
Q Consensus 91 i~IP~EVl~yID~G-rNPDiyTre~vE~~~ 119 (135)
+.|....|..||.| +||++-+..-|+.+.
T Consensus 108 lgvs~stI~~iE~G~~~Ps~~~l~kLak~l 137 (176)
T PRK08359 108 VGLSVNDLRRIAHGEYEPTIKEAKKLERYF 137 (176)
T ss_pred hCCCHHHHHHHHCCCcCCCHHHHHHHHHHh
Confidence 34556667777776 567777666666554
No 79
>PRK14002 potassium-transporting ATPase subunit C; Provisional
Probab=21.10 E-value=4.3e+02 Score=21.26 Aligned_cols=65 Identities=11% Similarity=0.137 Sum_probs=41.8
Q ss_pred chhHHHHHHHHHHHHHHHHHhhhhhcCCCCcHHHHHhhhcCCCchH---HHHHHHHHHHHhhhhhhhhHH
Q 032730 64 SQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGKNPDE---FTRDVINSCIAKNQVTKGKTD 130 (135)
Q Consensus 64 sq~~L~~kin~LV~~L~~L~~~a~~~~i~IP~EVl~yID~GrNPDi---yTre~vE~~~~~Nq~~kGK~~ 130 (135)
+-..|.+++.+-+..|..-+. ....-+||.|++..==-|=.|+| +-+=++.++.+.......++.
T Consensus 86 snp~L~~~v~~r~~~~~~~~~--~~~~~~vP~DlvTaSgSGLDPhISp~aA~~Qv~RVA~argl~~~~v~ 153 (186)
T PRK14002 86 SNPEYLAEVQARIDTFLVHHP--YLSRKDIPAEMVTASGSGLDPNISPQAAYVQVKRVAKARGMSEEKVK 153 (186)
T ss_pred CCHHHHHHHHHHHHHHHHhCC--CCCCCCCCHHHHhccccCCCCCCCHHHHHHHHHHHHHHhCcCHHHHH
Confidence 345577777777776654331 11235799999988888888987 455567777666554444443
No 80
>PF01261 AP_endonuc_2: Xylose isomerase-like TIM barrel; InterPro: IPR012307 This TIM alpha/beta barrel structure is found in xylose isomerase (P19148 from SWISSPROT) and in endonuclease IV (P12638 from SWISSPROT, 3.1.21.2 from EC). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae []. ; PDB: 3KWS_B 3DX5_A 3CQH_B 3CQI_A 3CQK_A 3CQJ_B 2G0W_B 1DXI_A 2ZDS_D 3TVA_B ....
Probab=20.97 E-value=2.5e+02 Score=20.32 Aligned_cols=54 Identities=15% Similarity=0.214 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHHHHhhh---hcccc--CCCchhHHHHHHHHHHHHHHHHHhhhhhc
Q 032730 36 LNQVINSVQKTLGLLHQLYL---TVSSF--NAASQLPLLQRLNSLVSELDNMVKLSEKC 89 (135)
Q Consensus 36 L~~~iesl~~~l~~L~ql~i---~Vs~f--~~~sq~~L~~kin~LV~~L~~L~~~a~~~ 89 (135)
=+..++.+.+.++....+++ .++.. ............+.+++.|+.+-+.+...
T Consensus 66 r~~~~~~~~~~i~~a~~lg~~~i~~~~g~~~~~~~~~~~~~~~~~~~~l~~l~~~a~~~ 124 (213)
T PF01261_consen 66 REEALEYLKKAIDLAKRLGAKYIVVHSGRYPSGPEDDTEENWERLAENLRELAEIAEEY 124 (213)
T ss_dssp HHHHHHHHHHHHHHHHHHTBSEEEEECTTESSSTTSSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHhCCCceeecCcccccccCCCHHHHHHHHHHHHHHHHhhhhhh
Confidence 33444466666777888773 33322 23445556688889999999988877543
No 81
>PF00435 Spectrin: Spectrin repeat; InterPro: IPR002017 Spectrin repeats [] are found in several proteins involved in cytoskeletal structure. These include spectrin alpha and beta subunits [, ], alpha-actinin [] and dystrophin. The spectrin repeat forms a three-helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.; GO: 0005515 protein binding; PDB: 1HCI_A 1QUU_A 3FB2_B 1S35_A 1U5P_A 1U4Q_A 1CUN_B 1YDI_B 3EDV_A 1AJ3_A ....
Probab=20.96 E-value=2.3e+02 Score=17.87 Aligned_cols=46 Identities=15% Similarity=0.174 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHhhhhccccCCCchhHHHHHHHHHHHHHHHHHhhh
Q 032730 41 NSVQKTLGLLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVKLS 86 (135)
Q Consensus 41 esl~~~l~~L~ql~i~Vs~f~~~sq~~L~~kin~LV~~L~~L~~~a 86 (135)
......+..+...+-.+.+-.|.....+..++..|-.....|....
T Consensus 51 ~~~~~~l~~l~~~~~~L~~~~~~~~~~i~~~~~~l~~~w~~l~~~~ 96 (105)
T PF00435_consen 51 ESRQERLESLNEQAQQLIDSGPEDSDEIQEKLEELNQRWEALCELV 96 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333344444444444444456677788888888888887776543
No 82
>PRK12802 flagellin; Provisional
Probab=20.90 E-value=2.6e+02 Score=22.89 Aligned_cols=49 Identities=10% Similarity=0.241 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHHhhhhcc--ccCCCchhHHHHHHHHHHHHHHHHHhhh
Q 032730 38 QVINSVQKTLGLLHQLYLTVS--SFNAASQLPLLQRLNSLVSELDNMVKLS 86 (135)
Q Consensus 38 ~~iesl~~~l~~L~ql~i~Vs--~f~~~sq~~L~~kin~LV~~L~~L~~~a 86 (135)
.-++++.+.|..++++-+... .+.++.+..+...++.|.++|..+-..+
T Consensus 80 ~~l~~i~~~l~r~rel~v~a~ngt~s~~dr~ai~~ei~~l~~~i~~~an~t 130 (282)
T PRK12802 80 GALQESTNILQRMRELAVQSRNDSNDSTDRAALNKEFTTMLDEITRIATST 130 (282)
T ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 344455555666777666663 3566778899999999999999887643
No 83
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=20.79 E-value=3e+02 Score=19.95 Aligned_cols=26 Identities=27% Similarity=0.368 Sum_probs=17.1
Q ss_pred CcHHHHHhhhcCC-CchHHHHHHHHHH
Q 032730 93 VPTEVLNLIDDGK-NPDEFTRDVINSC 118 (135)
Q Consensus 93 IP~EVl~yID~Gr-NPDiyTre~vE~~ 118 (135)
|+..-+..+++|+ +|..-+-+-+-.+
T Consensus 30 is~~~is~iE~g~~~ps~~~l~kIa~a 56 (120)
T PRK13890 30 VSISFLSDLTTGKANPSLKVMEAIADA 56 (120)
T ss_pred cCHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 6677777777774 7777665555444
No 84
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=20.72 E-value=99 Score=22.10 Aligned_cols=21 Identities=33% Similarity=0.681 Sum_probs=15.6
Q ss_pred hhhcCCCchHHHHHHHHHHHH
Q 032730 100 LIDDGKNPDEFTRDVINSCIA 120 (135)
Q Consensus 100 yID~GrNPDiyTre~vE~~~~ 120 (135)
.+++|++|..|.+++++..+.
T Consensus 40 l~~~G~d~~~~l~~L~~~~R~ 60 (143)
T PF12169_consen 40 LLEQGKDPKQFLDDLIEYLRD 60 (143)
T ss_dssp HHHCT--HHHHHHHHHHHHHH
T ss_pred HHHhCCCHHHHHHHHHHHHHH
Confidence 457899999999999987664
No 85
>PF05250 UPF0193: Uncharacterised protein family (UPF0193); InterPro: IPR007914 This family of proteins is functionally uncharacterised.
Probab=20.30 E-value=4.7e+02 Score=21.45 Aligned_cols=54 Identities=19% Similarity=0.173 Sum_probs=38.9
Q ss_pred cCChHHHHHHHHHHHHHHHHHHHHhhhhccccCCCchhHHHHHHHHHHHHHHHHHhhhh
Q 032730 29 ADDPKQNLNQVINSVQKTLGLLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVKLSE 87 (135)
Q Consensus 29 ~~~~~~~L~~~iesl~~~l~~L~ql~i~Vs~f~~~sq~~L~~kin~LV~~L~~L~~~a~ 87 (135)
..|.++.|-+-|+-=.+||.....+|- .......+...|-.-|.+|..|++...
T Consensus 149 ~~Drf~elv~EI~ER~efL~eMe~LG~-----gk~yr~~I~~EIsqrlrele~ld~~rs 202 (212)
T PF05250_consen 149 EKDRFEELVQEIEERREFLAEMEALGQ-----GKKYRGIILTEISQRLRELEKLDKKRS 202 (212)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHcCC-----chhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 446666666666666666666666665 456677888889999999999987653
No 86
>PF00137 ATP-synt_C: ATP synthase subunit C; InterPro: IPR002379 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases) and V-ATPases (or V1V0-ATPases) are each composed of two linked complexes: the F1 or V1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0 or V0 complex that forms the membrane-spanning pore. The F- and V-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. This entry represents subunit C (also called subunit 9, or proteolipid in F-ATPases, or the 16 kDa proteolipid in V-ATPases) found in the F0 or V0 complex of F- and V-ATPases, respectively. In F-ATPases, ten C subunits form an oligomeric ring that makes up the F0 rotor. The flux of protons through the ATPase channel drives the rotation of the C subunit ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the C subunit ring of F0. The sequential protonation and deprotonation of Asp61 of subunit C is coupled to the stepwise movement of the rotor []. In V-ATPases, there are three proteolipid subunits (c, c' and c'') that form part of the proton-conducting pore, each containing a buried glutamic acid residue that is essential for proton transport, and together they form a hexameric ring spanning the membrane [, ]. Structurally, the c subunits consist of a two antiparallel transmembrane helices. Both helices of one c subunit are connected by a loop on the cytoplasmic side []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015991 ATP hydrolysis coupled proton transport, 0033177 proton-transporting two-sector ATPase complex, proton-transporting domain; PDB: 3AOU_D 2DB4_H 2BL2_C 2CYD_A 2XQT_A 2XQS_A 2XQU_E 1WU0_A 1ATY_A 1C17_A ....
Probab=20.20 E-value=1.5e+02 Score=19.29 Aligned_cols=25 Identities=20% Similarity=0.353 Sum_probs=17.9
Q ss_pred CCCchHHHHHHHHHHHHhhhhhhhh
Q 032730 104 GKNPDEFTRDVINSCIAKNQVTKGK 128 (135)
Q Consensus 104 GrNPDiyTre~vE~~~~~Nq~~kGK 128 (135)
.|||+++++-++=.+.-+-...-|-
T Consensus 33 a~~p~~~~~~li~~~~~E~~~i~gl 57 (66)
T PF00137_consen 33 ARQPELFTKMLIGAAFIEALGIYGL 57 (66)
T ss_dssp HHSGGHHHHHHHHHHHHHHHHHHHH
T ss_pred HhccccchhhhhhHHHHHHHHHHHH
Confidence 5899999999887776655544443
No 87
>PRK12807 flagellin; Provisional
Probab=20.15 E-value=2.8e+02 Score=22.80 Aligned_cols=47 Identities=21% Similarity=0.321 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHHHhhhhc--cccCCCchhHHHHHHHHHHHHHHHHHh
Q 032730 38 QVINSVQKTLGLLHQLYLTV--SSFNAASQLPLLQRLNSLVSELDNMVK 84 (135)
Q Consensus 38 ~~iesl~~~l~~L~ql~i~V--s~f~~~sq~~L~~kin~LV~~L~~L~~ 84 (135)
..++++.+.|..++++-+.. ..+.++.+..+...++.|.++|..+-.
T Consensus 78 ~~L~~i~~~l~r~rel~v~a~ngt~s~~dr~ai~~Ei~~l~~~i~~~a~ 126 (287)
T PRK12807 78 SAMNSVSNILTRMRDIAVQSSNGTNTAENQSALQKEFAELQEQIDYIAK 126 (287)
T ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555566677777666 346677788999999999999998864
Done!