Query 028220
Match_columns 212
No_of_seqs 120 out of 146
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 08:08:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028220.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028220hhsearch_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 3.1E-47 6.8E-52 311.5 14.7 141 28-168 6-147 (147)
2 PF09748 Med10: Transcription 100.0 2.6E-42 5.6E-47 277.0 13.4 116 42-157 4-128 (128)
3 PF04129 Vps52: Vps52 / Sac2 f 82.2 50 0.0011 32.2 14.1 72 90-161 81-160 (508)
4 KOG4331 Polytopic membrane pro 78.1 47 0.001 35.2 12.9 98 100-201 326-455 (865)
5 PF07234 DUF1426: Protein of u 71.6 7.5 0.00016 31.4 4.3 29 173-201 10-38 (117)
6 PF02436 PYC_OADA: Conserved c 71.1 15 0.00032 31.9 6.4 107 49-161 36-161 (196)
7 PF05008 V-SNARE: Vesicle tran 67.8 15 0.00032 26.4 4.9 55 30-84 21-75 (79)
8 PF11074 DUF2779: Domain of un 66.5 9.8 0.00021 30.9 4.2 64 94-160 42-107 (130)
9 PF05823 Gp-FAR-1: Nematode fa 62.1 58 0.0013 27.1 8.1 34 122-155 108-141 (154)
10 PF11315 Med30: Mediator compl 60.3 96 0.0021 26.2 9.0 43 92-134 80-136 (150)
11 PRK14139 heat shock protein Gr 55.3 1.4E+02 0.003 25.9 10.7 52 1-52 1-53 (185)
12 cd08812 CARD_RIG-I_like Caspas 52.1 30 0.00065 26.1 4.4 61 90-156 17-78 (88)
13 PRK12999 pyruvate carboxylase; 51.8 55 0.0012 35.4 7.7 112 49-160 863-993 (1146)
14 PF12128 DUF3584: Protein of u 50.6 1.8E+02 0.0039 31.5 11.3 83 102-184 888-971 (1201)
15 PF11657 Activator-TraM: Trans 48.4 1.6E+02 0.0035 24.6 10.7 64 132-195 78-141 (144)
16 smart00503 SynN Syntaxin N-ter 46.4 1.2E+02 0.0026 22.5 11.2 29 133-161 84-112 (117)
17 PRK04358 hypothetical protein; 45.3 1E+02 0.0022 27.7 7.2 78 23-103 9-103 (217)
18 PF11333 DUF3135: Protein of u 43.6 63 0.0014 24.6 4.9 46 129-187 17-62 (83)
19 PF09164 VitD-bind_III: Vitami 43.5 55 0.0012 24.5 4.4 42 130-184 9-50 (68)
20 PF14823 Sirohm_synth_C: Siroh 42.0 44 0.00096 24.6 3.8 14 175-188 32-45 (70)
21 PF14712 Snapin_Pallidin: Snap 40.1 1.1E+02 0.0025 22.4 5.9 23 63-85 28-50 (92)
22 TIGR01235 pyruv_carbox pyruvat 39.5 1.1E+02 0.0024 33.3 7.7 113 49-161 861-992 (1143)
23 PF15508 NAAA-beta: beta subun 39.2 1.7E+02 0.0036 22.1 6.9 73 124-201 21-95 (95)
24 PF08535 KorB: KorB domain; I 39.0 1.1E+02 0.0023 22.8 5.5 54 65-123 6-59 (93)
25 PRK06771 hypothetical protein; 38.6 1E+02 0.0022 24.3 5.5 30 92-143 54-83 (93)
26 PHA03188 UL14 tegument protein 36.7 2.1E+02 0.0045 25.5 7.6 84 108-191 64-154 (199)
27 PF03433 EspA: EspA-like secre 35.8 12 0.00026 32.8 0.0 57 68-132 77-139 (188)
28 KOG1961 Vacuolar sorting prote 34.8 4.9E+02 0.011 27.1 10.9 72 68-139 115-196 (683)
29 PRK15364 pathogenicity island 34.5 52 0.0011 29.1 3.6 33 68-103 77-109 (196)
30 KOG1666 V-SNARE [Intracellular 34.0 3.6E+02 0.0077 24.4 17.4 57 28-84 30-86 (220)
31 TIGR02606 antidote_CC2985 puta 33.6 1.5E+02 0.0031 21.5 5.4 54 90-150 3-62 (69)
32 PF02106 Fanconi_C: Fanconi an 33.4 1.6E+02 0.0034 29.9 7.1 102 93-209 294-415 (559)
33 PF09602 PhaP_Bmeg: Polyhydrox 32.8 3.3E+02 0.0071 23.6 8.7 55 63-119 78-135 (165)
34 PHA03250 UL35; Provisional 32.2 4.6E+02 0.01 26.8 10.2 126 73-204 203-352 (564)
35 PF08745 UPF0278: UPF0278 fami 32.1 15 0.00033 32.6 0.0 79 23-104 5-100 (205)
36 PRK13740 conjugal transfer pro 32.0 64 0.0014 24.3 3.3 40 108-153 19-58 (70)
37 PF05430 Methyltransf_30: S-ad 31.6 22 0.00047 28.6 0.8 18 104-121 62-79 (124)
38 PRK14040 oxaloacetate decarbox 31.2 2.2E+02 0.0047 28.8 7.9 69 92-160 361-453 (593)
39 PF03997 VPS28: VPS28 protein; 31.1 1.7E+02 0.0036 25.5 6.2 29 100-128 18-46 (188)
40 PF02669 KdpC: K+-transporting 30.8 1.8E+02 0.0039 25.5 6.4 65 58-126 85-152 (188)
41 PF01934 DUF86: Protein of unk 30.3 2.4E+02 0.0052 21.2 6.7 73 55-142 15-92 (119)
42 TIGR02684 dnstrm_HI1420 probab 30.2 1.7E+02 0.0036 22.2 5.4 49 64-115 29-78 (89)
43 KOG4470 Proteasome activator s 30.1 3.5E+02 0.0075 24.8 8.2 93 99-205 137-230 (246)
44 TIGR03875 RNA_lig_partner RNA 30.0 87 0.0019 27.9 4.3 77 24-103 6-99 (206)
45 PRK09282 pyruvate carboxylase 29.6 2.1E+02 0.0045 28.9 7.4 92 60-160 337-444 (592)
46 TIGR02044 CueR Cu(I)-responsiv 29.4 2.5E+02 0.0055 22.0 6.5 54 91-144 56-110 (127)
47 TIGR00833 actII Transport prot 29.3 61 0.0013 33.8 3.8 10 89-98 657-666 (910)
48 cd08789 CARD_IPS-1_RIG-I Caspa 29.0 74 0.0016 23.9 3.3 57 92-156 18-74 (84)
49 PLN03229 acetyl-coenzyme A car 28.2 3.6E+02 0.0079 28.5 8.9 45 101-160 683-727 (762)
50 TIGR03200 dearomat_oah 6-oxocy 28.2 76 0.0016 30.3 3.9 55 105-159 221-293 (360)
51 PF10191 COG7: Golgi complex c 27.7 5.6E+02 0.012 26.6 10.3 141 29-185 110-258 (766)
52 PF13198 DUF4014: Protein of u 27.4 52 0.0011 24.9 2.2 13 184-196 16-28 (72)
53 PRK09432 metF 5,10-methylenete 26.9 91 0.002 28.4 4.1 29 79-107 217-245 (296)
54 PRK13713 conjugal transfer pro 26.6 1.3E+02 0.0029 24.7 4.5 50 101-150 50-117 (118)
55 KOG3547 Bestrophin (Best vitel 26.6 69 0.0015 31.5 3.4 23 179-201 30-52 (450)
56 PF01031 Dynamin_M: Dynamin ce 26.2 1.5E+02 0.0032 26.3 5.2 62 125-186 56-122 (295)
57 KOG3990 Uncharacterized conser 26.1 3.8E+02 0.0083 25.1 7.8 51 12-62 206-260 (305)
58 PF15168 TRIQK: Triple QxxK/R 26.1 3.1E+02 0.0067 21.1 6.1 21 160-180 36-56 (79)
59 PF01220 DHquinase_II: Dehydro 25.3 96 0.0021 26.0 3.6 30 49-78 37-66 (140)
60 PF05004 IFRD: Interferon-rela 25.2 2.3E+02 0.0049 25.9 6.3 62 102-165 34-103 (309)
61 COG1344 FlgL Flagellin and rel 25.0 1.4E+02 0.0031 27.5 5.1 50 37-86 77-128 (360)
62 MTH00169 ATP8 ATP synthase F0 24.8 2.3E+02 0.0049 20.8 5.1 34 173-206 5-38 (67)
63 PF01017 STAT_alpha: STAT prot 24.5 2.3E+02 0.0051 23.8 5.9 52 28-79 118-179 (182)
64 TIGR03764 ICE_PFGI_1_parB inte 23.9 2.4E+02 0.0052 25.9 6.1 36 110-148 210-245 (258)
65 TIGR02047 CadR-PbrR Cd(II)/Pb( 23.6 3.5E+02 0.0077 21.3 6.5 54 91-144 56-110 (127)
66 PLN03094 Substrate binding sub 23.6 1.4E+02 0.003 28.6 4.8 49 38-86 290-343 (370)
67 COG5094 TAF9 Transcription ini 23.4 1.6E+02 0.0034 24.8 4.4 54 88-147 31-87 (145)
68 PRK09174 F0F1 ATP synthase sub 22.9 1.3E+02 0.0028 26.1 4.1 34 173-206 48-81 (204)
69 PF07739 TipAS: TipAS antibiot 22.8 85 0.0018 23.4 2.6 45 139-183 29-75 (118)
70 PF14202 TnpW: Transposon-enco 22.6 67 0.0015 20.9 1.8 21 57-77 15-35 (37)
71 PRK05255 hypothetical protein; 22.4 4.9E+02 0.011 22.4 7.4 40 111-150 88-134 (171)
72 PF06569 DUF1128: Protein of u 22.3 3.4E+02 0.0075 20.4 5.8 36 31-66 4-39 (71)
73 PF11458 Mistic: Membrane-inte 21.8 2.9E+02 0.0063 21.3 5.3 53 30-82 5-75 (84)
74 PF07889 DUF1664: Protein of u 21.7 4.5E+02 0.0098 21.5 10.9 84 32-144 37-120 (126)
75 PRK07502 cyclohexadienyl dehyd 21.4 1.9E+02 0.0042 25.5 5.0 56 104-159 231-286 (307)
76 PRK13454 F0F1 ATP synthase sub 21.3 1.7E+02 0.0036 24.6 4.4 34 173-207 26-60 (181)
77 PF03682 UPF0158: Uncharacteri 21.3 2.5E+02 0.0054 23.5 5.4 47 100-160 77-124 (163)
78 KOG0484 Transcription factor P 21.1 67 0.0015 26.3 1.8 16 102-117 37-52 (125)
79 PF06657 Cep57_MT_bd: Centroso 21.0 3.6E+02 0.0078 20.1 6.1 54 24-80 3-67 (79)
80 PF09119 SicP-binding: SicP bi 20.8 36 0.00079 26.2 0.2 52 111-168 25-76 (81)
81 KOG3284 Vacuolar sorting prote 20.6 5.5E+02 0.012 23.1 7.5 56 100-169 44-99 (213)
82 TIGR00681 kdpC K+-transporting 20.4 3.7E+02 0.008 23.6 6.4 64 65-131 90-156 (187)
83 PF06831 H2TH: Formamidopyrimi 20.0 1.3E+02 0.0028 22.7 3.1 49 6-56 34-87 (92)
No 1
>KOG3046 consensus Transcription factor, subunit of SRB subcomplex of RNA polymerase II [Transcription]
Probab=100.00 E-value=3.1e-47 Score=311.50 Aligned_cols=141 Identities=50% Similarity=0.733 Sum_probs=137.1
Q ss_pred ccCChhHHHHHHHHHHHHHHHHHHHhhhhccccCCCchhhHHHHHHHHHHHHHhHHhhhhhCC-CCCchHHHHhhhcCCC
Q 028220 28 AADDPKQNLNQVINSVQKTLGLLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVKLSEKCN-IQVPTEVLNLIDDGKN 106 (212)
Q Consensus 28 ~~~~~~~qL~~~ieSLe~~L~~L~Ql~i~VsdFq~~Sq~~L~qKIn~LV~~L~~L~~~a~~~d-i~IPlEVl~yID~GRN 106 (212)
..++..++|.++.++++++++.+||+|++|++|+|.||+.|+++|++||..|++|++++++++ +.||+||++|||||||
T Consensus 6 ~~~q~~ekl~~l~~~le~~~e~~~~Lgl~vs~F~~tsq~~L~qrl~tLv~~L~~l~~~s~k~n~i~IPleVl~yIddGrN 85 (147)
T KOG3046|consen 6 NNDQMQEKLAQLENSLEKFLENFRQLGLIVSNFQPTSQDALNQRLNTLVRGLQDLDKLSSKLNDIQIPLEVLEYIDDGRN 85 (147)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhcCCCCcHHHHHHHHHHHHHHhhhhHHHHHhhccccCcHHHHHHHhcCCC
Confidence 567888999999999999999999999999999999999999999999999999999999987 9999999999999999
Q ss_pred ccHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHhhChhhHHHHHHHHhcchhhhHHH
Q 028220 107 PDEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQTFPDEVEAYREIRANSAAVSNAI 168 (212)
Q Consensus 107 PDiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~~FPel~~~yr~ir~~~~a~~~~~ 168 (212)
||+|||+|+|+|+++||++|||++||++||++|++||+++|||+++.||.||+.++++|+++
T Consensus 86 Pd~ytke~le~~~~kNq~vkGK~~~~K~fr~~l~eEl~q~fPe~~~~yr~Ir~e~~~~s~vs 147 (147)
T KOG3046|consen 86 PDLYTKEFLEKCLAKNQYVKGKIDAFKKFRKHLAEELSQEFPELVDPYRSIRAEDAPESKVS 147 (147)
T ss_pred ccHHHHHHHHHHHHhhhHHhhhHHHHHHHHHHHHHHHHHHChHHHHHHHHHHhccCcccccC
Confidence 99999999999999999999999999999999999999999999999999999999999874
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=2.6e-42 Score=276.99 Aligned_cols=116 Identities=41% Similarity=0.640 Sum_probs=111.0
Q ss_pred HHHHHHHHHHHhhhhccccC-CCchhhHHHHHHHHHHHHHhHHhhhhh--------CCCCCchHHHHhhhcCCCccHHHH
Q 028220 42 SVQKTLGLLHQLYLTVSSFN-AASQLPLLQRLNSLVSELDNMVKLSEK--------CNIQVPTEVLNLIDDGKNPDEFTR 112 (212)
Q Consensus 42 SLe~~L~~L~Ql~i~VsdFq-~~Sq~~L~qKIn~LV~~L~~L~~~a~~--------~di~IPlEVl~yID~GRNPDiYTR 112 (212)
+|++++++|+|++++|++|+ ++|+++|.+||+.|+++|++|++++.. ++++||+|||+|||+|||||+|||
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 45566778999999999999 999999999999999999999999987 789999999999999999999999
Q ss_pred HHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHhhChhhHHHHHHH
Q 028220 113 DVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQTFPDEVEAYREI 157 (212)
Q Consensus 113 EfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~~FPel~~~yr~i 157 (212)
||||+|+++||++|||++||++||++|+++|+++|||+.+.|++|
T Consensus 84 e~vE~~~~~Nq~~kGK~~a~~~fr~~L~~el~~~fPe~~~~~~~i 128 (128)
T PF09748_consen 84 EFVELVRRENQYVKGKMEAFKSFRDVLAEELASAFPELKEDVRRI 128 (128)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHChHHHHHHhhC
Confidence 999999999999999999999999999999999999999999975
No 3
>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=82.20 E-value=50 Score=32.24 Aligned_cols=72 Identities=15% Similarity=0.289 Sum_probs=41.6
Q ss_pred CCCCchHHHHhhhcCCCccHHHHHHHHHHHHHhhHhh----ccHHHHHHHHHHHH----HHHHhhChhhHHHHHHHHhcc
Q 028220 90 NIQVPTEVLNLIDDGKNPDEFTRDVINSCIAKNQVTK----GKTDAFKSLRKHLL----DELEQTFPDEVEAYREIRANS 161 (212)
Q Consensus 90 di~IPlEVl~yID~GRNPDiYTREfVE~~~~~NQ~~k----GKi~a~~~fR~~L~----eeL~~~FPel~~~yr~ir~~~ 161 (212)
++-||+++++-|-+|.==+-|-++.++...+.....+ ....|.+.++..|. ..+++...=+......+|...
T Consensus 81 ~i~ipP~lI~~I~~~~v~e~~~~~~~~~~~k~~~~~~~~~~~~~~a~~d~~~~Le~L~~ka~~rir~fl~~kI~~lr~~~ 160 (508)
T PF04129_consen 81 DIVIPPDLIRSICEGPVNEQYIEELLELLKKKIFFSKDQSFKDSKAIKDVKPELEKLKNKAVERIRDFLLKKIKSLRKPK 160 (508)
T ss_pred HHcCCHHHHHhHhcCCCCHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 6789999999998884333566666665555444332 33445555554443 233333344555666677543
No 4
>KOG4331 consensus Polytopic membrane protein Prominin [General function prediction only]
Probab=78.07 E-value=47 Score=35.15 Aligned_cols=98 Identities=18% Similarity=0.277 Sum_probs=54.0
Q ss_pred hhhcCCCccHH--------HHHHHHHHHHHhhHhhc-----------cHHHH-HHH----------HHHHHH-HHHhhCh
Q 028220 100 LIDDGKNPDEF--------TRDVINSCIAKNQVTKG-----------KTDAF-KSL----------RKHLLD-ELEQTFP 148 (212)
Q Consensus 100 yID~GRNPDiY--------TREfVE~~~~~NQ~~kG-----------Ki~a~-~~f----------R~~L~e-eL~~~FP 148 (212)
.+||--|||-| |-|+...+++.|+..|- -+..+ +.+ -..|.. .....||
T Consensus 326 ~~~qlp~vd~~~~gm~~V~~sei~~~~q~~~s~~n~l~~kvq~q~s~vv~~~~r~l~q~~~~l~~~a~~l~~ql~~~~~s 405 (865)
T KOG4331|consen 326 FFDQLPNVDAFLSGMPNVVTSEILQSVQRGNSLFNVLPDKVQYQTSGVVDDVMRDLPQIPGDLDGLAEKLPSQLANSVFS 405 (865)
T ss_pred hhhhCCCchHHHhccccchHHHHHHHHHhhhhhhhhhhHHHhhcccccchHHHHHHHhCCchHHHHHhhccHHHHHHHHH
Confidence 36666666655 45788888888887431 11111 111 111111 1223444
Q ss_pred hhHHHHHHHHhcchhhhHHHhhhhhHHHHHHH-HHHHHHHHHHHHHHHHHHHHH
Q 028220 149 DEVEAYREIRANSAAVSNAILSEAHHVEWMLS-ICCQFFMFLILYILLSVLYDI 201 (212)
Q Consensus 149 el~~~yr~ir~~~~a~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~ 201 (212)
........+-.+ .+.-...+.|..|.-+ +=|-++|++.|..++.+|+.|
T Consensus 406 ~~~~k~~~~s~~----~~~~~~ry~~y~wv~~LVicsl~llvll~~~~Gll~Gi 455 (865)
T KOG4331|consen 406 GVTLKVEASSLR----ALQKHLRYPLYRWVVSLVICSLQLLVLLIGLFGLLCGI 455 (865)
T ss_pred HHHHHHHHhhcc----ccchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444443332 2223345788888866 446788888888888888876
No 5
>PF07234 DUF1426: Protein of unknown function (DUF1426); InterPro: IPR009871 This family consists of several Banana bunchy top virus proteins of around 120 residues in length. Q9IGU4 from SWISSPROT is annotated a movement protein whereas most other family members are hypothetical. The function of this family is unknown.
Probab=71.61 E-value=7.5 Score=31.35 Aligned_cols=29 Identities=38% Similarity=0.792 Sum_probs=26.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028220 173 HHVEWMLSICCQFFMFLILYILLSVLYDI 201 (212)
Q Consensus 173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 (212)
-|-||.+-+..-|...-||||||.+|+..
T Consensus 10 lfFEwFLF~~AIFiAItIlYILLalL~Ev 38 (117)
T PF07234_consen 10 LFFEWFLFFGAIFIAITILYILLALLFEV 38 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 47899999999999999999999999875
No 6
>PF02436 PYC_OADA: Conserved carboxylase domain; InterPro: IPR003379 This domain represents a conserved region in pyruvate carboxylase (PYC) (6.4.1.1 from EC), oxaloacetate decarboxylase alpha chain (OADA) (4.1.1.3 from EC), and transcarboxylase 5s subunit (2.1.3.1 from EC). The domain is found adjacent to the HMGL-like domain (IPR000891 from INTERPRO) and often close to the biotin_lipoyl domain (IPR000089 from INTERPRO) of biotin requiring enzymes.; PDB: 2NX9_B 3HBL_A 3HB9_C 3HO8_A 3BG5_C 1S3H_A 1RQE_A 1U5J_A 1RQB_A 2QF7_B ....
Probab=71.11 E-value=15 Score=31.93 Aligned_cols=107 Identities=19% Similarity=0.270 Sum_probs=66.6
Q ss_pred HHHHhhhhccccCCCchhhHHHHHHHHHHHHHhHHhhhhhCCCCCchHHHHhhhc--CCCccHHHHHHHHHHHHHhhHhh
Q 028220 49 LLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDD--GKNPDEFTRDVINSCIAKNQVTK 126 (212)
Q Consensus 49 ~L~Ql~i~VsdFq~~Sq~~L~qKIn~LV~~L~~L~~~a~~~di~IPlEVl~yID~--GRNPDiYTREfVE~~~~~NQ~~k 126 (212)
.+++.-.-.-..+|.||=+=.+-+..+...+ ....-..||-+|++|+-- |+=|--|-.++.+++.+..+...
T Consensus 36 ~v~~~lG~~~~VTPsSqiVg~qA~~nV~~~~------~g~r~~~~p~~v~~~~~G~~G~pp~~~~~~l~~~vl~~~~~i~ 109 (196)
T PF02436_consen 36 RVRKDLGYPPKVTPSSQIVGDQAVFNVLNGL------LGERYKDFPDSVVDYLLGKYGKPPGGFPEELRKKVLKGEEPIT 109 (196)
T ss_dssp HHHHHTTS--SSTTHHHHHHHHHHHHHHTT-------HHTTTSS-BHHHHHHHTTTT---TTSS-HHHHHHHHTTS---S
T ss_pred HHHHHcCCccccCcHHHHHHHHHHHHHHhhh------cCccccchhHHHHHHhCcccCCCCCCCCHHHHHHHhcCCCCCC
Confidence 3444333333458888865555555544444 122456799999999954 89999999999999998877666
Q ss_pred ccHH------HHHHHHHHHHHHH-----------HhhChhhHHHHHHHHhcc
Q 028220 127 GKTD------AFKSLRKHLLDEL-----------EQTFPDEVEAYREIRANS 161 (212)
Q Consensus 127 GKi~------a~~~fR~~L~eeL-----------~~~FPel~~~yr~ir~~~ 161 (212)
++-. .|+++|+.|.+.. .--||+...+|.+-|...
T Consensus 110 ~RP~~~l~p~d~~~~r~~l~~~~g~~~~dedvlsyal~P~v~~~f~~~~~~~ 161 (196)
T PF02436_consen 110 GRPGDLLPPADLDKLRKELEEKAGREPTDEDVLSYALFPKVAEDFLKFRAKY 161 (196)
T ss_dssp SSGGGCS----HHHHHHHHHHHCTSTSCHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred CCccccCChhhHHHHHHHHHHHcCCCCCHHHHHHHhcCchhHHHHHHHHHhc
Confidence 5522 6888888888754 235899999998888743
No 7
>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=67.77 E-value=15 Score=26.37 Aligned_cols=55 Identities=24% Similarity=0.319 Sum_probs=46.1
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHhhhhccccCCCchhhHHHHHHHHHHHHHhHHh
Q 028220 30 DDPKQNLNQVINSVQKTLGLLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVK 84 (212)
Q Consensus 30 ~~~~~qL~~~ieSLe~~L~~L~Ql~i~VsdFq~~Sq~~L~qKIn~LV~~L~~L~~ 84 (212)
++.+..|..+=..|.+.-+.|.||.+-|.+..++....+..+|..+=+.|..+.+
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 6777777777778888777999999999999777888999999999999988865
No 8
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=66.51 E-value=9.8 Score=30.90 Aligned_cols=64 Identities=23% Similarity=0.379 Sum_probs=48.4
Q ss_pred chHHHHhhhc-CCCccHHHHHHHHHHHHHhhHhhccHHHHHH-HHHHHHHHHHhhChhhHHHHHHHHhc
Q 028220 94 PTEVLNLIDD-GKNPDEFTRDVINSCIAKNQVTKGKTDAFKS-LRKHLLDELEQTFPDEVEAYREIRAN 160 (212)
Q Consensus 94 PlEVl~yID~-GRNPDiYTREfVE~~~~~NQ~~kGKi~a~~~-fR~~L~eeL~~~FPel~~~yr~ir~~ 160 (212)
+++-.+|+++ |.+|-...-+-+-++..++- |-+-+|.+ |-+.-.++|++.||+..+....|.++
T Consensus 42 ~~~h~efL~~~~~DPr~~~~~~L~~~i~~~~---g~ivvyN~sfE~~rL~ela~~~p~~~~~l~~I~~r 107 (130)
T PF11074_consen 42 ELEHVEFLADPGEDPRRELIEALIKAIGSIY---GSIVVYNKSFEKTRLKELAELFPDYAEKLNSIIER 107 (130)
T ss_pred chhhHHHhccCCCCchHHHHHHHHHHhhhhc---CeEEEechHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 4566677754 68888766666655555554 77777766 88889999999999999999999843
No 9
>PF05823 Gp-FAR-1: Nematode fatty acid retinoid binding protein (Gp-FAR-1); InterPro: IPR008632 Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localises to the surface of the organism, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems [].; GO: 0008289 lipid binding; PDB: 2W9Y_A.
Probab=62.14 E-value=58 Score=27.07 Aligned_cols=34 Identities=26% Similarity=0.427 Sum_probs=20.1
Q ss_pred hhHhhccHHHHHHHHHHHHHHHHhhChhhHHHHH
Q 028220 122 NQVTKGKTDAFKSLRKHLLDELEQTFPDEVEAYR 155 (212)
Q Consensus 122 NQ~~kGKi~a~~~fR~~L~eeL~~~FPel~~~yr 155 (212)
.+..++-+..|+.+-..-.+.|.++||+...-..
T Consensus 108 k~~~k~~~~~ykaLs~~ak~dL~k~FP~i~~~~~ 141 (154)
T PF05823_consen 108 KQLAKKVIDSYKALSPEAKDDLKKNFPIIASFLQ 141 (154)
T ss_dssp HHHH----HHHHTS-HHHHHHHHHH-TT------
T ss_pred HHHHhhhHHHHHcCCHHHHHHHHHHCccchhhhh
Confidence 5668888999999999999999999999876544
No 10
>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=60.31 E-value=96 Score=26.25 Aligned_cols=43 Identities=23% Similarity=0.393 Sum_probs=31.2
Q ss_pred CCchH-HHHhhhcCCCccHHH-------------HHHHHHHHHHhhHhhccHHHHHH
Q 028220 92 QVPTE-VLNLIDDGKNPDEFT-------------RDVINSCIAKNQVTKGKTDAFKS 134 (212)
Q Consensus 92 ~IPlE-Vl~yID~GRNPDiYT-------------REfVE~~~~~NQ~~kGKi~a~~~ 134 (212)
+.|+| +|-|+|+..+...-+ +|.+|++..+|+.+|--|+-++.
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 57788899999998877775544
No 11
>PRK14139 heat shock protein GrpE; Provisional
Probab=55.32 E-value=1.4e+02 Score=25.88 Aligned_cols=52 Identities=15% Similarity=0.198 Sum_probs=28.8
Q ss_pred CCCCCCCCcccC-CCCCccCCCCcccccccCChhHHHHHHHHHHHHHHHHHHH
Q 028220 1 MDGPVGGSRASG-GNGMVSNQANDTTTVAADDPKQNLNQVINSVQKTLGLLHQ 52 (212)
Q Consensus 1 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~qL~~~ieSLe~~L~~L~Q 52 (212)
|+.+|..+|--- -..+...+.-.+++|++++....|+.-|+.+++-+..+.+
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~l~~~l~~le~e~~elkd 53 (185)
T PRK14139 1 MENTQQNPSEQEAEEAGAAAQAAAAAAAAAEDAAPALEAELAEAEAKAAELQD 53 (185)
T ss_pred CCCCCCCCCCccccCcccccccccccccccchhHHHHHHHHHHHHHHHHHHHH
Confidence 556655554311 1112223555555567777777788777777765555544
No 12
>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=52.06 E-value=30 Score=26.11 Aligned_cols=61 Identities=20% Similarity=0.306 Sum_probs=48.8
Q ss_pred CCCCchHHHHhhhcCCCccHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHH-HHHhhChhhHHHHHH
Q 028220 90 NIQVPTEVLNLIDDGKNPDEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLD-ELEQTFPDEVEAYRE 156 (212)
Q Consensus 90 di~IPlEVl~yID~GRNPDiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~e-eL~~~FPel~~~yr~ 156 (212)
..-.|.+|+.|+-+ .+|.+-.|...++ ...+|.+++...|=+.|.+ .=...||......+.
T Consensus 17 ~~l~p~~il~~l~~-----~L~~~~~e~I~a~-~~~~g~~~aa~~Ll~~L~~~r~~~wf~~Fl~AL~~ 78 (88)
T cd08812 17 DTIIPRDILDHLPE-----CLTDEDKEQILAE-ERNKGNIAAAEELLDRLERCDKPGWFQAFLDALRR 78 (88)
T ss_pred HhcCHHHHHHHHHH-----HcCHHHHHHHHHH-HhccChHHHHHHHHHHHHHhccCCcHHHHHHHHHH
Confidence 34589999999976 9999999998886 5567999999999888887 445678877776654
No 13
>PRK12999 pyruvate carboxylase; Reviewed
Probab=51.78 E-value=55 Score=35.45 Aligned_cols=112 Identities=14% Similarity=0.264 Sum_probs=69.0
Q ss_pred HHHHhhhhccccCCCchhhHHHHHHHHHHHHHhHHhhhhhCCCCCchHHHHhhhc--CCCccHHHHHHHHHHHHHhhHhh
Q 028220 49 LLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDD--GKNPDEFTRDVINSCIAKNQVTK 126 (212)
Q Consensus 49 ~L~Ql~i~VsdFq~~Sq~~L~qKIn~LV~~L~~L~~~a~~~di~IPlEVl~yID~--GRNPDiYTREfVE~~~~~NQ~~k 126 (212)
.++++-.-.--.+|.||=+=.+-+..+...|..=+=........||-+|++|+-- |+=|--|-.++.+++.+..+...
T Consensus 863 ~v~~~~G~~~~VTP~Sq~vg~~A~~~v~~~~~~~~~~~~~~~~~~~~~v~~~~~G~~G~~~~~~~~~~~~~~l~~~~~~~ 942 (1146)
T PRK12999 863 AVNRMFGDIVKVTPSSKVVGDMALFMVQNGLTPEDVYEPGEDLDFPDSVVSFLKGELGQPPGGFPEPLQKKVLKGEEPIT 942 (1146)
T ss_pred HHHHHcCCCceeCccchhhHHHHHHHHhhccchhhhhccCceeeCCHHHHHHhCcCCCCCCCCCCHHHHHHHhCCCCCCc
Confidence 4444333333357888865555544444433221111122245799999999954 89999999999999987665444
Q ss_pred ccH-----H-HHHHHHHHHHHHHHh-----------hChhhHHHHHHHHhc
Q 028220 127 GKT-----D-AFKSLRKHLLDELEQ-----------TFPDEVEAYREIRAN 160 (212)
Q Consensus 127 GKi-----~-a~~~fR~~L~eeL~~-----------~FPel~~~yr~ir~~ 160 (212)
++- . -|+++|+.|.+.... -||+...+|.+-|..
T Consensus 943 ~rp~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~ 993 (1146)
T PRK12999 943 VRPGELLEPVDFEAERAELEEKLGREVTDRDVLSYLLYPKVFEDYIKHREE 993 (1146)
T ss_pred CChhhhCCcccHHHHHHHHHHHhcCCCCHHHHHHHHhCcHHHHHHHHHHHh
Confidence 432 2 277788877776532 367777777776654
No 14
>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins.
Probab=50.58 E-value=1.8e+02 Score=31.45 Aligned_cols=83 Identities=11% Similarity=0.143 Sum_probs=53.2
Q ss_pred hcCCCccHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHhh-ChhhHHHHHHHHhcchhhhHHHhhhhhHHHHHHH
Q 028220 102 DDGKNPDEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQT-FPDEVEAYREIRANSAAVSNAILSEAHHVEWMLS 180 (212)
Q Consensus 102 D~GRNPDiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~~-FPel~~~yr~ir~~~~a~~~~~~~~~~~~~~~~~ 180 (212)
....+++....+++..+...-...++..+.++.+-+.+..-|... -+++.+.+...|....-.+...+...++-.|+..
T Consensus 888 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~f~~~l~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~ 967 (1201)
T PF12128_consen 888 PNAEDAEGSVDERLRDLEDLLQRRKRLREELKKAVERFKGVLTKHSGSELAENWEELRSEDSFLSDKGINSDDYRQWAPD 967 (1201)
T ss_pred CCchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHHHhccccccccccchhHHHHHHH
Confidence 445566666778888888877888888888887777777666433 3667777777755444444444444455666555
Q ss_pred HHHH
Q 028220 181 ICCQ 184 (212)
Q Consensus 181 ~~~~ 184 (212)
.|..
T Consensus 968 l~~~ 971 (1201)
T PF12128_consen 968 LQEL 971 (1201)
T ss_pred HHHH
Confidence 5443
No 15
>PF11657 Activator-TraM: Transcriptional activator TraM
Probab=48.44 E-value=1.6e+02 Score=24.64 Aligned_cols=64 Identities=17% Similarity=0.191 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHHhhChhhHHHHHHHHhcchhhhHHHhhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 028220 132 FKSLRKHLLDELEQTFPDEVEAYREIRANSAAVSNAILSEAHHVEWMLSICCQFFMFLILYILL 195 (212)
Q Consensus 132 ~~~fR~~L~eeL~~~FPel~~~yr~ir~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 195 (212)
+..-++.....|.+.+-+-...++.-..++-++.+..++...++-||+=.|--.+.+..+.+++
T Consensus 78 l~~ske~m~~~l~e~~~~~~~avk~~i~~~~~~~~~~~~~~r~~a~~nl~aa~~~~~aa~v~~~ 141 (144)
T PF11657_consen 78 LAASKEAMNKILQESAQEIVEAVKSEIDNSLAEVNDLVREARKAAILNLVAAVLVLLAACVALW 141 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344555555566666666666666556788888889999999999998888776655544443
No 16
>smart00503 SynN Syntaxin N-terminal domain. Three-helix domain that (in Sso1p) slows the rate of its reaction with the SNAP-25 homologue Sec9p
Probab=46.41 E-value=1.2e+02 Score=22.53 Aligned_cols=29 Identities=14% Similarity=0.374 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHhhChhhHHHHHHHHhcc
Q 028220 133 KSLRKHLLDELEQTFPDEVEAYREIRANS 161 (212)
Q Consensus 133 ~~fR~~L~eeL~~~FPel~~~yr~ir~~~ 161 (212)
..-|....+.|...|=+....|+.+....
T Consensus 84 ~r~~~~q~~~L~~~f~~~m~~fq~~Q~~~ 112 (117)
T smart00503 84 DRTRKAQTEKLRKKFKEVMNEFQRLQRKY 112 (117)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566677777888888888888877543
No 17
>PRK04358 hypothetical protein; Provisional
Probab=45.27 E-value=1e+02 Score=27.67 Aligned_cols=78 Identities=23% Similarity=0.491 Sum_probs=45.8
Q ss_pred cccccccCChhHHH--HHHHHHHHHHHHHHHH--hhhhccccCCCchhhHHHHHHHHHHH-------HHhHH-----hhh
Q 028220 23 DTTTVAADDPKQNL--NQVINSVQKTLGLLHQ--LYLTVSSFNAASQLPLLQRLNSLVSE-------LDNMV-----KLS 86 (212)
Q Consensus 23 ~~~~~~~~~~~~qL--~~~ieSLe~~L~~L~Q--l~i~VsdFq~~Sq~~L~qKIn~LV~~-------L~~L~-----~~a 86 (212)
||++-|-.+.++++ +++.+.+..+++.+.+ +...+|-|-|+| +-..+..++.. +.+++ +..
T Consensus 9 DTS~fT~p~vr~~fg~e~l~ea~~~~l~Lia~arl~l~is~YmPpS---Vy~El~~f~~~~~~~~e~~~kl~twi~~KsP 85 (217)
T PRK04358 9 DTSAFTDPDVREQFGVEDLEEAVEKFLDLIARARLKLGISCYMPPS---VYKELRGFLERNGCSPEVIAKLDTWIVKKSP 85 (217)
T ss_pred eccccCCHHHHHHcCCCCHHHHHHHHHHHHHHhhhccCceEEcCHH---HHHHHHHHHHhcCCCHHHHhhheeEEEEcCC
Confidence 34444555555544 3566677777777666 445678888865 55555544432 12222 222
Q ss_pred hhCCCCCchHHH-Hhhhc
Q 028220 87 EKCNIQVPTEVL-NLIDD 103 (212)
Q Consensus 87 ~~~di~IPlEVl-~yID~ 103 (212)
..+++.||-+++ +||++
T Consensus 86 ~ry~v~IPA~i~ye~I~~ 103 (217)
T PRK04358 86 NRYEIKIPAEIFYEYIED 103 (217)
T ss_pred CceeeeccHHHHHHHHHH
Confidence 356889999888 67764
No 18
>PF11333 DUF3135: Protein of unknown function (DUF3135); InterPro: IPR021482 This family of proteins with unkown function appears to be restricted to Proteobacteria.
Probab=43.55 E-value=63 Score=24.61 Aligned_cols=46 Identities=20% Similarity=0.373 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHhhChhhHHHHHHHHhcchhhhHHHhhhhhHHHHHHHHHHHHHH
Q 028220 129 TDAFKSLRKHLLDELEQTFPDEVEAYREIRANSAAVSNAILSEAHHVEWMLSICCQFFM 187 (212)
Q Consensus 129 i~a~~~fR~~L~eeL~~~FPel~~~yr~ir~~~~a~~~~~~~~~~~~~~~~~~~~~~~~ 187 (212)
=++|..||..+.+++-+.- ++.-.+|+-..++|++-..+.|+.=.-
T Consensus 17 Pe~fe~lr~~~~ee~I~~a-------------~~~~q~rL~~lQ~~Id~~~~~~knP~~ 62 (83)
T PF11333_consen 17 PEAFEQLRQELIEEMIESA-------------PEEMQPRLRALQFHIDMQRSRCKNPLH 62 (83)
T ss_pred HHHHHHHHHHHHHHHHHhC-------------CHHHHHHHHHHHHHHHHHHHHcCChHH
Confidence 3678888888888775544 444467888889999999999986443
No 19
>PF09164 VitD-bind_III: Vitamin D binding protein, domain III; InterPro: IPR015247 This domain is predominantly found in Vitamin D binding proteins, and adopts a multihelical structure. It is required for formation of an actin 'clamp', allowing the protein to bind to actin []. ; PDB: 1MA9_A 1KW2_A 1KXP_D 1J7E_A 1J78_A 1LOT_A.
Probab=43.52 E-value=55 Score=24.50 Aligned_cols=42 Identities=21% Similarity=0.553 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHhhChhhHHHHHHHHhcchhhhHHHhhhhhHHHHHHHHHHH
Q 028220 130 DAFKSLRKHLLDELEQTFPDEVEAYREIRANSAAVSNAILSEAHHVEWMLSICCQ 184 (212)
Q Consensus 130 ~a~~~fR~~L~eeL~~~FPel~~~yr~ir~~~~a~~~~~~~~~~~~~~~~~~~~~ 184 (212)
..|-.||+.|.+.|...||+- +|.+-+.++..-++ .-+.||.
T Consensus 9 ~tFtEyKKrL~e~l~~k~P~a----------t~~~l~~lve~Rsd---FAS~CC~ 50 (68)
T PF09164_consen 9 NTFTEYKKRLAERLRAKLPDA----------TPTELKELVEKRSD---FASKCCS 50 (68)
T ss_dssp S-HHHHHHHHHHHHHHH-TTS-----------HHHHHHHHHHHHH---HHHHHSS
T ss_pred ccHHHHHHHHHHHHHHHCCCC----------CHHHHHHHHHHHhh---HHHHhhc
Confidence 357889999999999999984 44455555544333 3456664
No 20
>PF14823 Sirohm_synth_C: Sirohaem biosynthesis protein C-terminal; PDB: 1KYQ_B.
Probab=41.97 E-value=44 Score=24.59 Aligned_cols=14 Identities=21% Similarity=0.667 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHH
Q 028220 175 VEWMLSICCQFFMF 188 (212)
Q Consensus 175 ~~~~~~~~~~~~~~ 188 (212)
-.||++.|-+|.+.
T Consensus 32 M~Wm~~vcd~w~l~ 45 (70)
T PF14823_consen 32 MRWMSQVCDYWSLE 45 (70)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHhcccCHH
Confidence 57999999999864
No 21
>PF14712 Snapin_Pallidin: Snapin/Pallidin
Probab=40.12 E-value=1.1e+02 Score=22.38 Aligned_cols=23 Identities=30% Similarity=0.445 Sum_probs=19.4
Q ss_pred CchhhHHHHHHHHHHHHHhHHhh
Q 028220 63 ASQLPLLQRLNSLVSELDNMVKL 85 (212)
Q Consensus 63 ~Sq~~L~qKIn~LV~~L~~L~~~ 85 (212)
.||..|...|..+...|+++...
T Consensus 28 ~sQ~~L~~~i~~~~~~L~~~~~~ 50 (92)
T PF14712_consen 28 QSQEELLQQIDRLNEKLKELNEV 50 (92)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 37889999999999999888764
No 22
>TIGR01235 pyruv_carbox pyruvate carboxylase. This enzyme plays a role in gluconeogensis but not glycolysis.
Probab=39.50 E-value=1.1e+02 Score=33.27 Aligned_cols=113 Identities=12% Similarity=0.229 Sum_probs=66.5
Q ss_pred HHHHhhhhccccCCCchhhHHHHHHHHHHHHHhHHhhhhhCCCCCchHHHHhhhc--CCCccHHHHHHHHHHHHHhhHhh
Q 028220 49 LLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDD--GKNPDEFTRDVINSCIAKNQVTK 126 (212)
Q Consensus 49 ~L~Ql~i~VsdFq~~Sq~~L~qKIn~LV~~L~~L~~~a~~~di~IPlEVl~yID~--GRNPDiYTREfVE~~~~~NQ~~k 126 (212)
.++++-.-.--.+|.||=+=.+-+--+...|..=+=........||-+|++|+-- |+=|--|-.++.+++.+..+...
T Consensus 861 ~v~~~lG~~~~VTP~Sq~vg~~A~~~v~~~l~~~~v~~~~~~~~~~~~v~~~~~G~~G~pp~~~~~~~~~~vl~~~~~~~ 940 (1143)
T TIGR01235 861 EANQMFGDIVKVTPSSKVVGDMALFMVSNDLTVDDVVEPAEELSFPDSVVEFLKGDIGQPHGGFPEPLQKKVLKGEKPIT 940 (1143)
T ss_pred HHHHHcCCCceECChhHhHHHHHHHHHHhccChhhhccccccccCCHHHHHHhCcCCCCCCCCCCHHHHHHHhCCCCCCc
Confidence 3444332222457888754333322222222211101112245799999999954 78888888888888887655443
Q ss_pred ccHH------HHHHHHHHHHHHHHh-----------hChhhHHHHHHHHhcc
Q 028220 127 GKTD------AFKSLRKHLLDELEQ-----------TFPDEVEAYREIRANS 161 (212)
Q Consensus 127 GKi~------a~~~fR~~L~eeL~~-----------~FPel~~~yr~ir~~~ 161 (212)
++-. -|+++|+.|.+.... -||+...+|..-|...
T Consensus 941 ~rp~~~l~p~~~~~~~~~~~~~~~~~~~~ed~~~y~~~p~v~~~~~~~~~~~ 992 (1143)
T TIGR01235 941 VRPGSLLEPADLDAIRKDLQEKHEREVSDFDVASYAMYPKVFTDFAKARDTY 992 (1143)
T ss_pred CCccccCCcccHHHHHHHHHHHhcCCCCHHHHHHHHcCcHHHHHHHHHHHhc
Confidence 3322 377888887776522 3788888888777653
No 23
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=39.19 E-value=1.7e+02 Score=22.07 Aligned_cols=73 Identities=21% Similarity=0.187 Sum_probs=42.7
Q ss_pred HhhccHHHHHHHHHHHHHHHHhhChh--hHHHHHHHHhcchhhhHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028220 124 VTKGKTDAFKSLRKHLLDELEQTFPD--EVEAYREIRANSAAVSNAILSEAHHVEWMLSICCQFFMFLILYILLSVLYDI 201 (212)
Q Consensus 124 ~~kGKi~a~~~fR~~L~eeL~~~FPe--l~~~yr~ir~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 (212)
.++-+-..++.+...+.+-+..-+|. .....+.+-+ ..-+.. .+.+.+=|.|+|+..-+-+-.-+++.++||+
T Consensus 21 i~~~~k~~i~~l~~~~~~~~~~~~~~~~~~~~v~~~~~----~l~~~~-~~~~~~EirGIA~~~gi~l~~iv~lN~~yEi 95 (95)
T PF15508_consen 21 IAKDYKDEIRELIEVLKDLLQSFVPSGKVLDFVDKLLP----HLLRYL-PQPYAEEIRGIAKAAGIPLGDIVLLNLFYEI 95 (95)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHH----HHHHhC-CHHHHHHHHHHHHHhCCCHHHHHHHHHHhhC
Confidence 33334455555666555555555555 2222222211 111111 3457777999999998888888889999985
No 24
>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=39.03 E-value=1.1e+02 Score=22.80 Aligned_cols=54 Identities=24% Similarity=0.271 Sum_probs=29.2
Q ss_pred hhhHHHHHHHHHHHHHhHHhhhhhCCCCCchHHHHhhhcCCCccHHHHHHHHHHHHHhh
Q 028220 65 QLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGKNPDEFTRDVINSCIAKNQ 123 (212)
Q Consensus 65 q~~L~qKIn~LV~~L~~L~~~a~~~di~IPlEVl~yID~GRNPDiYTREfVE~~~~~NQ 123 (212)
|..+..++..--+...+.-.+. ..|.+|.+.|++|+-.|..+..-+....++|.
T Consensus 6 q~eIA~~lGks~s~Vs~~l~Ll-----~lP~~i~~~v~~g~~~~~~a~~~L~~~~~~~~ 59 (93)
T PF08535_consen 6 QEEIAKRLGKSRSWVSNHLALL-----DLPEEIKELVRSGRISDIRALYELRKLAEKNP 59 (93)
T ss_dssp HHHHHHHTT--HHHHHHHHGGG-----S--HHHHHHHHTTS---HHHHHHHHHHHHH-H
T ss_pred HHHHHHHHCCCHHHHHHHHHHH-----cCCHHHHHHHHcCCCchHHHHHHHHHHHHhCH
Confidence 4455555543333333333222 48999999999999999888877766666653
No 25
>PRK06771 hypothetical protein; Provisional
Probab=38.55 E-value=1e+02 Score=24.29 Aligned_cols=30 Identities=27% Similarity=0.402 Sum_probs=22.8
Q ss_pred CCchHHHHhhhcCCCccHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHH
Q 028220 92 QVPTEVLNLIDDGKNPDEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDEL 143 (212)
Q Consensus 92 ~IPlEVl~yID~GRNPDiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL 143 (212)
.+|.||.+.+.+|+ |++|++.+|+.-.-.|
T Consensus 54 ~~~~e~~~Li~~Gk----------------------ki~AIK~~Re~tG~~L 83 (93)
T PRK06771 54 PVNKELRQLMEEGQ----------------------TVTAVKRVREAFGFSL 83 (93)
T ss_pred cccHHHHHHHHcCC----------------------chHHHHHHHHHcCCCH
Confidence 68889999998887 5778888777655444
No 26
>PHA03188 UL14 tegument protein; Provisional
Probab=36.73 E-value=2.1e+02 Score=25.49 Aligned_cols=84 Identities=17% Similarity=0.166 Sum_probs=56.7
Q ss_pred cHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHhhChhhHHHHHHHHhcchhhhHHHhhh-------hhHHHHHHH
Q 028220 108 DEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQTFPDEVEAYREIRANSAAVSNAILSE-------AHHVEWMLS 180 (212)
Q Consensus 108 DiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~~FPel~~~yr~ir~~~~a~~~~~~~~-------~~~~~~~~~ 180 (212)
.+.+.-.||.+.++=..+.-+|++-...|+.|...=.=-=|++.+.+..+=.+-...-.++-.+ -++.+||..
T Consensus 64 qLrs~aRve~veQK~r~Iq~rVeeQ~a~r~iL~~nRRfL~PdFid~lD~~ED~l~d~Ed~L~da~~~~~~~d~~~~wl~e 143 (199)
T PHA03188 64 NIRSAARIAAVEQKIADIQEKVEEQTSIQKILNANRRYIAPDFIEGLDKIEDDNCDGIDKLEDAVGGDIEHDHHEGWFCE 143 (199)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcChHHHHHHHHHHHHHHhhHHHHHhhhcCCCCCCcccccccc
Confidence 4667778888888888888888888777777776544445666665555443333323333222 246789999
Q ss_pred HHHHHHHHHHH
Q 028220 181 ICCQFFMFLIL 191 (212)
Q Consensus 181 ~~~~~~~~~~~ 191 (212)
-|.-+.+..+|
T Consensus 144 ~dEALLt~WmL 154 (199)
T PHA03188 144 DDEALLTQWML 154 (199)
T ss_pred hhHHHHHHHHH
Confidence 99999888776
No 27
>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=35.82 E-value=12 Score=32.78 Aligned_cols=57 Identities=21% Similarity=0.490 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHhHHhhhhhCCCCCchHHHHhhhc------CCCccHHHHHHHHHHHHHhhHhhccHHHH
Q 028220 68 LLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDD------GKNPDEFTRDVINSCIAKNQVTKGKTDAF 132 (212)
Q Consensus 68 L~qKIn~LV~~L~~L~~~a~~~di~IPlEVl~yID~------GRNPDiYTREfVE~~~~~NQ~~kGKi~a~ 132 (212)
+.++++++|-.+..=+ ++...++|.||++|+++ |++=+-|-++.=. -+.-+|+..|+
T Consensus 77 maN~vDevIA~~~k~~---dk~k~~lp~dVi~Ym~~ngI~VdG~si~~Yl~~n~~-----~~LdkG~LqaV 139 (188)
T PF03433_consen 77 MANRVDEVIAEVAKSD---DKAKAPLPDDVIDYMRDNGIKVDGKSIDDYLKKNGS-----GGLDKGQLQAV 139 (188)
T ss_dssp -----------------------------------------------------------------------
T ss_pred HHHHHHHHHHhccCCC---ccccccCCHHHHHHHHHcCCeecCeeccchhhhhhh-----ccCCchhHHHH
Confidence 6677777766555433 33455799999999965 6777777666543 44555665554
No 28
>KOG1961 consensus Vacuolar sorting protein VPS52/suppressor of actin Sac2 [Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=34.80 E-value=4.9e+02 Score=27.09 Aligned_cols=72 Identities=24% Similarity=0.344 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHhHHh----hhhhC-CCCCchHHHHhhhcCCCcc-HHHHH--HHHH-HHHHh-hHhhccHHHHHHHHH
Q 028220 68 LLQRLNSLVSELDNMVK----LSEKC-NIQVPTEVLNLIDDGKNPD-EFTRD--VINS-CIAKN-QVTKGKTDAFKSLRK 137 (212)
Q Consensus 68 L~qKIn~LV~~L~~L~~----~a~~~-di~IPlEVl~yID~GRNPD-iYTRE--fVE~-~~~~N-Q~~kGKi~a~~~fR~ 137 (212)
|.+|=+++-..|.+... +++.+ ++-||++++.-|=+|.=-+ -|... -+-. ...-+ +...|-..+++..+.
T Consensus 115 lqekS~~m~~~L~Nrq~v~s~Ls~fVdd~iVpp~lI~~I~~g~vne~~f~~~LeeL~~Kl~~v~~dq~~k~a~a~~Dv~~ 194 (683)
T KOG1961|consen 115 LQEKSNDMQLRLENRQAVESKLSQFVDDLIVPPELIKTIVDGDVNEPEFLEALEELSHKLKLVELDQSNKDAKALKDVEP 194 (683)
T ss_pred HHHHhhHHHHHHHhHHHHHHHHHHHhccccCCHHHHHHHHcCCCCchHHHHHHHHHHHHHHhhhhhhhccchhhhhhHHH
Confidence 34444444444444332 33333 7899999999998884333 33222 1111 11122 344455555555554
Q ss_pred HH
Q 028220 138 HL 139 (212)
Q Consensus 138 ~L 139 (212)
.|
T Consensus 195 lL 196 (683)
T KOG1961|consen 195 LL 196 (683)
T ss_pred HH
Confidence 44
No 29
>PRK15364 pathogenicity island 2 effector protein SseB; Provisional
Probab=34.50 E-value=52 Score=29.08 Aligned_cols=33 Identities=15% Similarity=0.361 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHhHHhhhhhCCCCCchHHHHhhhc
Q 028220 68 LLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDD 103 (212)
Q Consensus 68 L~qKIn~LV~~L~~L~~~a~~~di~IPlEVl~yID~ 103 (212)
+.+++++.|-.+++= -++...++|.||++|+.+
T Consensus 77 mAN~VDevIA~v~k~---ddK~k~~LPddVI~Ymrd 109 (196)
T PRK15364 77 KSNEMDEVIAKAAKG---DAKTKEEVPEDVIKYMRD 109 (196)
T ss_pred HHHHHHHHHHHHhcC---CCcccccCCHHHHHHHHH
Confidence 566666666555442 233456899999999943
No 30
>KOG1666 consensus V-SNARE [Intracellular trafficking, secretion, and vesicular transport]
Probab=34.03 E-value=3.6e+02 Score=24.39 Aligned_cols=57 Identities=21% Similarity=0.323 Sum_probs=50.9
Q ss_pred ccCChhHHHHHHHHHHHHHHHHHHHhhhhccccCCCchhhHHHHHHHHHHHHHhHHh
Q 028220 28 AADDPKQNLNQVINSVQKTLGLLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVK 84 (212)
Q Consensus 28 ~~~~~~~qL~~~ieSLe~~L~~L~Ql~i~VsdFq~~Sq~~L~qKIn~LV~~L~~L~~ 84 (212)
+.++.++.|..+=.++++.=+.|.||.+-|..-.|+....+..|+.++=+.|.+++.
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 456778888888888888888999999999999999999999999999999998875
No 31
>TIGR02606 antidote_CC2985 putative addiction module antidote protein, CC2985 family. This bacterial protein family has a very similar seed alignment to that of Pfam model pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15.
Probab=33.57 E-value=1.5e+02 Score=21.50 Aligned_cols=54 Identities=11% Similarity=0.247 Sum_probs=42.3
Q ss_pred CCCCchHHHHhhh----cCC--CccHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHhhChhh
Q 028220 90 NIQVPTEVLNLID----DGK--NPDEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQTFPDE 150 (212)
Q Consensus 90 di~IPlEVl~yID----~GR--NPDiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~~FPel 150 (212)
++.+|.+.-.+|+ .|+ |...+-|+-+......++ .++.+|+.+.+.+....|+.
T Consensus 3 ~isL~~~~~~~i~~~V~sG~Y~s~SEVir~aLR~le~~e~-------~~~~Lr~~i~~g~~sg~~~~ 62 (69)
T TIGR02606 3 SVSLGEHLESFIRSQVQSGRYGSASEVVRAALRLLEERET-------KLQALRDAIEEGEQSGEAGR 62 (69)
T ss_pred eeecCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhCCCCCC
Confidence 6778888887764 474 888888988887777763 36789999999998887765
No 32
>PF02106 Fanconi_C: Fanconi anaemia group C protein; InterPro: IPR000686 Fanconi anaemia (FA) [, , ] is a recessive inherited disease characterised by defective DNA repair. FA cells are sensitive to DNA cross-linking agents that cause chromosomal instability and cell death. The disease is manifested clinically by progressive pancytopenia, variable physical anomalies, and predisposition to malignancy. Four complementation groups have been identified, designated A to D. The gene for group C (FACC) has been cloned. Expression of the FACC cDNA corrects the phenotypic defect of FA(C) cells, resulting in normalized cell growth in the presence of DNA cross-linking agents such as mitomycin C (MMC). Gene transfer of the FACC gene should provide a survival advantage to transduced hematopoietic cells, suggesting that FA might be an ideal candidate for gene therapy []. The function of the FACC gene is not known. Immunofluorescence and sub-cellular fractionation studies of human cell lines, and COS-7 cells transiently expressing human FACC, showed the protein to be located primarily in the cytoplasm. Yet, placement of a nuclear localisation signal at the N terminus of FACC directed the hybrid protein to the nuclei of transfected COS-7 cells. Such findings suggest an indirect role for FACC in regulating DNA repair in this group of Fanconi anaemia [].; GO: 0006281 DNA repair
Probab=33.41 E-value=1.6e+02 Score=29.94 Aligned_cols=102 Identities=18% Similarity=0.244 Sum_probs=66.0
Q ss_pred CchHHHHhh--hcCCCcc------HHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHhhChhhHHHHHHHHhcchhh
Q 028220 93 VPTEVLNLI--DDGKNPD------EFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQTFPDEVEAYREIRANSAAV 164 (212)
Q Consensus 93 IPlEVl~yI--D~GRNPD------iYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~~FPel~~~yr~ir~~~~a~ 164 (212)
|=-|+++++ +-..+|. +||+=|+|...++|.+.|=-..+| ||--....-..--..|.+
T Consensus 294 iVdeifr~aLlEtdGa~eV~~~iqvFT~cFveal~~enkQ~kf~Lkay--------------FP~~~~sLv~~Ll~~P~d 359 (559)
T PF02106_consen 294 IVDEIFRNALLETDGAPEVLTAIQVFTRCFVEALEKENKQLKFPLKAY--------------FPYSSPSLVMVLLQHPKD 359 (559)
T ss_pred HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHhccccccchHHHh--------------CCCCchHHHHHHHhChhh
Confidence 444555544 6677775 699999999999998887555544 666555444443344444
Q ss_pred hHHHhhhhhHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 028220 165 SNAILSEAHHVEWMLSI------------CCQFFMFLILYILLSVLYDIRVEQIVKG 209 (212)
Q Consensus 165 ~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 209 (212)
-++-+. -.|..||+.. |.-.|=-..|+|=..--+||-+||.+++
T Consensus 360 lpq~~w-~qhL~~Is~~Lk~~vEd~~~~s~~~~fE~WFL~vhFg~W~diAae~Ll~s 415 (559)
T PF02106_consen 360 LPQEAW-LQHLKHISEMLKEIVEDQTHGSCGGPFESWFLFVHFGGWVDIAAEQLLMS 415 (559)
T ss_pred cChHHH-HHHHHHHHHHHHHHhcccccCCCCChHHHHHHHHHHhhHHHHHHHHHHhc
Confidence 444332 3566777654 3334444556677788899999999875
No 33
>PF09602 PhaP_Bmeg: Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg); InterPro: IPR011728 This entry describes a protein found in polyhydroxyalkanoic acid (PHA) gene regions and incorporated into PHA inclusions in Bacillus cereus and Bacillus megaterium. The role of the protein may include amino acid storage [].
Probab=32.82 E-value=3.3e+02 Score=23.57 Aligned_cols=55 Identities=15% Similarity=0.172 Sum_probs=32.6
Q ss_pred CchhhHHHHHHHHHHHHHhHHhhhhhC---CCCCchHHHHhhhcCCCccHHHHHHHHHHH
Q 028220 63 ASQLPLLQRLNSLVSELDNMVKLSEKC---NIQVPTEVLNLIDDGKNPDEFTRDVINSCI 119 (212)
Q Consensus 63 ~Sq~~L~qKIn~LV~~L~~L~~~a~~~---di~IPlEVl~yID~GRNPDiYTREfVE~~~ 119 (212)
.+...|.+.||++-+.+.++...-+.. ....-.+.+..++.| -+..++.+|+...
T Consensus 78 ~~~~~l~d~inE~t~k~~El~~~i~el~~~~~Ks~~~~l~q~~~~--~eEtv~~~ieqqk 135 (165)
T PF09602_consen 78 ATGNSLNDSINEWTDKLNELSAKIQELLLSPSKSSFSLLSQISKQ--YEETVKQLIEQQK 135 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcchHHHHHHHHHHHHhh--HHHHHHHHHHHHH
Confidence 456678888888888777776544322 223455666666554 3455555555433
No 34
>PHA03250 UL35; Provisional
Probab=32.24 E-value=4.6e+02 Score=26.77 Aligned_cols=126 Identities=16% Similarity=0.350 Sum_probs=87.8
Q ss_pred HHHHHHHHhHHhhhhhCCCCCchHHHHhhhcCCCccHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHh-------
Q 028220 73 NSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGKNPDEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQ------- 145 (212)
Q Consensus 73 n~LV~~L~~L~~~a~~~di~IPlEVl~yID~GRNPDiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~------- 145 (212)
.-+.+.|+.|.+- .+=|+.++.-++..+-|+-.--|.+..+.-.|...+=+ .+++.+|.-+..++..
T Consensus 203 ~lY~~NL~dLt~~-----~~~pl~Llt~~~~s~~~edvlND~~FLLS~~~Mi~~~~-~~L~~LR~wI~~qln~L~e~lYl 276 (564)
T PHA03250 203 ELYAENLADITQR-----NNRPFRLLTVIKRSKDPEDVLNDMMFLLSLRHLQFRHQ-EELQALRKWIVLKLNRLCSDLYF 276 (564)
T ss_pred HHHHHHHHHHhhc-----cCCceeeeeeccCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344555555432 34599999999998888889999999999999888765 4577888888887764
Q ss_pred ---hChhhHHHHHHHHhcchhhhHH-Hhhhhh---HHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHH
Q 028220 146 ---TFPDEVEAYREIRANSAAVSNA-ILSEAH---HVEWMLSICCQF----------FMFLILYILLSVLYDIRVE 204 (212)
Q Consensus 146 ---~FPel~~~yr~ir~~~~a~~~~-~~~~~~---~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~ 204 (212)
.+|++.+.|+++-..-+..-+. .-..++ -..|+...|.++ ||+.-+|.+|.-+||++-.
T Consensus 277 aY~QvPelR~~f~~La~~v~~~~~s~~~d~p~f~p~l~~lf~flr~~~~A~vyvcP~Yvr~a~~~~l~r~~~~~~~ 352 (564)
T PHA03250 277 AYTQVPETRQTFRNLARELHLLRQSRSPEDPAFRPVLANLLQFLRQLHEADVYLCPGYLHFAIFALLLRLYNLRDA 352 (564)
T ss_pred HHhcCcchHHHHHHHHHHHHHHhccCCCCCchhHHHHHHHHHHHHHHHhCCEeeChHHHHHHHHHHHHHhcccccc
Confidence 5799999999887643332111 000122 346777766543 6788888899988887644
No 35
>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=32.07 E-value=15 Score=32.59 Aligned_cols=79 Identities=19% Similarity=0.437 Sum_probs=0.0
Q ss_pred cccccccCChhHH--HHHHHHHHHHHHHHHHH--hhhhccccCCCchhhHHHHHHHHHH-------HHHhHH-----hhh
Q 028220 23 DTTTVAADDPKQN--LNQVINSVQKTLGLLHQ--LYLTVSSFNAASQLPLLQRLNSLVS-------ELDNMV-----KLS 86 (212)
Q Consensus 23 ~~~~~~~~~~~~q--L~~~ieSLe~~L~~L~Q--l~i~VsdFq~~Sq~~L~qKIn~LV~-------~L~~L~-----~~a 86 (212)
||++-|-.+.+++ .+++-+++..+++.+.+ +...+|-|-|+| +-..+..++. -+.+++ +..
T Consensus 5 DTS~fTdp~vr~~fG~~~l~ea~~~~l~Lia~arl~l~is~YmPpS---Vy~El~~fl~~~~~~~e~~~k~~twvv~KsP 81 (205)
T PF08745_consen 5 DTSAFTDPEVREQFGDEDLCEAVEKFLDLIARARLKLGISCYMPPS---VYKELKNFLERNGCDEEVISKLDTWVVKKSP 81 (205)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccc---ccccccccccccccccccccccccccccccc
Confidence 4444455556664 35667777777877776 566778888865 4444444443 122222 333
Q ss_pred hhCCCCCchHHH-HhhhcC
Q 028220 87 EKCNIQVPTEVL-NLIDDG 104 (212)
Q Consensus 87 ~~~di~IPlEVl-~yID~G 104 (212)
...++.||-+++ +||++=
T Consensus 82 ~ryev~IPA~i~yEyI~em 100 (205)
T PF08745_consen 82 DRYEVKIPAEIFYEYIEEM 100 (205)
T ss_dssp -------------------
T ss_pred ccccccccccccccccccc
Confidence 467899999998 788763
No 36
>PRK13740 conjugal transfer protein TraY; Provisional
Probab=32.02 E-value=64 Score=24.30 Aligned_cols=40 Identities=28% Similarity=0.346 Sum_probs=30.9
Q ss_pred cHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHhhChhhHHH
Q 028220 108 DEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQTFPDEVEA 153 (212)
Q Consensus 108 DiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~~FPel~~~ 153 (212)
|--|-+.+..+...+-..|.+--.+ .++|||.. |||....
T Consensus 19 d~etn~lL~~A~~RSGRSK~~EA~l-RL~DHL~r-----FpDfy~s 58 (70)
T PRK13740 19 DEDTNNKLIEAKERSGRSKTNEVQI-RLRDHLKR-----FPDFYNS 58 (70)
T ss_pred CHHHHHHHHHHHHHcCCcccHHHHH-HHHHHHHh-----Cccccch
Confidence 3456677888888888888775555 79999976 9998765
No 37
>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=31.55 E-value=22 Score=28.56 Aligned_cols=18 Identities=17% Similarity=0.407 Sum_probs=15.7
Q ss_pred CCCccHHHHHHHHHHHHH
Q 028220 104 GKNPDEFTRDVINSCIAK 121 (212)
Q Consensus 104 GRNPDiYTREfVE~~~~~ 121 (212)
.+||++||.|++..+.+-
T Consensus 62 ~~nPelWs~e~~~~l~~~ 79 (124)
T PF05430_consen 62 AKNPELWSEELFKKLARL 79 (124)
T ss_dssp TTSGGGSSHHHHHHHHHH
T ss_pred cCCcccCCHHHHHHHHHH
Confidence 699999999999987654
No 38
>PRK14040 oxaloacetate decarboxylase; Provisional
Probab=31.18 E-value=2.2e+02 Score=28.77 Aligned_cols=69 Identities=14% Similarity=0.277 Sum_probs=47.3
Q ss_pred CCchHHHHhhhc--CCCccHHHHHHHHHHHHHhhHhhcc-----HHHHHHHHHHHHHHHHh-----------------hC
Q 028220 92 QVPTEVLNLIDD--GKNPDEFTRDVINSCIAKNQVTKGK-----TDAFKSLRKHLLDELEQ-----------------TF 147 (212)
Q Consensus 92 ~IPlEVl~yID~--GRNPDiYTREfVE~~~~~NQ~~kGK-----i~a~~~fR~~L~eeL~~-----------------~F 147 (212)
.||-||.+|+-- |+=|--+-.+..+++.+..+...++ -..|+++|+.+.+...+ -|
T Consensus 361 ~~~~~v~~~~~G~~G~~p~~~~~~~~~~~l~~~~~~~~rp~~~~~p~~~~~~~~~~~~~~~~~~~~~~e~~e~~l~~~~~ 440 (593)
T PRK14040 361 TITKETAGVLKGEYGATPAPVNAELQARVLEGAEPITCRPADLLAPELDKLEAELRRQAQEKGITLAENAIDDVLTYALF 440 (593)
T ss_pred eCCHHHHHHhCcCCCCCCCCCCHHHHHHHhCCCCCCcCChhhhcCchHHHHHHHHHHHhhhcCCCcccCCHHHHHHHHhc
Confidence 699999999954 7888888888888887544332222 12377788887665522 37
Q ss_pred hhhHHHHHHHHhc
Q 028220 148 PDEVEAYREIRAN 160 (212)
Q Consensus 148 Pel~~~yr~ir~~ 160 (212)
|....+|..-|..
T Consensus 441 p~v~~~f~~~~~~ 453 (593)
T PRK14040 441 PQIGLKFLENRHN 453 (593)
T ss_pred cHHHHHHHHhhcc
Confidence 8888888888864
No 39
>PF03997 VPS28: VPS28 protein; InterPro: IPR007143 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ].; PDB: 2J9W_B 2J9U_C 2G3K_A 2F66_E 2F6M_D 2J9V_A 2CAZ_E 2P22_B.
Probab=31.13 E-value=1.7e+02 Score=25.53 Aligned_cols=29 Identities=17% Similarity=0.125 Sum_probs=21.0
Q ss_pred hhhcCCCccHHHHHHHHHHHHHhhHhhcc
Q 028220 100 LIDDGKNPDEFTRDVINSCIAKNQVTKGK 128 (212)
Q Consensus 100 yID~GRNPDiYTREfVE~~~~~NQ~~kGK 128 (212)
||.+.-+|+-||..|-....+=.-..+.-
T Consensus 18 yikD~It~~eYt~~c~kLl~Qyk~~~~~~ 46 (188)
T PF03997_consen 18 YIKDSITEKEYTTACNKLLNQYKTILKQL 46 (188)
T ss_dssp HHTTSS-HHHHHHHHHHHHHHHHHHHTST
T ss_pred HhhccCCHHHHHHHHHHHHHHHHHHHHHc
Confidence 89999999999999987765544444443
No 40
>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=30.81 E-value=1.8e+02 Score=25.47 Aligned_cols=65 Identities=12% Similarity=0.191 Sum_probs=42.4
Q ss_pred cccCCCchhhHHHHHHHHHHHHHhHHhhhhhCCCCCchHHHHhhhcCCCccH---HHHHHHHHHHHHhhHhh
Q 028220 58 SSFNAASQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGKNPDE---FTRDVINSCIAKNQVTK 126 (212)
Q Consensus 58 sdFq~~Sq~~L~qKIn~LV~~L~~L~~~a~~~di~IPlEVl~yID~GRNPDi---YTREfVE~~~~~NQ~~k 126 (212)
|++-|.+ ..|.+++.+-+..+..-+ .....+||.|++..==-|=+||| +-+=++.++.+......
T Consensus 85 SNl~psn-~~l~~~v~~~~~~~~~~~---~~~~~~vP~dlvtaSgSGLDP~IS~~aA~~Qv~RVA~argl~~ 152 (188)
T PF02669_consen 85 SNLGPSN-PELRERVEERIAALRKEN---PVAPSPVPADLVTASGSGLDPHISPAAALIQVPRVAKARGLSE 152 (188)
T ss_pred ccCCCCC-hHHHHHHHHHHHHHHhhc---ccCCCCCCHHHHhcccccCCCCcCHHHHHHHHHHHHHHhCcCH
Confidence 3444444 347777777666554433 22355899999999889999998 55667777777654433
No 41
>PF01934 DUF86: Protein of unknown function DUF86; InterPro: IPR008201 This entry describes prokaryotic proteins of unknown function.; PDB: 1YLM_A.
Probab=30.28 E-value=2.4e+02 Score=21.21 Aligned_cols=73 Identities=10% Similarity=0.218 Sum_probs=37.8
Q ss_pred hhccccC--CCchhhHHHHHHHHHHHHHhHHhhhhhCCCCCchHHHHhhhcCCCccHHHHHHHHHHHHHh---hHhhccH
Q 028220 55 LTVSSFN--AASQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGKNPDEFTRDVINSCIAKN---QVTKGKT 129 (212)
Q Consensus 55 i~VsdFq--~~Sq~~L~qKIn~LV~~L~~L~~~a~~~di~IPlEVl~yID~GRNPDiYTREfVE~~~~~N---Q~~kGKi 129 (212)
...++|. .--+.++...++.+++.+..+... ++. ....+.|+-| +++.....+ ....-+.
T Consensus 15 ~~~eef~~d~~~~~av~~~l~~~~e~~~di~~~-----------i~~-~~~~~~p~~~---~~~~L~~~~ii~~~~~~~l 79 (119)
T PF01934_consen 15 ISREEFLSDRMLQDAVERNLQLIIEAIIDIAKH-----------IIS-EEGLGKPGSY---IFEILAEHGIISEEPAEPL 79 (119)
T ss_dssp -----TT-SHHHHHHHHHHHHHHHHHHHHHHHH-----------HHH-HTT----SSH---HHHHHHHTTSS-HHHHHHH
T ss_pred ccHHHHhcCHHHHHHHHHHHHHHHHHHhhhHHH-----------HHH-HhCCCCCccH---HHHHHHHcCCccchhHHHH
Confidence 4456665 234667777777777777666543 222 1234555656 566555555 5566666
Q ss_pred HHHHHHHHHHHHH
Q 028220 130 DAFKSLRKHLLDE 142 (212)
Q Consensus 130 ~a~~~fR~~L~ee 142 (212)
..+..||..|...
T Consensus 80 ~~~~g~RN~lvH~ 92 (119)
T PF01934_consen 80 RKMVGFRNRLVHD 92 (119)
T ss_dssp HHHHTTHHHHHT-
T ss_pred HHHHHHHHHHccc
Confidence 6777777766643
No 42
>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=30.16 E-value=1.7e+02 Score=22.25 Aligned_cols=49 Identities=22% Similarity=0.186 Sum_probs=33.7
Q ss_pred chhhHHHHHHHHHHHHHhHHhhhhhCCCCCchHHHHhhhcCC-CccHHHHHHH
Q 028220 64 SQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGK-NPDEFTRDVI 115 (212)
Q Consensus 64 Sq~~L~qKIn~LV~~L~~L~~~a~~~di~IPlEVl~yID~GR-NPDiYTREfV 115 (212)
....+...|.++.... .+..++..+. |+..-|..|++|+ ||.+-|-.-|
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 3445667777776653 4555555444 8999999999995 9988665444
No 43
>KOG4470 consensus Proteasome activator subunit [Posttranslational modification, protein turnover, chaperones]
Probab=30.14 E-value=3.5e+02 Score=24.79 Aligned_cols=93 Identities=18% Similarity=0.249 Sum_probs=54.7
Q ss_pred HhhhcCCCccHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHhhChhhHHHHHHHHhcchhhh-HHHhhhhhHHHH
Q 028220 99 NLIDDGKNPDEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQTFPDEVEAYREIRANSAAVS-NAILSEAHHVEW 177 (212)
Q Consensus 99 ~yID~GRNPDiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~~FPel~~~yr~ir~~~~a~~-~~~~~~~~~~~~ 177 (212)
--||||.|=.+ -.=|.+..+=..++-|++|| .+.|+.-|-+=...+..+-..+--.. +|+.+..+--+|
T Consensus 137 PkIEDGNnFGV---aIQEkvle~v~aV~tk~eaF-------~tqISrYf~~RgklV~K~aK~pHV~DYR~~v~e~DE~ey 206 (246)
T KOG4470|consen 137 PKIEDGNNFGV---AIQEKVLERVNAVKTKVEAF-------QTQISRYFSERGKLVTKAAKYPHVDDYRRLVHELDEKEY 206 (246)
T ss_pred cccccCCccce---eehHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHhHHHHHHhcCccHHHHHHHHhcccHHHH
Confidence 36899999544 44455666666788888877 34556666555555555554444444 556666666666
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028220 178 MLSICCQFFMFLILYILLSVLYDIRVEQ 205 (212)
Q Consensus 178 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 (212)
++--- |-+=+=-..+.||||-...
T Consensus 207 ~~lrl----~v~e~Rn~ya~L~dii~kN 230 (246)
T KOG4470|consen 207 ISLRL----MVLELRNFYATLHDIILKN 230 (246)
T ss_pred HHHHH----HHHHHHHHHHHHHHHHHhh
Confidence 64321 2222223457888886543
No 44
>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=30.00 E-value=87 Score=27.94 Aligned_cols=77 Identities=18% Similarity=0.447 Sum_probs=43.8
Q ss_pred ccccccCChhHHHH--HHHHHHHHHHHHHHH--hhhhccccCCCchhhHHHHHHHHHHH-------HHhHH-----hhhh
Q 028220 24 TTTVAADDPKQNLN--QVINSVQKTLGLLHQ--LYLTVSSFNAASQLPLLQRLNSLVSE-------LDNMV-----KLSE 87 (212)
Q Consensus 24 ~~~~~~~~~~~qL~--~~ieSLe~~L~~L~Q--l~i~VsdFq~~Sq~~L~qKIn~LV~~-------L~~L~-----~~a~ 87 (212)
|++-|-.+.++++. ++-+++.+++..+.+ +...+|-|-|+| +-..+..++.. +.+++ +...
T Consensus 6 TS~fTdp~vr~~fg~~~l~ea~~~~l~Lia~arl~l~iscYmPps---Vy~El~~fl~~~~~~~e~~~kl~twv~~KsP~ 82 (206)
T TIGR03875 6 TSAFTDPELREQLGDEDLCEAVRTFLDLIARARLKLGIECYMPPS---VYKELRRFLERNGCDPETLAKLDTWVVKKSPN 82 (206)
T ss_pred ccccCCHHHHHHcCCCCHHHHHHHHHHHHHHhhhccCceeecCHH---HHHHHHHHHHhcCCCHHHHHhheeEEEEcCCC
Confidence 34434445555443 444566666666655 456677788865 44555444431 22222 2223
Q ss_pred hCCCCCchHHH-Hhhhc
Q 028220 88 KCNIQVPTEVL-NLIDD 103 (212)
Q Consensus 88 ~~di~IPlEVl-~yID~ 103 (212)
.+++.||-+++ +||++
T Consensus 83 rye~~IPA~i~ye~I~e 99 (206)
T TIGR03875 83 RYEVKIPAEIFYEYIEE 99 (206)
T ss_pred eeeeeccHHHHHHHHHH
Confidence 56889999988 67764
No 45
>PRK09282 pyruvate carboxylase subunit B; Validated
Probab=29.62 E-value=2.1e+02 Score=28.88 Aligned_cols=92 Identities=15% Similarity=0.234 Sum_probs=58.9
Q ss_pred cCCCchhhHHHHHHHHHHHHHhHHhhhhhCCCCCchHHHHhhhc--CCCccHHHHHHHHHHHHHhhHhhcc-----HHHH
Q 028220 60 FNAASQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDD--GKNPDEFTRDVINSCIAKNQVTKGK-----TDAF 132 (212)
Q Consensus 60 Fq~~Sq~~L~qKIn~LV~~L~~L~~~a~~~di~IPlEVl~yID~--GRNPDiYTREfVE~~~~~NQ~~kGK-----i~a~ 132 (212)
.+|.||-+=.+-+-.++. ...-..||-||.+|+-- |+=|--|-.+..+++.+..+...++ -..|
T Consensus 337 VTP~Sq~vg~~A~~nv~~---------~~~~~~~~~~~~~~~~G~~G~~p~~~~~~~~~~~l~~~~~~~~rp~~~~~p~~ 407 (592)
T PRK09282 337 VTPTSQIVGTQAVLNVLT---------GERYKVITKEVKDYVKGLYGRPPAPINEELRKKIIGDEEPITCRPADLLEPEL 407 (592)
T ss_pred ECChhHhHHHHHHHHHHc---------CCccccCCHHHHHHhCcCCCCCCCCCCHHHHHHHhCCCCCCcCCcccccCCCH
Confidence 478887554444332221 12244699999999944 7888888888888887654332221 1256
Q ss_pred HHHHHHHHHHHHh---------hChhhHHHHHHHHhc
Q 028220 133 KSLRKHLLDELEQ---------TFPDEVEAYREIRAN 160 (212)
Q Consensus 133 ~~fR~~L~eeL~~---------~FPel~~~yr~ir~~ 160 (212)
.++|+.|.+.... -||+...+|.+-|..
T Consensus 408 ~~~~~~~~~~~~~~~e~~l~~~~~p~~~~~~~~~~~~ 444 (592)
T PRK09282 408 EKARKEAEELGKSEKEDVLTYALFPQIAKKFLEEREA 444 (592)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHhCcHHHHHHHHHHhc
Confidence 7777777665422 388888888888865
No 46
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=29.36 E-value=2.5e+02 Score=21.96 Aligned_cols=54 Identities=19% Similarity=0.237 Sum_probs=37.6
Q ss_pred CCCchHHHH-hhhcCCCccHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHH
Q 028220 91 IQVPTEVLN-LIDDGKNPDEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELE 144 (212)
Q Consensus 91 i~IPlEVl~-yID~GRNPDiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~ 144 (212)
.-+|++-+. +++...+|+.-..+..+....+-+.+..++..+...++.|...+.
T Consensus 56 ~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~ 110 (127)
T TIGR02044 56 VGFSLEECKELLNLWNDPNRTSADVKARTLEKVAEIERKISELQSMRDQLEALAQ 110 (127)
T ss_pred CCCCHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346766664 555444444334555666777888999999999999999987663
No 47
>TIGR00833 actII Transport protein. Characterized members of the RND superfamily all probably catalyze substrate efflux via an H+ antiport mechanism. These proteins are found ubiquitously in bacteria, archaea and eukaryotes. This sub-family includes the S. coelicolor ActII3 protein, which may play a role in drug resistance, and the M. tuberculosis MmpL7 protein, which catalyzes export of an outer membrane lipid, phthiocerol dimycocerosate.
Probab=29.29 E-value=61 Score=33.76 Aligned_cols=10 Identities=10% Similarity=0.494 Sum_probs=6.4
Q ss_pred CCCCCchHHH
Q 028220 89 CNIQVPTEVL 98 (212)
Q Consensus 89 ~di~IPlEVl 98 (212)
.+..||.+.+
T Consensus 657 ~~f~~p~~~~ 666 (910)
T TIGR00833 657 VDFYAPPRIF 666 (910)
T ss_pred CCcccChHHh
Confidence 3566777765
No 48
>cd08789 CARD_IPS-1_RIG-I Caspase activation and recruitment domains (CARDs) found in IPS-1 and RIG-I-like RNA helicases. Caspase activation and recruitment domains (CARDs) found in IPS-1 (Interferon beta promoter stimulator protein 1) and Retinoic acid Inducible Gene I (RIG-I)-like DEAD box helicases. RIG-I-like helicases and IPS-1 play important roles in the induction of interferons in response to viral infection. They are crucial in triggering innate immunity and in developing adaptive immunity against viral pathogens. RIG-I-like 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. MDA5 and RIG-I associate with IPS-1 through a CARD-CAR
Probab=29.00 E-value=74 Score=23.91 Aligned_cols=57 Identities=21% Similarity=0.166 Sum_probs=45.0
Q ss_pred CCchHHHHhhhcCCCccHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHhhChhhHHHHHH
Q 028220 92 QVPTEVLNLIDDGKNPDEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQTFPDEVEAYRE 156 (212)
Q Consensus 92 ~IPlEVl~yID~GRNPDiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~~FPel~~~yr~ 156 (212)
-.|.+|+.|+- .+|.+-.|...++ .-.+|..++-..|=+.|. .=...||.+....+.
T Consensus 18 l~~~~il~~L~------~Lt~~d~e~I~a~-~~~~G~~~aa~~Ll~~L~-r~~~Wf~~Fl~AL~~ 74 (84)
T cd08789 18 IDVEEVLPYLT------CLTAEDKERIQAA-ENNSGNIKAAWTLLDTLV-RRDNWLEPFLDALRE 74 (84)
T ss_pred CcHHHHHhhCC------cCCHHHHHHHHHH-HhcCChHHHHHHHHHHHh-ccCChHHHHHHHHHH
Confidence 58999999987 9999999988887 456799999988888888 445667776665544
No 49
>PLN03229 acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha; Provisional
Probab=28.16 E-value=3.6e+02 Score=28.49 Aligned_cols=45 Identities=18% Similarity=0.358 Sum_probs=34.3
Q ss_pred hhcCCCccHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHhhChhhHHHHHHHHhc
Q 028220 101 IDDGKNPDEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQTFPDEVEAYREIRAN 160 (212)
Q Consensus 101 ID~GRNPDiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~~FPel~~~yr~ir~~ 160 (212)
.+.|+-||.-.++-||+.-. ..|..|++.| .+|++.+.|.+++..
T Consensus 683 aka~~~pd~~~k~kieal~~-------------qik~~~~~a~--~~~~lkek~e~l~~e 727 (762)
T PLN03229 683 AKASKTPDVTEKEKIEALEQ-------------QIKQKIAEAL--NSSELKEKFEELEAE 727 (762)
T ss_pred HhcCCCCCcchHHHHHHHHH-------------HHHHHHHHHh--ccHhHHHHHHHHHHH
Confidence 78899999988877665432 3566677766 578999999999874
No 50
>TIGR03200 dearomat_oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase. Members of this protein family are 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase, a ring-hydrolyzing enzyme in the anaerobic metabolism of aromatic enzymes by way of benzoyl-CoA, as seen in Thauera aromatica, Geobacter metallireducens, and Azoarcus sp. Note that Rhodopseudomonas palustris uses a different pathway to perform a similar degradation of benzoyl-CoA to 3-hydroxpimelyl-CoA.
Probab=28.16 E-value=76 Score=30.29 Aligned_cols=55 Identities=25% Similarity=0.271 Sum_probs=30.6
Q ss_pred CCccHHHHHHHHH-HHHHhhHhhc--cHHHHHH-----------HHHH---HHHHHHhhChhhHH-HHHHHHh
Q 028220 105 KNPDEFTRDVINS-CIAKNQVTKG--KTDAFKS-----------LRKH---LLDELEQTFPDEVE-AYREIRA 159 (212)
Q Consensus 105 RNPDiYTREfVE~-~~~~NQ~~kG--Ki~a~~~-----------fR~~---L~eeL~~~FPel~~-~yr~ir~ 159 (212)
+||+..|-+.++. .+.-+..-+. +..++|. +.+. |..++...||+-.- ....||.
T Consensus 221 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 293 (360)
T TIGR03200 221 ANPLVVTDRYLDEFGRIVHGEFKAGDELKAGKELIKQGTIDLSLLDEAVEALCAKLLNTFPECLTKSIEELRK 293 (360)
T ss_pred cCcccchHHHHHHHhHHhcCCCcchhHHHHHHHHHhcccchHhHHHHHHHHHHHHHHHhchHHHHHHHHHhhh
Confidence 8999999888876 2222222222 3333333 3333 66778888887443 3335554
No 51
>PF10191 COG7: Golgi complex component 7 (COG7); InterPro: IPR019335 The conserved oligomeric Golgi (COG) complex is an eight-subunit (Cog1-8) peripheral Golgi protein involved in membrane trafficking and glycoconjugate synthesis []. COG7 is required for normal Golgi morphology and trafficking. Mutation in COG7 causes a congenital disorder of glycosylation [].
Probab=27.70 E-value=5.6e+02 Score=26.57 Aligned_cols=141 Identities=14% Similarity=0.182 Sum_probs=71.6
Q ss_pred cCChhHHHHHHHHHHHHHHHHHHHhhhhcccc-CCCchhhHHHHHHHHHHHHHhHHhhhhhCCCCCchHHHHhhhcCCCc
Q 028220 29 ADDPKQNLNQVINSVQKTLGLLHQLYLTVSSF-NAASQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGKNP 107 (212)
Q Consensus 29 ~~~~~~qL~~~ieSLe~~L~~L~Ql~i~VsdF-q~~Sq~~L~qKIn~LV~~L~~L~~~a~~~di~IPlEVl~yID~GRNP 107 (212)
-|.++..++..-++|++ -.....+.-.|.++ ....-..+.+||.++=++|.-+.+..+..+...=+|.+
T Consensus 110 ld~vK~rm~~a~~~L~E-A~~w~~l~~~v~~~~~~~d~~~~a~~l~~m~~sL~~l~~~pd~~~r~~~le~l--------- 179 (766)
T PF10191_consen 110 LDSVKSRMEAARETLQE-ADNWSTLSAEVDDLFESGDIAKIADRLAEMQRSLAVLQDVPDYEERRQQLEAL--------- 179 (766)
T ss_pred HHHHHHHHHHHHHHHHH-HHhHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHcCCCchhHHHHHHHHH---------
Confidence 34445555554454443 22233333333332 23333456666666666555554433222222222222
Q ss_pred cHHHHHHHHHHHH---HhhHhhccHHHHHHHHHHHHHHHHhhChhhHHHHHHHHhcchhhhHHHh----hhhhHHHHHHH
Q 028220 108 DEFTRDVINSCIA---KNQVTKGKTDAFKSLRKHLLDELEQTFPDEVEAYREIRANSAAVSNAIL----SEAHHVEWMLS 180 (212)
Q Consensus 108 DiYTREfVE~~~~---~NQ~~kGKi~a~~~fR~~L~eeL~~~FPel~~~yr~ir~~~~a~~~~~~----~~~~~~~~~~~ 180 (212)
++.+|.... -....+..++.-+.|++++.. | .-+|++...|...|..+-...-... +..++.+|+.+
T Consensus 180 ----~nrLEa~vsp~Lv~al~~~~~~~~~~~~~if~~-i-~R~~~l~~~Y~~~r~~~l~~~W~~~~~~~~~~~~~~~L~~ 253 (766)
T PF10191_consen 180 ----KNRLEALVSPQLVQALNSRDVDAAKEYVKIFSS-I-GREPQLEQYYCKCRKAPLQRLWQEYCQSDQSQSFAEWLPS 253 (766)
T ss_pred ----HHHHHHHhhHHHHHHHHhcCHHHHHHHHHHHHH-c-CCHHHHHHHHHHHHHHHHHHHHHHHhhhccchhHHHHHHH
Confidence 233333222 223456677888999988874 4 8899999999999874322221111 11457777766
Q ss_pred HHHHH
Q 028220 181 ICCQF 185 (212)
Q Consensus 181 ~~~~~ 185 (212)
-|..+
T Consensus 254 fyd~l 258 (766)
T PF10191_consen 254 FYDEL 258 (766)
T ss_pred HHHHH
Confidence 55443
No 52
>PF13198 DUF4014: Protein of unknown function (DUF4014)
Probab=27.41 E-value=52 Score=24.88 Aligned_cols=13 Identities=46% Similarity=0.932 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHH
Q 028220 184 QFFMFLILYILLS 196 (212)
Q Consensus 184 ~~~~~~~~~~~~~ 196 (212)
--|+|+|+||++.
T Consensus 16 ~efLF~ilfIvlm 28 (72)
T PF13198_consen 16 TEFLFFILFIVLM 28 (72)
T ss_pred HHHHHHHHHHHHH
Confidence 3478888888765
No 53
>PRK09432 metF 5,10-methylenetetrahydrofolate reductase; Provisional
Probab=26.90 E-value=91 Score=28.39 Aligned_cols=29 Identities=14% Similarity=0.394 Sum_probs=21.7
Q ss_pred HHhHHhhhhhCCCCCchHHHHhhhcCCCc
Q 028220 79 LDNMVKLSEKCNIQVPTEVLNLIDDGKNP 107 (212)
Q Consensus 79 L~~L~~~a~~~di~IPlEVl~yID~GRNP 107 (212)
++++..++..+.+.||.++++.++..++.
T Consensus 217 ~~~~~~~~~~~Gv~vP~~l~~~l~~~~d~ 245 (296)
T PRK09432 217 FKQLKKFADMTNVRIPAWMAKMFDGLDDD 245 (296)
T ss_pred HHHHHHHHHccCCCCCHHHHHHHHhcCCC
Confidence 34455555668899999999999997543
No 54
>PRK13713 conjugal transfer protein TraM; Provisional
Probab=26.65 E-value=1.3e+02 Score=24.66 Aligned_cols=50 Identities=20% Similarity=0.519 Sum_probs=37.3
Q ss_pred hhcCCCccHHHHHHHHHHHHHhhHh-------------hcc-----HHHHHHHHHHHHHHHHhhChhh
Q 028220 101 IDDGKNPDEFTRDVINSCIAKNQVT-------------KGK-----TDAFKSLRKHLLDELEQTFPDE 150 (212)
Q Consensus 101 ID~GRNPDiYTREfVE~~~~~NQ~~-------------kGK-----i~a~~~fR~~L~eeL~~~FPel 150 (212)
=|.|-|-+.|.|-.+|.|.+.+..+ .|+ -.....+|+-..++|..=||+.
T Consensus 50 kes~Fnq~eFnK~lLE~v~kt~~~~~~IL~~~~lsp~v~~~~~~ey~~mv~~I~~~v~e~m~~FFpe~ 117 (118)
T PRK13713 50 KESGFNQTEFNKLLLECVVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSEEMERFFPEN 117 (118)
T ss_pred hcCcccHHHHHHHHHHHHHHHHHHHHHHHccccccHhhcCCCcccHHHHHHHHHHHHHHHHHhcCCCC
Confidence 3678999999999999999885543 222 2345677888888888888873
No 55
>KOG3547 consensus Bestrophin (Best vitelliform macular dystrophy-associated protein) [General function prediction only]
Probab=26.59 E-value=69 Score=31.49 Aligned_cols=23 Identities=35% Similarity=0.762 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 028220 179 LSICCQFFMFLILYILLSVLYDI 201 (212)
Q Consensus 179 ~~~~~~~~~~~~~~~~~~~~~~~ 201 (212)
..+|+.+++||++|.++++.|-.
T Consensus 30 Kai~~el~~~l~~Y~~i~~iYR~ 52 (450)
T KOG3547|consen 30 KAIWKELLIWLILYYIISVIYRF 52 (450)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 56899999999999999999964
No 56
>PF01031 Dynamin_M: Dynamin central region; InterPro: IPR000375 Dynamin is a microtubule-associated force-producing protein of 100 Kd which is involved in the production of microtubule bundles. At the N terminus of dynamin is a GTPase domain (see IPR001401 from INTERPRO), and at the C terminus is a PH domain (see IPR001849 from INTERPRO). Between these two domains lies a central region of unknown function, which this entry represents.; GO: 0005525 GTP binding; PDB: 3ZVR_A 2AKA_B 2X2F_D 2X2E_D 3SNH_A 3ZYS_D 3ZYC_D 1JWY_B 1JX2_B 3SZR_A ....
Probab=26.17 E-value=1.5e+02 Score=26.31 Aligned_cols=62 Identities=13% Similarity=0.212 Sum_probs=42.2
Q ss_pred hhccHHHHHHHHHHHHHHHHhhChhhHHHHHHHHhcchhhhHHHhhh-----hhHHHHHHHHHHHHH
Q 028220 125 TKGKTDAFKSLRKHLLDELEQTFPDEVEAYREIRANSAAVSNAILSE-----AHHVEWMLSICCQFF 186 (212)
Q Consensus 125 ~kGKi~a~~~fR~~L~eeL~~~FPel~~~yr~ir~~~~a~~~~~~~~-----~~~~~~~~~~~~~~~ 186 (212)
..|--.=-+++-..|.+++.+.+|++....+......-.+-+++-.. .+-..++.+++..|.
T Consensus 56 ~~G~~~L~~~L~~~L~~~I~~~LP~l~~~I~~~l~~~~~eL~~lG~~~~~~~~~~~~~l~~~~~~f~ 122 (295)
T PF01031_consen 56 RCGTPALRKRLSELLVEHIRKSLPSLKSEIQKKLQEAEKELKRLGPPRPETPEEQRAYLLQIISKFS 122 (295)
T ss_dssp GSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHCSSSCHHHHHHHHHHHHHHHH
T ss_pred ccchHHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHH
Confidence 44553344678889999999999999999998877766666555332 233445666555543
No 57
>KOG3990 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.15 E-value=3.8e+02 Score=25.10 Aligned_cols=51 Identities=22% Similarity=0.085 Sum_probs=26.1
Q ss_pred CCCCCccCCCCcccccccCChhHHHHHHHHHHHHHHHHHHH----hhhhccccCC
Q 028220 12 GGNGMVSNQANDTTTVAADDPKQNLNQVINSVQKTLGLLHQ----LYLTVSSFNA 62 (212)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~qL~~~ieSLe~~L~~L~Q----l~i~VsdFq~ 62 (212)
|+||...+..-|.-..---..-++|++-|.+|++.|-.=+| -.-.+++..+
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 45664433322322211122457889989988886543333 2344555544
No 58
>PF15168 TRIQK: Triple QxxK/R motif-containing protein family
Probab=26.05 E-value=3.1e+02 Score=21.12 Aligned_cols=21 Identities=14% Similarity=0.090 Sum_probs=17.7
Q ss_pred cchhhhHHHhhhhhHHHHHHH
Q 028220 160 NSAAVSNAILSEAHHVEWMLS 180 (212)
Q Consensus 160 ~~~a~~~~~~~~~~~~~~~~~ 180 (212)
...||+|+.+---.-|.||..
T Consensus 36 k~kAeaKKta~gikev~l~l~ 56 (79)
T PF15168_consen 36 KLKAEAKKTAIGIKEVALVLA 56 (79)
T ss_pred HHHHHHHhhhhhhHHHHHHHH
Confidence 467899999998899999964
No 59
>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=25.35 E-value=96 Score=25.98 Aligned_cols=30 Identities=13% Similarity=0.183 Sum_probs=24.5
Q ss_pred HHHHhhhhccccCCCchhhHHHHHHHHHHH
Q 028220 49 LLHQLYLTVSSFNAASQLPLLQRLNSLVSE 78 (212)
Q Consensus 49 ~L~Ql~i~VsdFq~~Sq~~L~qKIn~LV~~ 78 (212)
...++++.+.-||.++.+.|.++|++-...
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 456789999999999999999999886543
No 60
>PF05004 IFRD: Interferon-related developmental regulator (IFRD); InterPro: IPR007701 Interferon-related developmental regulator (IFRD1) is the human homologue of the Rattus norvegicus early response protein PC4 and its murine homologue TIS7 []. The exact function of IFRD1 is unknown but it has been shown that PC4 is necessary for muscle differentiation and that it might have a role in signal transduction. This entry also contains IFRD2 and its murine equivalent SKMc15, which are highly expressed soon after gastrulation and in the hepatic primordium, suggesting an involvement in early hematopoiesis [].
Probab=25.18 E-value=2.3e+02 Score=25.93 Aligned_cols=62 Identities=13% Similarity=0.205 Sum_probs=42.9
Q ss_pred hcCCCccHHH--HHHHHHHHHHhhHhhccHHHHHHHHHHHHH-----HHHhhChhhHHHHHH-HHhcchhhh
Q 028220 102 DDGKNPDEFT--RDVINSCIAKNQVTKGKTDAFKSLRKHLLD-----ELEQTFPDEVEAYRE-IRANSAAVS 165 (212)
Q Consensus 102 D~GRNPDiYT--REfVE~~~~~NQ~~kGKi~a~~~fR~~L~e-----eL~~~FPel~~~yr~-ir~~~~a~~ 165 (212)
|++.+=+++. +++|+....++ .+++..+++.+.+.|.. .+...+..+.+.... +|+.+.-|.
T Consensus 34 e~~~~~~~e~~L~~~Id~l~eK~--~~~Re~aL~~l~~~l~~~~~~d~v~~~~~tL~~~~~k~lkkg~~~E~ 103 (309)
T PF05004_consen 34 EESSQEDLEDKLKEAIDLLTEKS--SSTREAALEALIRALSSRYLPDFVEDRRETLLDALLKSLKKGKSEEQ 103 (309)
T ss_pred cccchhHHHHHHHHHHHHHHhcC--HHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHhccCCHHHH
Confidence 4556666664 67888877766 88999999999999865 455556666666654 666655343
No 61
>COG1344 FlgL Flagellin and related hook-associated proteins [Cell motility and secretion]
Probab=24.95 E-value=1.4e+02 Score=27.49 Aligned_cols=50 Identities=18% Similarity=0.404 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHHHhhhhccc--cCCCchhhHHHHHHHHHHHHHhHHhhh
Q 028220 37 NQVINSVQKTLGLLHQLYLTVSS--FNAASQLPLLQRLNSLVSELDNMVKLS 86 (212)
Q Consensus 37 ~~~ieSLe~~L~~L~Ql~i~Vsd--Fq~~Sq~~L~qKIn~LV~~L~~L~~~a 86 (212)
+.-++++.++|+.++++-+...+ +.+..+..+...|+.|.++|.++-..+
T Consensus 77 e~aL~~~~~~lqrirelavqaan~t~s~~dr~~iq~Ei~~l~~el~~iantt 128 (360)
T COG1344 77 EGALSEISKILQRIKELAVQAANGTLSDADRAAIQKEIEQLLDELDNIANTT 128 (360)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 34455666677788898888886 778888999999999999999998766
No 62
>MTH00169 ATP8 ATP synthase F0 subunit 8; Provisional
Probab=24.78 E-value=2.3e+02 Score=20.77 Aligned_cols=34 Identities=15% Similarity=0.296 Sum_probs=22.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028220 173 HHVEWMLSICCQFFMFLILYILLSVLYDIRVEQI 206 (212)
Q Consensus 173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 206 (212)
+..-|++|.-.-+..|.++|+++|...=-|+..+
T Consensus 5 d~~~f~sQ~~Wl~i~f~~ly~l~s~~iLPri~~~ 38 (67)
T MTH00169 5 DSVTYLTQYIWTLIILFFLFSLLVNYILPKIQQQ 38 (67)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445888887777788888888776444444443
No 63
>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=24.47 E-value=2.3e+02 Score=23.79 Aligned_cols=52 Identities=19% Similarity=0.258 Sum_probs=29.3
Q ss_pred ccCChhHHHHHHHHHHHHHHHHHHHhhhhc----c--ccCCC----chhhHHHHHHHHHHHH
Q 028220 28 AADDPKQNLNQVINSVQKTLGLLHQLYLTV----S--SFNAA----SQLPLLQRLNSLVSEL 79 (212)
Q Consensus 28 ~~~~~~~qL~~~ieSLe~~L~~L~Ql~i~V----s--dFq~~----Sq~~L~qKIn~LV~~L 79 (212)
+.++..++|+.--++|.+.++.++|--.-+ . .|.++ ....|.+++..+.+.|
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 356778899998999999999888722222 1 23332 2336666666666655
No 64
>TIGR03764 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein. Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.
Probab=23.90 E-value=2.4e+02 Score=25.89 Aligned_cols=36 Identities=11% Similarity=0.201 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHhhCh
Q 028220 110 FTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQTFP 148 (212)
Q Consensus 110 YTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~~FP 148 (212)
|.-=|-+.|.+=| .+-.=.++.|||.|..+|.++.|
T Consensus 210 f~~~f~~~~~~~d---~~~~~~~~~~~deli~~~~~~l~ 245 (258)
T TIGR03764 210 FEEVFQEVLARFD---DPEEFSLERFRDELIGEMAKALG 245 (258)
T ss_pred HHHHHHHHHHhcC---CcccCCHHHHHHHHHHHHHHHcC
Confidence 4444555555544 33444678999999999999998
No 65
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=23.65 E-value=3.5e+02 Score=21.26 Aligned_cols=54 Identities=13% Similarity=0.160 Sum_probs=38.3
Q ss_pred CCCchHHHH-hhhcCCCccHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHH
Q 028220 91 IQVPTEVLN-LIDDGKNPDEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELE 144 (212)
Q Consensus 91 i~IPlEVl~-yID~GRNPDiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~ 144 (212)
.-+|++-|. +++...+|+.-..+..+.....-+.+..++..++..++.|...+.
T Consensus 56 lG~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~ 110 (127)
T TIGR02047 56 LDMSLAEIRQLLRYQDKPEKSCSDVNALLDEHISHVRARIIKLQALIEQLVDLRG 110 (127)
T ss_pred cCCCHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346776664 455444555444566667788889999999999999999887553
No 66
>PLN03094 Substrate binding subunit of ER-derived-lipid transporter; Provisional
Probab=23.59 E-value=1.4e+02 Score=28.57 Aligned_cols=49 Identities=14% Similarity=0.189 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHhhhhcccc-----CCCchhhHHHHHHHHHHHHHhHHhhh
Q 028220 38 QVINSVQKTLGLLHQLYLTVSSF-----NAASQLPLLQRLNSLVSELDNMVKLS 86 (212)
Q Consensus 38 ~~ieSLe~~L~~L~Ql~i~VsdF-----q~~Sq~~L~qKIn~LV~~L~~L~~~a 86 (212)
+++..++.+...|.+-.-.+..| +|.....|.+-+.++...+.++++..
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 44444444444444433222222 23344455555555555555555544
No 67
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=23.39 E-value=1.6e+02 Score=24.81 Aligned_cols=54 Identities=20% Similarity=0.453 Sum_probs=45.6
Q ss_pred hCCCCCchHHHHhhhcCCCccHHHHHHHHHHHHHhhHh-hccHHH--HHHHHHHHHHHHHhhC
Q 028220 88 KCNIQVPTEVLNLIDDGKNPDEFTRDVINSCIAKNQVT-KGKTDA--FKSLRKHLLDELEQTF 147 (212)
Q Consensus 88 ~~di~IPlEVl~yID~GRNPDiYTREfVE~~~~~NQ~~-kGKi~a--~~~fR~~L~eeL~~~F 147 (212)
.+.-+||++++++- ..||.+.++-++--|..+ +|.+.. .+..|=.|+.++...|
T Consensus 31 ~ye~~VplQLl~FA------hRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~v~~~F 87 (145)
T COG5094 31 EYEPKVPLQLLEFA------HRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATKVGRHF 87 (145)
T ss_pred hhCccchHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHHhcCCc
Confidence 35668999999985 579999999999999998 777765 5788889999988888
No 68
>PRK09174 F0F1 ATP synthase subunit B'; Validated
Probab=22.90 E-value=1.3e+02 Score=26.12 Aligned_cols=34 Identities=15% Similarity=0.260 Sum_probs=20.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028220 173 HHVEWMLSICCQFFMFLILYILLSVLYDIRVEQI 206 (212)
Q Consensus 173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 206 (212)
++.-|-.+.--++..|+|||++|+-+.=-++..+
T Consensus 48 ~~~~~~~~l~w~~I~FliL~~lL~k~~~~pI~~v 81 (204)
T PRK09174 48 DSTHYASQLLWLAITFGLFYLFMSRVILPRIGGI 81 (204)
T ss_pred cchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555666666778888888865432244433
No 69
>PF07739 TipAS: TipAS antibiotic-recognition domain; InterPro: IPR012925 TipAL is a bacterial transcriptional regulator of the MerR family. The tipA gene can be expressed as a long form, TipAL, and a short form, TipAS, which constitutes the C-terminal part of TipAL. TipAS forms the antibiotic-recognition domain []. This domain, which has an alpha-helical globin-like fold, is also found at the C terminus of other MerR family transcription factors, including Mta, a central regulator of multidrug resistance in Bacillus subtilis [], and SkgA from Caulobacter crescentus []. ; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1NY9_A 3HH0_A 3QAO_A.
Probab=22.77 E-value=85 Score=23.41 Aligned_cols=45 Identities=7% Similarity=0.069 Sum_probs=23.1
Q ss_pred HHHHHHhhChhhHHHHHHHHhc--chhhhHHHhhhhhHHHHHHHHHH
Q 028220 139 LLDELEQTFPDEVEAYREIRAN--SAAVSNAILSEAHHVEWMLSICC 183 (212)
Q Consensus 139 L~eeL~~~FPel~~~yr~ir~~--~~a~~~~~~~~~~~~~~~~~~~~ 183 (212)
-..++.+++.++....+..... +|.-..-..-...|.+|++..+.
T Consensus 29 ~~~~~~~~~~~l~~~l~~~~~~g~~p~s~evq~l~~~~~~~~~~~~~ 75 (118)
T PF07739_consen 29 EWQELQKEWDELFAELAALMEEGVDPDSPEVQELAERWMELINQFTG 75 (118)
T ss_dssp ----TTHHHHHHHHHHHHHHHHT--TT-HHHHHHHHHHHHHHHHSS-
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHhC
Confidence 3445556667777777766655 44444444445567777765443
No 70
>PF14202 TnpW: Transposon-encoded protein TnpW
Probab=22.59 E-value=67 Score=20.94 Aligned_cols=21 Identities=14% Similarity=0.343 Sum_probs=18.1
Q ss_pred ccccCCCchhhHHHHHHHHHH
Q 028220 57 VSSFNAASQLPLLQRLNSLVS 77 (212)
Q Consensus 57 VsdFq~~Sq~~L~qKIn~LV~ 77 (212)
-..|++.+.+.+.+||..|+.
T Consensus 15 ~~~F~~~s~et~~DKi~rli~ 35 (37)
T PF14202_consen 15 EVHFSETSKETMQDKIKRLIR 35 (37)
T ss_pred EEEECCCccccHHHHHHHHHh
Confidence 356889999999999999985
No 71
>PRK05255 hypothetical protein; Provisional
Probab=22.36 E-value=4.9e+02 Score=22.38 Aligned_cols=40 Identities=20% Similarity=0.395 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHhhHhhccHHHHHHHHHHHHH-------HHHhhChhh
Q 028220 111 TRDVINSCIAKNQVTKGKTDAFKSLRKHLLD-------ELEQTFPDE 150 (212)
Q Consensus 111 TREfVE~~~~~NQ~~kGKi~a~~~fR~~L~e-------eL~~~FPel 150 (212)
-+..++.....++....+.+.++..|+.|.+ ++-+.||+.
T Consensus 88 I~~al~~~~~~~~~~~~~~h~lE~wRdrLi~~~d~al~e~~~~~P~~ 134 (171)
T PRK05255 88 IRAALDKLKNKHNQETARFHKLERWRDRLLAEGDDALTEFLEEYPDA 134 (171)
T ss_pred HHHHHHHHhchhHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHCchh
Confidence 5677888888889999999999999999988 466777754
No 72
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=22.34 E-value=3.4e+02 Score=20.37 Aligned_cols=36 Identities=11% Similarity=0.273 Sum_probs=25.4
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHhhhhccccCCCchh
Q 028220 31 DPKQNLNQVINSVQKTLGLLHQLYLTVSSFNAASQL 66 (212)
Q Consensus 31 ~~~~qL~~~ieSLe~~L~~L~Ql~i~VsdFq~~Sq~ 66 (212)
..++|++..|+.|.+-|.-+..=-+..++|+...-+
T Consensus 4 ~s~ENv~~MIe~Ik~KL~mvN~~~i~~~~f~~~~ye 39 (71)
T PF06569_consen 4 PSQENVEYMIEEIKQKLNMVNAGAIKPEDFSEEKYE 39 (71)
T ss_pred ccHHHHHHHHHHHHHHHHHhhHHhCCHHhCChhhHH
Confidence 457788899998887776666666667777765433
No 73
>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=21.80 E-value=2.9e+02 Score=21.35 Aligned_cols=53 Identities=23% Similarity=0.389 Sum_probs=33.9
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHhhhhccc------cCC------------CchhhHHHHHHHHHHHHHhH
Q 028220 30 DDPKQNLNQVINSVQKTLGLLHQLYLTVSS------FNA------------ASQLPLLQRLNSLVSELDNM 82 (212)
Q Consensus 30 ~~~~~qL~~~ieSLe~~L~~L~Ql~i~Vsd------Fq~------------~Sq~~L~qKIn~LV~~L~~L 82 (212)
+.-+.||.+-|+.+-+-|..+.|+.--... |.. -.++.+++|+|++|.++-.+
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 345678888787777777766665432111 110 15778999999999887543
No 74
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=21.66 E-value=4.5e+02 Score=21.50 Aligned_cols=84 Identities=15% Similarity=0.322 Sum_probs=56.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhhhccccCCCchhhHHHHHHHHHHHHHhHHhhhhhCCCCCchHHHHhhhcCCCccHHH
Q 028220 32 PKQNLNQVINSVQKTLGLLHQLYLTVSSFNAASQLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGKNPDEFT 111 (212)
Q Consensus 32 ~~~qL~~~ieSLe~~L~~L~Ql~i~VsdFq~~Sq~~L~qKIn~LV~~L~~L~~~a~~~di~IPlEVl~yID~GRNPDiYT 111 (212)
.+-+|.+-..++-+-|+.+.+ .+ .....-|.+||+.+-..|++..+.... |
T Consensus 37 Trr~m~~A~~~v~kql~~vs~---~l----~~tKkhLsqRId~vd~klDe~~ei~~~----------------------i 87 (126)
T PF07889_consen 37 TRRSMSDAVASVSKQLEQVSE---SL----SSTKKHLSQRIDRVDDKLDEQKEISKQ----------------------I 87 (126)
T ss_pred HHHhHHHHHHHHHHHHHHHHH---HH----HHHHHHHHHHHHHHHhhHHHHHHHHHH----------------------H
Confidence 355666666665554444443 11 235667999999999999988876543 5
Q ss_pred HHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHH
Q 028220 112 RDVINSCIAKNQVTKGKTDAFKSLRKHLLDELE 144 (212)
Q Consensus 112 REfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~ 144 (212)
++-|..++.+=...+++++.+...=.-|..+|.
T Consensus 88 ~~eV~~v~~dv~~i~~dv~~v~~~V~~Le~ki~ 120 (126)
T PF07889_consen 88 KDEVTEVREDVSQIGDDVDSVQQMVEGLEGKID 120 (126)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666677777777778888877777777766664
No 75
>PRK07502 cyclohexadienyl dehydrogenase; Validated
Probab=21.42 E-value=1.9e+02 Score=25.54 Aligned_cols=56 Identities=14% Similarity=0.109 Sum_probs=37.1
Q ss_pred CCCccHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHhhChhhHHHHHHHHh
Q 028220 104 GKNPDEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQTFPDEVEAYREIRA 159 (212)
Q Consensus 104 GRNPDiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~~FPel~~~yr~ir~ 159 (212)
+-||++|+-=|+...-.--+..+.-++.++.||+.|..+=.+++-+..+.-++.|.
T Consensus 231 ~~~~~~w~~i~~~N~~~~~~~l~~~~~~l~~~~~~l~~~d~~~l~~~~~~~~~~r~ 286 (307)
T PRK07502 231 ASDPTMWRDVFLHNKDAVLEMLGRFTEDLAALQRAIRWGDGDALFDLFTRTRAIRR 286 (307)
T ss_pred cCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 47999998877765444446677788888888888875444444444444444443
No 76
>PRK13454 F0F1 ATP synthase subunit B'; Provisional
Probab=21.27 E-value=1.7e+02 Score=24.65 Aligned_cols=34 Identities=12% Similarity=0.319 Sum_probs=19.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHh
Q 028220 173 HHVEWMLSICCQFFMFLILYILLSVL-YDIRVEQIV 207 (212)
Q Consensus 173 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~ 207 (212)
+..-|.++.-.++.-|+|||++|+-+ |. +|..++
T Consensus 26 d~~t~~~q~~~~lI~F~iL~~ll~k~l~~-PI~~~l 60 (181)
T PRK13454 26 DFSTFPNQIFWLLVTLVAIYFVLTRVALP-RIGAVL 60 (181)
T ss_pred cHHhcchHHHHHHHHHHHHHHHHHHHHHH-HHHHHH
Confidence 33344455555566678888777543 44 444443
No 77
>PF03682 UPF0158: Uncharacterised protein family (UPF0158); InterPro: IPR005361 This is a small family of hypothetical bacterial proteins of unknown function.
Probab=21.26 E-value=2.5e+02 Score=23.55 Aligned_cols=47 Identities=23% Similarity=0.554 Sum_probs=30.1
Q ss_pred hhhc-CCCccHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHhhChhhHHHHHHHHhc
Q 028220 100 LIDD-GKNPDEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQTFPDEVEAYREIRAN 160 (212)
Q Consensus 100 yID~-GRNPDiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~~FPel~~~yr~ir~~ 160 (212)
+|+. =+||++ |+.+..+.+ || .||+.||+.|. .+|++.+.+-+.|..
T Consensus 77 Fv~~~v~d~~l--~~~L~~ai~------gr-gafrrFKd~L~-----~~~~~~e~Wy~F~~~ 124 (163)
T PF03682_consen 77 FVEEKVEDPDL--RERLLRAIQ------GR-GAFRRFKDILS-----EYPELRERWYAFREE 124 (163)
T ss_pred HHHHhCCCHHH--HHHHHHHHh------CC-cHHHHHHHHHH-----HCHHHHHHHHHHHHH
Confidence 4444 355543 555665553 43 28999999885 478887777777653
No 78
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=21.06 E-value=67 Score=26.32 Aligned_cols=16 Identities=31% Similarity=0.518 Sum_probs=11.9
Q ss_pred hcCCCccHHHHHHHHH
Q 028220 102 DDGKNPDEFTRDVINS 117 (212)
Q Consensus 102 D~GRNPDiYTREfVE~ 117 (212)
-+-+=|||||||-|-.
T Consensus 37 ~ETHYPDIYTREEiA~ 52 (125)
T KOG0484|consen 37 AETHYPDIYTREEIAL 52 (125)
T ss_pred HhhcCCcchhHHHHHH
Confidence 3456799999997643
No 79
>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=21.01 E-value=3.6e+02 Score=20.10 Aligned_cols=54 Identities=20% Similarity=0.430 Sum_probs=32.7
Q ss_pred ccccccCChhHHHHHHHHHHHHHHHHHHHhhhhcccc-------CC----CchhhHHHHHHHHHHHHH
Q 028220 24 TTTVAADDPKQNLNQVINSVQKTLGLLHQLYLTVSSF-------NA----ASQLPLLQRLNSLVSELD 80 (212)
Q Consensus 24 ~~~~~~~~~~~qL~~~ieSLe~~L~~L~Ql~i~VsdF-------q~----~Sq~~L~qKIn~LV~~L~ 80 (212)
++......+...|..+|..|+.=++ ++...-..+ ++ .....|...|..||..|.
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 4445667788888888888776433 333222222 23 234677888888877664
No 80
>PF09119 SicP-binding: SicP binding; InterPro: IPR015203 Members of this family bind the chaperone SicP, which is required both to maintain the stability of SptP, as well as to ensure the eventual secretion of the protein. The domain is found in the Salmonella effector protein SptP, which interacts with SicP chaperone dimers mainly through four regions of its chaperone-binding domain. The structure of the SptP-SicP complex contains four molecules of SicP, aligned in a linear fashion and arranged in two sets of tightly bound homodimers that bind two SptP molecules. The SicP homodimers do not interact with each other, but are held together by a molecular interface formed between two SptP molecules. Each SptP molecule is wrapped around by three SicP chaperones (two chaperones from one homodimer and a third one from the opposite homodimer pair) []. ; GO: 0005615 extracellular space; PDB: 1JYO_F.
Probab=20.83 E-value=36 Score=26.22 Aligned_cols=52 Identities=12% Similarity=0.180 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHhhChhhHHHHHHHHhcchhhhHHH
Q 028220 111 TRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQTFPDEVEAYREIRANSAAVSNAI 168 (212)
Q Consensus 111 TREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~~FPel~~~yr~ir~~~~a~~~~~ 168 (212)
.++++|....+||++ +.-|-..|.++-+++|-.-.-.+-++++.+|.-+++.
T Consensus 25 Vq~~~e~~~~~nqkt------L~vFl~ALa~~YGe~~a~~~~~~~~ls~~tPLt~r~i 76 (81)
T PF09119_consen 25 VQKYVENQRVENQKT------LQVFLEALAERYGEETANKVLDKMDLSGGTPLTQRRI 76 (81)
T ss_dssp HHHHHHCS--S-HHH------HHHHHHHHHHTTSCHHHHHHHHHHHH-----GGGS-E
T ss_pred HHHHHHHHhHHHHHH------HHHHHHHHHHHHhHHHHHHHHHHhccCCCCCccHHHH
Confidence 467888888888875 4468888888888888888888888999999887765
No 81
>KOG3284 consensus Vacuolar sorting protein VPS28 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.59 E-value=5.5e+02 Score=23.05 Aligned_cols=56 Identities=18% Similarity=0.239 Sum_probs=38.8
Q ss_pred hhhcCCCccHHHHHHHHHHHHHhhHhhccHHHHHHHHHHHHHHHHhhChhhHHHHHHHHhcchhhhHHHh
Q 028220 100 LIDDGKNPDEFTRDVINSCIAKNQVTKGKTDAFKSLRKHLLDELEQTFPDEVEAYREIRANSAAVSNAIL 169 (212)
Q Consensus 100 yID~GRNPDiYTREfVE~~~~~NQ~~kGKi~a~~~fR~~L~eeL~~~FPel~~~yr~ir~~~~a~~~~~~ 169 (212)
|+.|.--|..||-+|-... ..|+-.+...=.++||...+--+..|=+.||.-+|+-
T Consensus 44 yirD~is~sey~s~c~kLi--------------~Q~k~~~~~~~~~~f~SiE~Fc~kyrl~cp~Ai~Ri~ 99 (213)
T KOG3284|consen 44 YIRDCISPSEYTSECSKLI--------------VQYKVAFRSVQGTEFPSIEDFCKKYRLDCPAAIERIR 99 (213)
T ss_pred HHHccCCHHHHHHHHHHHH--------------HHHHHHHHHhcccccCcHHHHHHHHccCChHHHHHHH
Confidence 8888999999999986543 2344444444445788877777777777766666654
No 82
>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=20.43 E-value=3.7e+02 Score=23.58 Aligned_cols=64 Identities=14% Similarity=0.210 Sum_probs=43.4
Q ss_pred hhhHHHHHHHHHHHHHhHHhhhhhCCCCCchHHHHhhhcCCCccH---HHHHHHHHHHHHhhHhhccHHH
Q 028220 65 QLPLLQRLNSLVSELDNMVKLSEKCNIQVPTEVLNLIDDGKNPDE---FTRDVINSCIAKNQVTKGKTDA 131 (212)
Q Consensus 65 q~~L~qKIn~LV~~L~~L~~~a~~~di~IPlEVl~yID~GRNPDi---YTREfVE~~~~~NQ~~kGKi~a 131 (212)
-..|.+++.+-+..+..-+. ...-+||.|++..==-|=+||| +-+-++.++.+.......++..
T Consensus 90 np~l~~~v~~r~~~~~~~~~---~~~~~vP~DlvTaSgSGLDPhISp~aA~~Qv~RVA~argl~~~~v~~ 156 (187)
T TIGR00681 90 NPDLLSRIAARVEAQRLENL---DAAVQVPVDLVTSSGSGLDPHISPAAAQAQFPRVAKARNISPQQLQS 156 (187)
T ss_pred CHHHHHHHHHHHHHHHHhCC---CCCCCCCHHHHhcccccCCCCCCHHHHHHHHHHHHHHhCcCHHHHHH
Confidence 34577777776666544321 1235899999999889999998 5566777777776665555443
No 83
>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=20.04 E-value=1.3e+02 Score=22.74 Aligned_cols=49 Identities=12% Similarity=0.094 Sum_probs=30.5
Q ss_pred CCCcccCCCC-----CccCCCCcccccccCChhHHHHHHHHHHHHHHHHHHHhhhh
Q 028220 6 GGSRASGGNG-----MVSNQANDTTTVAADDPKQNLNQVINSVQKTLGLLHQLYLT 56 (212)
Q Consensus 6 ~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~qL~~~ieSLe~~L~~L~Ql~i~ 56 (212)
...+|+| |- -....++|.+. +.+=.+.+++.+.+++.+++....+.+..
T Consensus 34 ~~iaGiG-Niy~~EiLf~a~i~P~~~-~~~L~~~~~~~l~~~~~~vl~~ai~~gg~ 87 (92)
T PF06831_consen 34 SVIAGIG-NIYADEILFRAGIHPERP-ASSLSEEELRRLHEAIKRVLREAIEVGGT 87 (92)
T ss_dssp TTSTT---HHHHHHHHHHTTB-TTSB-GGGSHHHHHHHHHHHHHHHHHHHHHTT-B
T ss_pred CccccCc-HHHHHHHHHHcCCCccCc-cccCCHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 4456666 54 12345565554 66777888999999999988877776543
Done!