Query 022787
Match_columns 292
No_of_seqs 125 out of 519
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 06:08:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022787.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022787hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1860 Nuclear protein export 100.0 2.8E-51 6.1E-56 407.6 23.4 243 5-258 157-422 (927)
2 COG5079 SAC3 Nuclear protein e 100.0 2.8E-50 6.1E-55 377.8 22.6 241 5-259 125-384 (646)
3 PF03399 SAC3_GANP: SAC3/GANP/ 100.0 4.2E-50 9.2E-55 350.3 22.0 201 5-235 2-204 (204)
4 KOG1861 Leucine permease trans 100.0 5.3E-49 1.1E-53 366.9 20.3 227 3-265 292-519 (540)
5 PF10075 PCI_Csn8: COP9 signal 99.3 3.4E-11 7.3E-16 99.6 10.7 129 125-261 3-133 (143)
6 KOG3151 26S proteasome regulat 98.4 3.1E-05 6.7E-10 68.2 16.9 166 62-252 54-222 (260)
7 KOG4414 COP9 signalosome, subu 98.2 1.3E-05 2.8E-10 65.6 8.9 106 149-260 60-167 (197)
8 PF01399 PCI: PCI domain; Int 96.6 0.027 5.9E-07 42.9 9.6 74 169-245 4-82 (105)
9 KOG3252 Uncharacterized conser 96.3 0.029 6.3E-07 47.9 8.7 101 155-262 88-189 (217)
10 KOG1464 COP9 signalosome, subu 93.5 6.3 0.00014 36.4 16.5 140 95-247 241-388 (440)
11 smart00753 PAM PCI/PINT associ 89.2 1.1 2.4E-05 33.1 5.4 42 201-245 5-46 (88)
12 smart00088 PINT motif in prote 89.2 1.1 2.4E-05 33.1 5.4 42 201-245 5-46 (88)
13 KOG2908 26S proteasome regulat 88.6 12 0.00027 35.3 12.8 87 164-251 233-323 (380)
14 KOG0687 26S proteasome regulat 86.0 31 0.00068 32.6 15.1 100 157-259 241-358 (393)
15 COG5187 RPN7 26S proteasome re 84.3 2.6 5.7E-05 39.0 6.0 119 155-283 250-389 (412)
16 KOG2581 26S proteasome regulat 78.9 12 0.00026 36.2 8.5 113 159-276 308-434 (493)
17 smart00874 B5 tRNA synthetase 64.0 12 0.00027 26.3 3.9 32 223-254 5-38 (71)
18 PF13986 DUF4224: Domain of un 63.9 16 0.00035 24.1 4.1 38 224-261 3-41 (47)
19 PF04800 ETC_C1_NDUFA4: ETC co 62.9 4.6 0.0001 31.3 1.5 23 232-254 52-75 (101)
20 PF02042 RWP-RK: RWP-RK domain 60.4 21 0.00047 24.2 4.3 27 224-250 16-42 (52)
21 PF12324 HTH_15: Helix-turn-he 57.4 42 0.00091 24.7 5.7 46 209-260 28-74 (77)
22 PF08784 RPA_C: Replication pr 55.2 27 0.00059 26.5 4.7 51 203-253 45-98 (102)
23 PF03683 UPF0175: Uncharacteri 54.5 36 0.00079 24.7 5.0 34 218-251 29-62 (76)
24 KOG3389 NADH:ubiquinone oxidor 53.3 8.1 0.00018 31.9 1.5 31 223-253 119-150 (178)
25 PF03484 B5: tRNA synthetase B 52.3 20 0.00044 25.4 3.4 32 223-254 5-38 (70)
26 PF09759 Atx10homo_assoc: Spin 51.5 26 0.00055 27.3 4.0 68 192-261 32-99 (102)
27 PRK13239 alkylmercury lyase; P 45.8 63 0.0014 28.4 6.0 50 206-260 23-72 (206)
28 PF14555 UBA_4: UBA-like domai 45.6 28 0.0006 22.2 2.9 27 226-252 4-30 (43)
29 PF08727 P3A: Poliovirus 3A pr 45.2 6.6 0.00014 27.1 -0.1 27 226-252 17-44 (57)
30 PF09494 Slx4: Slx4 endonuclea 44.4 30 0.00065 24.2 3.1 32 219-252 22-62 (64)
31 PF04760 IF2_N: Translation in 44.0 25 0.00054 23.5 2.6 29 223-251 3-32 (54)
32 PF13994 PgaD: PgaD-like prote 37.9 49 0.0011 26.9 3.9 53 203-259 84-136 (138)
33 PF12833 HTH_18: Helix-turn-he 37.5 1.1E+02 0.0023 21.7 5.4 47 202-252 27-76 (81)
34 PF00627 UBA: UBA/TS-N domain; 35.8 51 0.0011 20.1 2.9 25 226-251 6-30 (37)
35 PF03634 TCP: TCP family trans 35.0 25 0.00054 28.5 1.7 17 228-244 34-51 (138)
36 PF07643 DUF1598: Protein of u 34.9 1.1E+02 0.0025 22.8 5.0 64 13-85 6-71 (84)
37 KOG1076 Translation initiation 33.4 2.3E+02 0.005 29.7 8.4 71 167-239 656-734 (843)
38 PRK13503 transcriptional activ 32.3 1E+02 0.0022 27.3 5.5 46 202-252 219-267 (278)
39 PF14726 RTTN_N: Rotatin, an a 32.0 84 0.0018 24.2 4.1 41 205-246 2-56 (98)
40 PRK11511 DNA-binding transcrip 31.4 1.4E+02 0.003 23.6 5.5 47 201-252 56-105 (127)
41 PF00165 HTH_AraC: Bacterial r 31.0 81 0.0018 19.6 3.3 30 223-252 8-38 (42)
42 PF04182 B-block_TFIIIC: B-blo 29.9 1.5E+02 0.0033 21.2 5.0 46 206-253 3-51 (75)
43 COG1654 BirA Biotin operon rep 29.5 2E+02 0.0043 21.2 5.6 38 222-259 18-59 (79)
44 PF05491 RuvB_C: Holliday junc 29.4 84 0.0018 23.1 3.5 53 205-259 8-64 (76)
45 smart00550 Zalpha Z-DNA-bindin 28.9 2.1E+02 0.0045 20.0 6.4 46 206-254 7-56 (68)
46 PF10978 DUF2785: Protein of u 28.9 1.6E+02 0.0034 24.9 5.7 87 96-188 87-173 (175)
47 KOG0686 COP9 signalosome, subu 28.6 2.7E+02 0.0058 27.3 7.6 82 169-254 309-400 (466)
48 PF03374 ANT: Phage antirepres 27.6 1.7E+02 0.0037 22.3 5.3 42 209-253 13-54 (111)
49 KOG2753 Uncharacterized conser 27.3 5.5E+02 0.012 24.5 10.2 74 165-244 240-315 (378)
50 cd04764 HTH_MlrA-like_sg1 Heli 27.1 1.1E+02 0.0023 21.1 3.7 35 224-258 1-35 (67)
51 TIGR03862 flavo_PP4765 unchara 26.3 66 0.0014 30.9 3.3 34 227-260 45-79 (376)
52 PRK13501 transcriptional activ 26.1 1.7E+02 0.0038 26.2 5.9 48 200-252 222-272 (290)
53 PF06056 Terminase_5: Putative 24.0 2.4E+02 0.0052 19.3 4.9 29 223-251 13-41 (58)
54 KOG4329 DNA-binding protein [G 24.0 50 0.0011 31.5 1.9 44 208-251 246-299 (445)
55 smart00342 HTH_ARAC helix_turn 22.4 2.6E+02 0.0057 19.0 5.8 29 223-251 50-80 (84)
56 PF12840 HTH_20: Helix-turn-he 22.2 2.5E+02 0.0055 18.8 5.3 44 205-252 10-56 (61)
57 KOG0775 Transcription factor S 21.6 2E+02 0.0043 26.5 5.1 104 146-252 80-218 (304)
58 PF11360 DUF3110: Protein of u 21.3 94 0.002 23.3 2.6 31 232-262 52-83 (86)
59 COG1510 Predicted transcriptio 20.7 1.3E+02 0.0028 25.7 3.5 54 221-279 39-95 (177)
60 COG4189 Predicted transcriptio 20.5 3.5E+02 0.0077 24.5 6.3 51 199-253 17-70 (308)
61 PF08279 HTH_11: HTH domain; 20.2 2.6E+02 0.0056 18.1 4.9 42 209-253 4-48 (55)
No 1
>KOG1860 consensus Nuclear protein export factor [Intracellular trafficking, secretion, and vesicular transport; Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2.8e-51 Score=407.61 Aligned_cols=243 Identities=35% Similarity=0.595 Sum_probs=216.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHH-HHcCCCCChhhHHHhhhhhHHHHHhhhhhhhcCChhhHHHHHHHHHHHHHHHhhhhh
Q 022787 5 EVRASDVRPLPVLEETLNYLLS-LLDSTEHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRS 83 (292)
Q Consensus 5 ~~~P~~vRP~~vL~kT~~yL~~-~~~~~~~~~~~~y~Fi~DRlRaIRQDltvQ~i~~~~~i~v~E~~~Rf~i~~~~~l~~ 83 (292)
.|.|++||||+||.+||+||+. ++...+.++..+|+|+|||+||||||+|+||+.+..||.++|+|+||||++.|+||+
T Consensus 157 ~pLPsdvRP~~VL~~T~dYLl~~v~~~~~~sl~~~y~FvwDRtRAVR~D~t~Q~~~d~~Av~llE~i~RfhI~~~h~Lce 236 (927)
T KOG1860|consen 157 RPLPSDVRPPPVLVKTVDYLLGKVLCDKDISLREMYDFVWDRTRAVRQDFTIQNYSDQEAVELLERIARFHILFRHRLCE 236 (927)
T ss_pred CCCccccCCHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHhcc
Confidence 5699999999999999999997 445566689999999999999999999999999999999999999999999999997
Q ss_pred cCCCCCCChhhhhcHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHhhcCCCCchhhhHHHHhhhCChhhhcCH
Q 022787 84 SCSSSSISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSK 163 (292)
Q Consensus 84 ~~~~~~f~~~~~~n~~ql~qcl~~L~~lY~~~~~~~~~~~ne~EF~aY~iL~~l~~~~~~~~~~l~~~l~~l~~~i~~sp 163 (292)
.+ +.| +.++|+|||++|+.+|.++|++++++|++|+||+||+||++|++|++++. .+.. +.+|+++++++
T Consensus 237 ~~--~~F--da~~nlEQL~K~l~sL~elYdD~r~~g~~cpnE~EFR~Y~vLl~Lgd~~~--~~~i----q~~~~evr~~~ 306 (927)
T KOG1860|consen 237 EP--EQF--DAQQNLEQLQKCLQSLGELYDDLRKGGIPCPNEPEFRGYYVLLSLGDPQV--VRDI----QAWPDEVRQDS 306 (927)
T ss_pred Cc--ccC--ChhHHHHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHhcCCchH--HHHH----HhcCcccccch
Confidence 64 356 47899999999999999999999999999999999999999999998762 3223 45699999999
Q ss_pred hHHHHHHHHHHHHhCcHHHHHH------------------HHHh-cchHHHHHHHhhhHHHHHHHHHHHHHhhhcC--CC
Q 022787 164 EMWFARQALRYFQMGNYRRFLS------------------TVAA-EASYLQYCIIEPYIDEVRSLALCCIHNCCYK--LH 222 (292)
Q Consensus 164 ~v~~Al~v~~a~~~~Ny~rfFk------------------ll~~-~~~~L~~cll~~~~~~vR~~aL~~i~~a~yk--~~ 222 (292)
+|++|+.++.|+++|||.+||+ +... ..++|+.|+++.||+.+|..|++.|.+ +|+ ..
T Consensus 307 ~Vk~al~~~~a~~~nn~~~~~r~~~~~t~a~~~l~~~~~~l~q~p~~~~L~~~v~~~~f~~ir~~al~~~~~-~~~~~~~ 385 (927)
T KOG1860|consen 307 EVKLALCLRRAFQSNNFRRFFRLSSLRTEALQNLYTRFFKLMQSPALPYLMGCVLELFFPDIRWAALRAMSH-AYNSKHV 385 (927)
T ss_pred hHHHHHHHHHHhccCCeeeeeeccchhHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHHHH-HHhccCC
Confidence 9999999999999999988874 3322 468899999999999999999999999 574 46
Q ss_pred CcCHHHHHHHhcCCc-hHHHHHHHHhCCeecccCCCc
Q 022787 223 PYPLGHLSKVLMMEE-SDVELFCNAYGLQTCIDEVGN 258 (292)
Q Consensus 223 ~ipl~~l~~~L~f~~-~e~~~f~~~~Gl~~~~d~~g~ 258 (292)
+||+..+..+|+|+. ++...+|..|||+++.|..+.
T Consensus 386 ~vp~~~l~~~l~f~~~e~~~~~~~~y~Leis~~~~~~ 422 (927)
T KOG1860|consen 386 PVPLGKLDRILLFDGEEELKVVCNYYGLEISVDDKIV 422 (927)
T ss_pred CcchhHHHHHHhcCChhhhHhhhhheeeEeecccccc
Confidence 899999999999995 679999999999997655444
No 2
>COG5079 SAC3 Nuclear protein export factor [Intracellular trafficking and secretion / Cell division and chromosome partitioning]
Probab=100.00 E-value=2.8e-50 Score=377.84 Aligned_cols=241 Identities=33% Similarity=0.480 Sum_probs=213.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHcCCCCChhhHHHhhhhhHHHHHhhhhhhhcCChhhHHHHHHHHHHHHHHHhhhhhc
Q 022787 5 EVRASDVRPLPVLEETLNYLLSLLDSTEHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRSS 84 (292)
Q Consensus 5 ~~~P~~vRP~~vL~kT~~yL~~~~~~~~~~~~~~y~Fi~DRlRaIRQDltvQ~i~~~~~i~v~E~~~Rf~i~~~~~l~~~ 84 (292)
.+.|+|||||+||++|++||+..+.. .++...|.|+|||+||||||+|+||..+..||.|+|+|+||||++.|.|++.
T Consensus 125 p~LPsDVRPp~VLvktidylv~~c~~--d~l~e~~~Fv~drtRavrqDftiQN~~g~dAV~c~EriaRfhIl~lh~L~~~ 202 (646)
T COG5079 125 PELPSDVRPPEVLVKTIDYLVKLCAG--DQLIEMHRFVRDRTRAVRQDFTIQNEKGKDAVECHERIARFHILFLHLLHDH 202 (646)
T ss_pred CCCcccCCChHHHHHHHHHHHHHhcC--cchHHHHHHHHhhhHHHHhhceeecccCchHHHHHHHHHHHHHHHHHHHhcC
Confidence 34999999999999999999966654 2567899999999999999999999999999999999999999999999964
Q ss_pred CCCCCCChhhhhcHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHhhcCCCCchhhhHHHHhhhCChhhhcCHh
Q 022787 85 CSSSSISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKE 164 (292)
Q Consensus 85 ~~~~~f~~~~~~n~~ql~qcl~~L~~lY~~~~~~~~~~~ne~EF~aY~iL~~l~~~~~~~~~~l~~~l~~l~~~i~~sp~ 164 (292)
++|+ .+|++|||.+.+.+|.++||+++.++..||||+||+||.||.+|+|.. .+...+ .+|..++..+.
T Consensus 203 ---p~Fs--~qqeleQL~ksL~sL~elYdd~r~~~~~cpneaEFraYaiL~slgDp~--yv~~iq----~wp~~if~d~~ 271 (646)
T COG5079 203 ---PHFS--KQQELEQLKKSLASLIELYDDGRAGKKECPNEAEFRAYAILASLGDPR--YVAGIQ----GWPGGIFCDLP 271 (646)
T ss_pred ---cccc--HHhHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhCCch--hhhccc----cCCccccccch
Confidence 5787 468999999999999999999999989999999999999999999865 343334 45899999999
Q ss_pred HHHHHHHHHHHHhCc---------------HHHHHHHHHh-cchHHHHHHHhhhHHHHHHHHHHHHHhhhc--CCCCcCH
Q 022787 165 MWFARQALRYFQMGN---------------YRRFLSTVAA-EASYLQYCIIEPYIDEVRSLALCCIHNCCY--KLHPYPL 226 (292)
Q Consensus 165 v~~Al~v~~a~~~~N---------------y~rfFkll~~-~~~~L~~cll~~~~~~vR~~aL~~i~~a~y--k~~~ipl 226 (292)
|+.|+++.+-.+.|| |.|||+++.+ +++|||+|+++.|+..+|..||..|.++ + .-.++|.
T Consensus 272 vq~alkl~~laq~nn~r~~~~rnteac~nlytrFfkl~qSpsv~~lmg~lle~h~~sir~~aLkAm~k~-~~sahk~ipf 350 (646)
T COG5079 272 VQIALKLMQLAQSNNFRLLGRRNTEACFNLYTRFFKLIQSPSVQYLMGCLLEKHNISIRGGALKAMEKE-IESAHKNIPF 350 (646)
T ss_pred HHHHHHHHHHhhccCeeeccccchhhhhHHHHHHHHHHhCccHHHHHHHHHHHhhHHHHHHHHHHHHHH-HHHhhcCCCe
Confidence 999999988777666 7899998865 7899999999999999999999999885 4 1127999
Q ss_pred HHHHHHhcCCc-hHHHHHHHHhCCeecccCCCcc
Q 022787 227 GHLSKVLMMEE-SDVELFCNAYGLQTCIDEVGNK 259 (292)
Q Consensus 227 ~~l~~~L~f~~-~e~~~f~~~~Gl~~~~d~~g~~ 259 (292)
.++..+|.|++ .|+++||+.||+++..+.+|++
T Consensus 351 ~~l~~il~f~~~~e~~efckyy~lei~~ed~~~l 384 (646)
T COG5079 351 VDLSGILDFEEKGEGEEFCKYYGLEIRIEDSVKL 384 (646)
T ss_pred ehhhhhccccccchhHHHhhhcceeeeccccccc
Confidence 99999999996 6799999999999975556665
No 3
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=100.00 E-value=4.2e-50 Score=350.25 Aligned_cols=201 Identities=39% Similarity=0.615 Sum_probs=160.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHcCCCCChhhHHHhhhhhHHHHHhhhhhhhcCChhhHHHHHHHHHHHHHHHhhhhhc
Q 022787 5 EVRASDVRPLPVLEETLNYLLSLLDSTEHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRSS 84 (292)
Q Consensus 5 ~~~P~~vRP~~vL~kT~~yL~~~~~~~~~~~~~~y~Fi~DRlRaIRQDltvQ~i~~~~~i~v~E~~~Rf~i~~~~~l~~~ 84 (292)
+|+|++|||++||++|++||++++ ++.++|+|||||+||||||++|||+.+++++.|||.+|||+|++
T Consensus 2 ~p~p~~vRp~~vL~~t~~~l~~~~-----~~~~~y~fi~drlRsiRqDl~vQ~~~~~~~i~v~E~~ar~~i~~------- 69 (204)
T PF03399_consen 2 EPNPSDVRPPEVLKKTLNYLLRKI-----PFKDDYNFIWDRLRSIRQDLTVQNIENDFAIKVYERIARFAIES------- 69 (204)
T ss_dssp ---------HHHHHHHHHHHHHHT-----CCCCHHHHHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHHHHHH-------
T ss_pred CCChHhCCCHHHHHHHHHHHHHHh-----hhhhhhHHHHHHhHHHHhhHHHHhcCCHHHHHHHHHHHHHHhhc-------
Confidence 799999999999999999999998 34469999999999999999999999999999999999999988
Q ss_pred CCCCCCChhhhhcHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHhhcCC-CCchhhhHHHHhhhCChhhhcCH
Q 022787 85 CSSSSISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSN-GQPVGESLSLWFRHVPSPIIKSK 163 (292)
Q Consensus 85 ~~~~~f~~~~~~n~~ql~qcl~~L~~lY~~~~~~~~~~~ne~EF~aY~iL~~l~~~-~~~~~~~l~~~l~~l~~~i~~sp 163 (292)
.|.+||++|+++|+++|++.+. +.+++|++||.||+||+++.+. .+. +...+..+|++++++|
T Consensus 70 -----------~d~~qf~~c~~~L~~lY~~~~~-~~~~~~~~ef~~y~lL~~l~~~~~~~----~~~~l~~l~~~~~~~~ 133 (204)
T PF03399_consen 70 -----------GDLEQFNQCLSQLKELYDDLRD-LPPSPNEAEFIAYYLLYLLCQNNIPD----FHMELELLPSEILSSP 133 (204)
T ss_dssp -----------HHHHHHHHHHHHHHHHHHHHHH-T---TTHHHHHHHHHHHTT-T---TH----HHHHHTTS-HHHHTSH
T ss_pred -----------CCHHHHHHHHHHHHHHHHhhcc-CCCCCCHHHHHHHHHHHHHHcccchH----HHHHHHHCchhhhcCH
Confidence 3678999999999999999743 4578999999999999998443 222 2334567899999999
Q ss_pred hHHHHHHHHHHHHhCcHHHHHHHHH-hcchHHHHHHHhhhHHHHHHHHHHHHHhhhcCCCCcCHHHHHHHhcC
Q 022787 164 EMWFARQALRYFQMGNYRRFLSTVA-AEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMM 235 (292)
Q Consensus 164 ~v~~Al~v~~a~~~~Ny~rfFkll~-~~~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f 235 (292)
.|++|++|.+|+.+|||++||+++. +.+|++++|+++.+++.+|..||++|++ +|++ ++|++.+++||+|
T Consensus 134 ~i~~al~l~~a~~~gny~~ff~l~~~~~~~~l~~~l~~~~~~~iR~~al~~i~~-ay~~-~i~l~~l~~~L~F 204 (204)
T PF03399_consen 134 YIQFALELCRALMEGNYVRFFRLYRSKSAPYLFACLMERFFNRIRLRALQSISK-AYRS-SIPLSFLAELLGF 204 (204)
T ss_dssp HHHHHHHHHHHH--TTHHHHHHHHT-TTS-HHHHHHHGGGHHHHHHHHHHHHHH-HS-T--EEHHHHHHHTT-
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHhccCCChHHHHHHHHHHHHHHHHHHHHHHH-HcCC-CCCHHHHHHHcCC
Confidence 9999999999999999999999762 5899999999999999999999999999 6984 5999999999997
No 4
>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]
Probab=100.00 E-value=5.3e-49 Score=366.87 Aligned_cols=227 Identities=21% Similarity=0.332 Sum_probs=199.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHcCCCCChhhHHHhhhhhHHHHHhhhhhhhcCChhhHHHHHHHHHHHHHHHhhhh
Q 022787 3 AKEVRASDVRPLPVLEETLNYLLSLLDSTEHPFEVIHDFVFDRTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLR 82 (292)
Q Consensus 3 ~~~~~P~~vRP~~vL~kT~~yL~~~~~~~~~~~~~~y~Fi~DRlRaIRQDltvQ~i~~~~~i~v~E~~~Rf~i~~~~~l~ 82 (292)
|++|+|+.|||++||++++.-|..+|..+ ..|.|++|||||||||||||+|.++|+|+|||+++|+.+.
T Consensus 292 TsAPdPstVRP~~VL~ksL~~vkdk~k~~-----~~Y~y~CdQ~KSiRQDLTVQ~IrneFTveVYEtHARIALE------ 360 (540)
T KOG1861|consen 292 TSAPDPSTVRPLEVLKKSLCLVKDKWKAK-----ANYAYLCDQFKSIRQDLTVQRIRNEFTVEVYETHARIALE------ 360 (540)
T ss_pred ccCCCccccCCHHHHHHHHHHHHHHHHhh-----ccHHHHHHHHHHHhhhhhhheeccceeeeeehhhhHHHHh------
Confidence 78999999999999999999999999764 5799999999999999999999999999999996665442
Q ss_pred hcCCCCCCChhhhhcHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHhhcCCCCchhhhHHHHhhhCChhhhcC
Q 022787 83 SSCSSSSISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKS 162 (292)
Q Consensus 83 ~~~~~~~f~~~~~~n~~ql~qcl~~L~~lY~~~~~~~~~~~ne~EF~aY~iL~~l~~~~~~~~~~l~~~l~~l~~~i~~s 162 (292)
+.|+++||||+++|+.||.+. + ..+..||.||+|||.+-..+. .+ +..-++.+++|++.+
T Consensus 361 ------------kGD~~EfNQCQtQLk~LY~eg----i-pg~~~EF~AYriLY~i~tkN~--~d-i~sll~~lt~E~ked 420 (540)
T KOG1861|consen 361 ------------KGDLEEFNQCQTQLKALYSEG----I-PGAYLEFTAYRILYYIFTKNY--PD-ILSLLRDLTEEDKED 420 (540)
T ss_pred ------------cCCHHHHHHHHHHHHHHHccC----C-CCchhhHHHHHHHHHHHhcCc--hH-HHHHHHhccHhhccC
Confidence 368999999999999999654 2 334899999999998754442 12 233468999999999
Q ss_pred HhHHHHHHHHHHHHhCcHHHHHHHHHhcchHHHHHHHhhhHHHHHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCc-hHHH
Q 022787 163 KEMWFARQALRYFQMGNYRRFLSTVAAEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEE-SDVE 241 (292)
Q Consensus 163 p~v~~Al~v~~a~~~~Ny~rfFkll~~~~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~-~e~~ 241 (292)
+.|.+||+|+.|+..|||++||+| +..+|.|..|||+.|+++.|..||.+|+| +|++ .||+++|++.|.|++ ++|.
T Consensus 421 ~~V~hAL~vR~A~~~GNY~kFFrL-Y~~AP~M~~yLmdlF~erER~~Al~ii~K-syrP-~i~~~fi~~~laf~~~e~c~ 497 (540)
T KOG1861|consen 421 EAVAHALEVRSAVTLGNYHKFFRL-YLTAPNMSGYLMDLFLERERKKALTIICK-SYRP-TITVDFIASELAFDSMEDCV 497 (540)
T ss_pred HHHHHHHHHHHHHHhccHHHHHHH-HhhcccchhHHHHHHHHHHHHHHHHHHHH-HcCC-CccHHHHhhhhhhchHHHHH
Confidence 999999999999999999999996 67999999999999999999999999999 6997 599999999999996 6799
Q ss_pred HHHHHhCCeecccCCCccccccCC
Q 022787 242 LFCNAYGLQTCIDEVGNKLLPTKQ 265 (292)
Q Consensus 242 ~f~~~~Gl~~~~d~~g~~~l~~k~ 265 (292)
.|++++|++- |+.|..+++++.
T Consensus 498 ~~l~~~~~~~--~~~g~~~~~~~~ 519 (540)
T KOG1861|consen 498 NFLNEQNLTY--DSLGPQILDKNA 519 (540)
T ss_pred HHHhccCccc--cccCCccccccc
Confidence 9999999776 667888777653
No 5
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=99.28 E-value=3.4e-11 Score=99.61 Aligned_cols=129 Identities=19% Similarity=0.280 Sum_probs=90.7
Q ss_pred HHHHHHHHHHHhhcCCCCchhhhHHHHhhhCChhhhcC-HhHHHHHHHHHHHHhCcHHHHHHHHHhc-chHHHHHHHhhh
Q 022787 125 EAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKS-KEMWFARQALRYFQMGNYRRFLSTVAAE-ASYLQYCIIEPY 202 (292)
Q Consensus 125 e~EF~aY~iL~~l~~~~~~~~~~l~~~l~~l~~~i~~s-p~v~~Al~v~~a~~~~Ny~rfFkll~~~-~~~L~~cll~~~ 202 (292)
..++.+-.++..|-+.+. .+ ...-+.++|.++..+ |.|+..+.+.+++++++|.+|+..+++. .+.-..-.+..+
T Consensus 3 ~~~~~~~~Ll~~L~~~~~--~d-f~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~ 79 (143)
T PF10075_consen 3 NPEIYALILLKYLMQNDL--SD-FRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGF 79 (143)
T ss_dssp -HHHHHHHHHHHHHTTTS--TH-HHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTH
T ss_pred chhHHHHHHHHHHHcCCc--hH-HHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHH
Confidence 467777766666654432 22 222347899999995 9999999999999999999999976532 223344567778
Q ss_pred HHHHHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCchHHHHHHHHhCCeecccCCCcccc
Q 022787 203 IDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGNKLL 261 (292)
Q Consensus 203 ~~~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e~~~f~~~~Gl~~~~d~~g~~~l 261 (292)
...+|.+++..+.+ +|. +|+++.++++||++++|+.++|+..||++ |++|..+.
T Consensus 80 ~~~iR~~i~~~i~~-aY~--sIs~~~la~~Lg~~~~el~~~~~~~gW~~--d~~~~~~~ 133 (143)
T PF10075_consen 80 EDTIRERIAHLISK-AYS--SISLSDLAEMLGLSEEELEKFIKSRGWTV--DGDGVLFP 133 (143)
T ss_dssp HHHHHHHHHHHHHH-H-S--EE-HHHHHHHTTS-HHHHHHHHHHHT-EE-------EE-
T ss_pred HHHHHHHHHHHHHH-HHh--HcCHHHHHHHhCCCHHHHHHHHHHcCCEE--CCCccEEe
Confidence 88999999999998 698 79999999999999888999999999999 44566554
No 6
>KOG3151 consensus 26S proteasome regulatory complex, subunit RPN12/PSMD8 [Posttranslational modification, protein turnover, chaperones]
Probab=98.39 E-value=3.1e-05 Score=68.17 Aligned_cols=166 Identities=14% Similarity=0.230 Sum_probs=127.8
Q ss_pred hhHHHHHHHHHHHHHHHhhhhhcCCCCCCChhhhhcHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHhhcCCC
Q 022787 62 KAINMFEKIVKFHVISHHKLRSSCSSSSISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNG 141 (292)
Q Consensus 62 ~~i~v~E~~~Rf~i~~~~~l~~~~~~~~f~~~~~~n~~ql~qcl~~L~~lY~~~~~~~~~~~ne~EF~aY~iL~~l~~~~ 141 (292)
.+-+|||-.|=..|.. -|.+.|..=+.+|+-.|-+....=..+++.--+.+..+|+-|..+.
T Consensus 54 ~aR~ilEi~vl~SI~t------------------~D~~sFerY~~Qlk~YY~d~~~~l~~S~~~~~l~GLnLL~LLsqNR 115 (260)
T KOG3151|consen 54 IARDILEIGVLLSILT------------------KDFESFERYMNQLKPYYFDYNEKLSESEKKHKLLGLNLLYLLSQNR 115 (260)
T ss_pred HHHHHHHHHHHHHHHh------------------ccHHHHHHHHHHhcchhcccccccCcchhhhHHHHHHHHHHHHhcc
Confidence 4678888854333322 3567888899999998887655333567888899999998876554
Q ss_pred CchhhhHHHHhhhCChhhhcC-HhHHHHHHHHHHHHhCcHHHHHHHHHhcchH-HHHHHHhhhHHHHHHHHHHHHHhhhc
Q 022787 142 QPVGESLSLWFRHVPSPIIKS-KEMWFARQALRYFQMGNYRRFLSTVAAEASY-LQYCIIEPYIDEVRSLALCCIHNCCY 219 (292)
Q Consensus 142 ~~~~~~l~~~l~~l~~~i~~s-p~v~~Al~v~~a~~~~Ny~rfFkll~~~~~~-L~~cll~~~~~~vR~~aL~~i~~a~y 219 (292)
.+ .+-.-+..+|..++.+ |.|++++++=+.++.|-|-+.+... +.+|. .-...|+...+.+|...-..+-| +|
T Consensus 116 ia---eFHteLe~lp~~~l~~~~~I~~~v~LEq~~MEGaYnKv~~a~-~s~p~~~y~~FmdIl~~tiRdEIA~c~EK-sY 190 (260)
T KOG3151|consen 116 IA---EFHTELELLPKKILQHNPYISHPVSLEQSLMEGAYNKVLSAK-QSIPSEEYTYFMDILLDTIRDEIAGCIEK-SY 190 (260)
T ss_pred HH---HHHHHHHhccHHHhhccchhhhHHHHHHHHHhhHHHHHHHHH-hcCCcHHHHHHHHHHHHHHHHHHHHHHHH-HH
Confidence 22 1333356889888887 9999999999999999999999864 45543 33456777777799988888888 68
Q ss_pred CCCCcCHHHHHHHhcCC-chHHHHHHHHhCCeec
Q 022787 220 KLHPYPLGHLSKVLMME-ESDVELFCNAYGLQTC 252 (292)
Q Consensus 220 k~~~ipl~~l~~~L~f~-~~e~~~f~~~~Gl~~~ 252 (292)
. .+|++..+.+|+|+ +++...|.++-+|.+.
T Consensus 191 d--~l~~s~a~~~L~f~~~~e~~~~~~~r~W~l~ 222 (260)
T KOG3151|consen 191 D--KLSASDATQMLLFNNDKELKKFATERQWPLD 222 (260)
T ss_pred h--hcCHHHHHHHHhcCChHHHHHHHHhcCCccc
Confidence 7 69999999999999 5679999999999984
No 7
>KOG4414 consensus COP9 signalosome, subunit CSN8 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=98.16 E-value=1.3e-05 Score=65.63 Aligned_cols=106 Identities=18% Similarity=0.211 Sum_probs=86.3
Q ss_pred HHHhhhCChhhhc-CHhHHHHHHHHHHHHhCcHHHHHHHHHh-cchHHHHHHHhhhHHHHHHHHHHHHHhhhcCCCCcCH
Q 022787 149 SLWFRHVPSPIIK-SKEMWFARQALRYFQMGNYRRFLSTVAA-EASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPL 226 (292)
Q Consensus 149 ~~~l~~l~~~i~~-sp~v~~Al~v~~a~~~~Ny~rfFkll~~-~~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~ipl 226 (292)
..| +++|+.|+. .|++--||.|.+.+|+.||...+..++. .-+--..-+|..+-+.-|.++++.+.. +|. +|-.
T Consensus 60 fLW-KRIP~AIKe~k~El~aaWgiGQkiWq~Df~GiYeaI~~~dWSeeak~imaAf~D~~~kR~FaLl~q-AYs--sI~~ 135 (197)
T KOG4414|consen 60 FLW-KRIPPAIKEAKPELGAAWGIGQKIWQHDFAGIYEAINAHDWSEEAKDIMAAFRDATRKRAFALLLQ-AYS--SIIA 135 (197)
T ss_pred HHH-HhCCHHHhhcCchhhhhhhhhHHHHhcccchHHHHHhhhcchHHHHHHHHHHHHHHHHHHHHHHHH-HHH--HHHH
Confidence 456 789999987 5999999999999999999999988763 233334445555566689999999988 687 7999
Q ss_pred HHHHHHhcCCchHHHHHHHHhCCeecccCCCccc
Q 022787 227 GHLSKVLMMEESDVELFCNAYGLQTCIDEVGNKL 260 (292)
Q Consensus 227 ~~l~~~L~f~~~e~~~f~~~~Gl~~~~d~~g~~~ 260 (292)
++++-.||+..+|+....-+.||+. |....+.
T Consensus 136 ~D~A~FlGl~~ddAtk~ilEnGWqa--DaasqMa 167 (197)
T KOG4414|consen 136 DDFAAFLGLPEDDATKGILENGWQA--DAASQMA 167 (197)
T ss_pred HHHHHHhCCCHHHHHHHHHHcccch--hhHHHHh
Confidence 9999999999999999999999998 4444443
No 8
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=96.58 E-value=0.027 Score=42.88 Aligned_cols=74 Identities=20% Similarity=0.323 Sum_probs=54.9
Q ss_pred HHHHHHHHhCcHHHHHHHHHhc-chHH----HHHHHhhhHHHHHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCchHHHHH
Q 022787 169 RQALRYFQMGNYRRFLSTVAAE-ASYL----QYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELF 243 (292)
Q Consensus 169 l~v~~a~~~~Ny~rfFkll~~~-~~~L----~~cll~~~~~~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e~~~f 243 (292)
.++.+|+..||+..|...+.+. ..++ ..-.++.....+|..+|..+.+ .|+ +++++.+++.|+++.++++.+
T Consensus 4 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~-~y~--~i~~~~ia~~l~~~~~~vE~~ 80 (105)
T PF01399_consen 4 SELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSK-PYS--SISISEIAKALQLSEEEVESI 80 (105)
T ss_dssp HHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHH-C-S--EEEHHHHHHHHTCCHHHHHHH
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHH-Hhc--ccchHHHHHHhccchHHHHHH
Confidence 4578999999999999988643 1221 1235566677799999999988 687 799999999999998776665
Q ss_pred HH
Q 022787 244 CN 245 (292)
Q Consensus 244 ~~ 245 (292)
+.
T Consensus 81 l~ 82 (105)
T PF01399_consen 81 LI 82 (105)
T ss_dssp HH
T ss_pred HH
Confidence 44
No 9
>KOG3252 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.30 E-value=0.029 Score=47.95 Aligned_cols=101 Identities=17% Similarity=0.228 Sum_probs=79.1
Q ss_pred CChhhhcCHhHHHHHHHHHHHHhCcHHHHHHHHHhcchHHHHHHHhhhHHHHHHHHHHHHHhhhcCCCCcCHHHHHHHhc
Q 022787 155 VPSPIIKSKEMWFARQALRYFQMGNYRRFLSTVAAEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLM 234 (292)
Q Consensus 155 l~~~i~~sp~v~~Al~v~~a~~~~Ny~rfFkll~~~~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~ 234 (292)
|++....+..++..+.+...+.+++|..|+...... +.|. --+..|=+.+|..|=..+.- +|. .|+=..|+++||
T Consensus 88 i~~~~~~ee~~r~ii~L~~~LEt~~Fq~FW~~~~~N-~~ml-e~itGFedsvr~yachvv~i-TyQ--kI~k~lLaellG 162 (217)
T KOG3252|consen 88 IDERVQMEEPFRSIIDLGDYLETCRFQQFWQEADEN-RDML-EGITGFEDSVRKYACHVVGI-TYQ--KIDKWLLAELLG 162 (217)
T ss_pred cCHHHhcccchhHHHhHHHHHhhchHHHHhhhhccc-hHHh-cCCCcHHHHHHHHHHHheec-hHh--hchHHHHHHhhC
Confidence 677777888999999999999999999999864322 2221 22445666788888777765 465 699999999999
Q ss_pred CC-chHHHHHHHHhCCeecccCCCccccc
Q 022787 235 ME-ESDVELFCNAYGLQTCIDEVGNKLLP 262 (292)
Q Consensus 235 f~-~~e~~~f~~~~Gl~~~~d~~g~~~l~ 262 (292)
-. |++.+.+.+.+||.. +++|..+++
T Consensus 163 ~~sDs~le~~~~~~GW~a--~e~G~ifv~ 189 (217)
T KOG3252|consen 163 GLSDSQLEVWMTKYGWIA--DESGQIFVA 189 (217)
T ss_pred cccHHHHHHHHHHcccee--cCCceEEEe
Confidence 65 789999999999998 678977775
No 10
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=93.46 E-value=6.3 Score=36.36 Aligned_cols=140 Identities=18% Similarity=0.257 Sum_probs=97.7
Q ss_pred hhcHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHhhc--CCCCchhhhHHHHhhhCChhhhcCHhHHHHHHHH
Q 022787 95 YLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLD--SNGQPVGESLSLWFRHVPSPIIKSKEMWFARQAL 172 (292)
Q Consensus 95 ~~n~~ql~qcl~~L~~lY~~~~~~~~~~~ne~EF~aY~iL~~l~--~~~~~~~~~l~~~l~~l~~~i~~sp~v~~Al~v~ 172 (292)
|+--+++.+.-+...+.+.....+| +|.+.-..-|-+|.++- +.-.++.. +--.+.+++|+|-..-.+.
T Consensus 241 Hlreg~fe~AhTDFFEAFKNYDEsG--spRRttCLKYLVLANMLmkS~iNPFDs-------QEAKPyKNdPEIlAMTnlv 311 (440)
T KOG1464|consen 241 HLREGEFEKAHTDFFEAFKNYDESG--SPRRTTCLKYLVLANMLMKSGINPFDS-------QEAKPYKNDPEILAMTNLV 311 (440)
T ss_pred ccccchHHHHHhHHHHHHhcccccC--CcchhHHHHHHHHHHHHHHcCCCCCcc-------cccCCCCCCHHHHHHHHHH
Confidence 5666788888888877765544444 57788888888887742 11111100 0123456789998888999
Q ss_pred HHHHhCcHHHHHHHHHhc------chHHHHHHHhhhHHHHHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCchHHHHHHHH
Q 022787 173 RYFQMGNYRRFLSTVAAE------ASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNA 246 (292)
Q Consensus 173 ~a~~~~Ny~rfFkll~~~------~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e~~~f~~~ 246 (292)
.|++.++...|=+++++. -|++--. ++-.+..+|.+.|-.+.+ .|. .|-+.++++-|..+..|.+.++-.
T Consensus 312 ~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh-~EdLl~niRTQVLlkLIk-PYt--~i~Ipfis~~Lnv~~~dV~~LLV~ 387 (440)
T KOG1464|consen 312 AAYQNNDIIEFERILKSNRSNIMDDPFIREH-IEDLLRNIRTQVLLKLIK-PYT--NIGIPFISKELNVPEADVESLLVS 387 (440)
T ss_pred HHHhcccHHHHHHHHHhhhccccccHHHHHH-HHHHHHHHHHHHHHHHhc-ccc--ccCchhhHhhcCCCHHHHHHHHHH
Confidence 999999999999988752 3444333 444577899998888777 687 588888999999987777666655
Q ss_pred h
Q 022787 247 Y 247 (292)
Q Consensus 247 ~ 247 (292)
+
T Consensus 388 ~ 388 (440)
T KOG1464|consen 388 C 388 (440)
T ss_pred H
Confidence 5
No 11
>smart00753 PAM PCI/PINT associated module.
Probab=89.17 E-value=1.1 Score=33.11 Aligned_cols=42 Identities=21% Similarity=0.304 Sum_probs=33.9
Q ss_pred hhHHHHHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCchHHHHHHH
Q 022787 201 PYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCN 245 (292)
Q Consensus 201 ~~~~~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e~~~f~~ 245 (292)
.....+|.+++..+++ .|+ .++++.+++.++++.++++.++.
T Consensus 5 ~l~~~~~~~~l~~l~~-~y~--~i~~~~i~~~~~l~~~~vE~~i~ 46 (88)
T smart00753 5 RLQRKIRLTNLLQLSE-PYS--SISLSDLAKLLGLSVPEVEKLVS 46 (88)
T ss_pred HHHHHHHHHHHHHHhH-Hhc--eeeHHHHHHHhCcCHHHHHHHHH
Confidence 3456699999999998 587 79999999999999766555544
No 12
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=89.17 E-value=1.1 Score=33.11 Aligned_cols=42 Identities=21% Similarity=0.304 Sum_probs=33.9
Q ss_pred hhHHHHHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCchHHHHHHH
Q 022787 201 PYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCN 245 (292)
Q Consensus 201 ~~~~~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e~~~f~~ 245 (292)
.....+|.+++..+++ .|+ .++++.+++.++++.++++.++.
T Consensus 5 ~l~~~~~~~~l~~l~~-~y~--~i~~~~i~~~~~l~~~~vE~~i~ 46 (88)
T smart00088 5 RLQRKIRLTNLLQLSE-PYS--SISLSDLAKLLGLSVPEVEKLVS 46 (88)
T ss_pred HHHHHHHHHHHHHHhH-Hhc--eeeHHHHHHHhCcCHHHHHHHHH
Confidence 3456699999999998 587 79999999999999766555544
No 13
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=88.61 E-value=12 Score=35.28 Aligned_cols=87 Identities=20% Similarity=0.227 Sum_probs=59.4
Q ss_pred hHHHHHHHHHHHHhCcHHHHHHHHHh--cchHHHHHHHhhhHHHHHHHHHHHHHhhhc-CCCCcCHHHHHHHhcCCchHH
Q 022787 164 EMWFARQALRYFQMGNYRRFLSTVAA--EASYLQYCIIEPYIDEVRSLALCCIHNCCY-KLHPYPLGHLSKVLMMEESDV 240 (292)
Q Consensus 164 ~v~~Al~v~~a~~~~Ny~rfFkll~~--~~~~L~~cll~~~~~~vR~~aL~~i~~a~y-k~~~ipl~~l~~~L~f~~~e~ 240 (292)
..++-.++..|+..||..+|+++... ..|-|.+.- ..-..++|.-||--|+-+-. ....+|++.+++....+.+|+
T Consensus 233 ~~eWL~dll~Afn~Gdl~~f~~l~~~~~~~p~L~~~e-~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip~~eV 311 (380)
T KOG2908|consen 233 NREWLKDLLIAFNSGDLKRFESLKGVWGKQPDLASNE-DFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIPNKEV 311 (380)
T ss_pred cHHHHHHHHHHhccCCHHHHHHHHHHhccCchHHHHH-HHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCCHHHH
Confidence 35777889999999999999997532 445554432 22345688888888764200 123799999999999997775
Q ss_pred HHH-HHHhCCee
Q 022787 241 ELF-CNAYGLQT 251 (292)
Q Consensus 241 ~~f-~~~~Gl~~ 251 (292)
+-. +++.++-+
T Consensus 312 E~LVMKAlslgL 323 (380)
T KOG2908|consen 312 ELLVMKALSLGL 323 (380)
T ss_pred HHHHHHHHhccc
Confidence 443 55665533
No 14
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=86.05 E-value=31 Score=32.59 Aligned_cols=100 Identities=21% Similarity=0.249 Sum_probs=68.6
Q ss_pred hhhhcCHhHHHHH-------HHHHHHHhCcHHHHHHHHHh------cchHHHHHHHhhhHHHHHHHHHHHHHhhhcCCCC
Q 022787 157 SPIIKSKEMWFAR-------QALRYFQMGNYRRFLSTVAA------EASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHP 223 (292)
Q Consensus 157 ~~i~~sp~v~~Al-------~v~~a~~~~Ny~rfFkll~~------~~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~ 223 (292)
..+.++|+|.-.+ +....+-..||..||.-|+. +......--...|...||.++-..+.- +|| +
T Consensus 241 tKVi~~~Evl~vl~~l~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLE-SYr--s 317 (393)
T KOG0687|consen 241 TKVIKCPEVLEVLHKLPSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLE-SYR--S 317 (393)
T ss_pred hhhcCcHHHHHHhhcCchHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHH-HHH--H
Confidence 4456677765443 45567789999999998853 112222223455777899999999887 699 7
Q ss_pred cCHHHHHHHhcCCc----hHHHHHHHHhCCeecccC-CCcc
Q 022787 224 YPLGHLSKVLMMEE----SDVELFCNAYGLQTCIDE-VGNK 259 (292)
Q Consensus 224 ipl~~l~~~L~f~~----~e~~~f~~~~Gl~~~~d~-~g~~ 259 (292)
+.++.+++-+|-+- .|...|.-.-.|-...|. +|.+
T Consensus 318 l~l~~MA~aFgVSVefiDreL~rFI~~grL~ckIDrVnGVV 358 (393)
T KOG0687|consen 318 LTLESMAKAFGVSVEFIDRELGRFIAAGRLHCKIDRVNGVV 358 (393)
T ss_pred HHHHHHHHHhCchHHHHHhHHHHhhccCceeeeeeccccee
Confidence 99999999999873 468888776555444444 3443
No 15
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=84.31 E-value=2.6 Score=39.02 Aligned_cols=119 Identities=18% Similarity=0.183 Sum_probs=77.1
Q ss_pred CChhhhcCHhHHH----------HHHHHHHHHhCcHHHHHHHHHh-cchHHHHHH-----HhhhHHHHHHHHHHHHHhhh
Q 022787 155 VPSPIIKSKEMWF----------ARQALRYFQMGNYRRFLSTVAA-EASYLQYCI-----IEPYIDEVRSLALCCIHNCC 218 (292)
Q Consensus 155 l~~~i~~sp~v~~----------Al~v~~a~~~~Ny~rfFkll~~-~~~~L~~cl-----l~~~~~~vR~~aL~~i~~a~ 218 (292)
+...|..+|++-- .-++...+-..||..||..+.. -+..|+.|. .+.|...||.++...+.- +
T Consensus 250 iktki~dspevl~vi~~~e~l~sl~~l~~SLy~cdY~~~F~~ll~~~~n~L~~d~fl~rh~d~fvREMRrrvYaQlLE-S 328 (412)
T COG5187 250 IKTKILDSPEVLDVIGSSEKLGSLVQLATSLYECDYGGDFMNLLYLFCNSLQDDVFLGRHVDLFVREMRRRVYAQLLE-S 328 (412)
T ss_pred hhhhhcCCHHHHHhccchhhhhhHHHHHHHHHHhccchhhHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHH-H
Confidence 3455667775432 2345566778899998876532 233333332 466788999999988887 6
Q ss_pred cCCCCcCHHHHHHHhcCCc----hHHHHHHHHhCCeecccC-CCccccccCCCcccCCcCcccccchhhh
Q 022787 219 YKLHPYPLGHLSKVLMMEE----SDVELFCNAYGLQTCIDE-VGNKLLPTKQTTFCRPKGGLQNYSFLGF 283 (292)
Q Consensus 219 yk~~~ipl~~l~~~L~f~~----~e~~~f~~~~Gl~~~~d~-~g~~~l~~k~~~f~~~~~~~~~~~~~~~ 283 (292)
|+ .++++.++.-+|.+- -|..+|.-.-.+-...|- +|.+.. +.|.++-|+|+..+-
T Consensus 329 Yr--~lsl~sMA~tFgVSV~yvdrDLg~FIp~~~LncvIDRvnGvVet-------nrpdekn~qy~~vVk 389 (412)
T COG5187 329 YR--LLSLESMAQTFGVSVEYVDRDLGEFIPEGRLNCVIDRVNGVVET-------NRPDEKNQQYSSVVK 389 (412)
T ss_pred HH--HhhHHHHHHHhCccHHHHhhhHHhhCCCCceeeeeecccceEec-------cCcchhhhhHHHHHh
Confidence 98 699999999999873 367788765444332232 565543 457777777776543
No 16
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=78.95 E-value=12 Score=36.23 Aligned_cols=113 Identities=16% Similarity=0.159 Sum_probs=65.9
Q ss_pred hhcCHhHHHH----HHHHHHHHhCcHHHHHHHHHhcchHHHH----HHHhhhHHHHHHHHHHHHHhhhcCCCCcCHHHHH
Q 022787 159 IIKSKEMWFA----RQALRYFQMGNYRRFLSTVAAEASYLQY----CIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLS 230 (292)
Q Consensus 159 i~~sp~v~~A----l~v~~a~~~~Ny~rfFkll~~~~~~L~~----cll~~~~~~vR~~aL~~i~~a~yk~~~ipl~~l~ 230 (292)
++..|..+-+ +.+.+|+..||-.+|=..+.+-.+-+++ -++-+.-..|-..+++.|+- +|+ .|++.+++
T Consensus 308 ~F~Qp~~~ksL~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISl-sYS--RISl~DIA 384 (493)
T KOG2581|consen 308 VFRQPGMRKSLRPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISL-SYS--RISLQDIA 384 (493)
T ss_pred hhcCccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheee-eee--eccHHHHH
Confidence 4455644444 4677899999999988766532222221 12222122244456777766 587 69999999
Q ss_pred HHhcCCchHHHHHH----HHhCCee--cccCCCccccccCCCcccCCcCccc
Q 022787 231 KVLMMEESDVELFC----NAYGLQT--CIDEVGNKLLPTKQTTFCRPKGGLQ 276 (292)
Q Consensus 231 ~~L~f~~~e~~~f~----~~~Gl~~--~~d~~g~~~l~~k~~~f~~~~~~~~ 276 (292)
..|+.+++|..+++ .+-|+.- .++++| ++..|.+.....+.++|
T Consensus 385 ~kL~l~Seed~EyiVakAIRDGvIea~Id~~~g--~m~skE~~diy~t~epQ 434 (493)
T KOG2581|consen 385 KKLGLNSEEDAEYIVAKAIRDGVIEAKIDHEDG--FMQSKETFDIYSTREPQ 434 (493)
T ss_pred HHhcCCCchhHHHHHHHHHHhccceeeeccccC--ceehhhhhhhhccCCch
Confidence 99999987644443 2345522 134455 55555555554444444
No 17
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=63.97 E-value=12 Score=26.31 Aligned_cols=32 Identities=9% Similarity=0.297 Sum_probs=27.5
Q ss_pred CcCHHHHHHHhcCC--chHHHHHHHHhCCeeccc
Q 022787 223 PYPLGHLSKVLMME--ESDVELFCNAYGLQTCID 254 (292)
Q Consensus 223 ~ipl~~l~~~L~f~--~~e~~~f~~~~Gl~~~~d 254 (292)
.++.+.+.+++|.+ ++++.+.++..|+++..+
T Consensus 5 ~~~~~~i~~llG~~i~~~ei~~~L~~lg~~~~~~ 38 (71)
T smart00874 5 TLRRERINRLLGLDLSAEEIEEILKRLGFEVEVS 38 (71)
T ss_pred EecHHHHHHHHCCCCCHHHHHHHHHHCCCeEEec
Confidence 47899999999987 467999999999998654
No 18
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=63.95 E-value=16 Score=24.13 Aligned_cols=38 Identities=11% Similarity=0.125 Sum_probs=31.7
Q ss_pred cCHHHHHHHhcCCc-hHHHHHHHHhCCeecccCCCcccc
Q 022787 224 YPLGHLSKVLMMEE-SDVELFCNAYGLQTCIDEVGNKLL 261 (292)
Q Consensus 224 ipl~~l~~~L~f~~-~e~~~f~~~~Gl~~~~d~~g~~~l 261 (292)
++-++|.++-|+.. ..-.++|..+|+.+..+.+|.+++
T Consensus 3 LT~~El~elTG~k~~~~Q~~~L~~~Gi~~~~~~~G~p~V 41 (47)
T PF13986_consen 3 LTDEELQELTGYKRPSKQIRWLRRNGIPFVVRADGRPIV 41 (47)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHHHCCCeeEECCCCCEEe
Confidence 45678999999884 567899999999998888998866
No 19
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=62.88 E-value=4.6 Score=31.35 Aligned_cols=23 Identities=13% Similarity=0.268 Sum_probs=17.3
Q ss_pred HhcCCc-hHHHHHHHHhCCeeccc
Q 022787 232 VLMMEE-SDVELFCNAYGLQTCID 254 (292)
Q Consensus 232 ~L~f~~-~e~~~f~~~~Gl~~~~d 254 (292)
-|.|++ +||+.||+.+|+.....
T Consensus 52 ~l~F~skE~Ai~yaer~G~~Y~V~ 75 (101)
T PF04800_consen 52 RLKFDSKEDAIAYAERNGWDYEVE 75 (101)
T ss_dssp EEEESSHHHHHHHHHHCT-EEEEE
T ss_pred EeeeCCHHHHHHHHHHcCCeEEEe
Confidence 467886 67999999999987543
No 20
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=60.41 E-value=21 Score=24.18 Aligned_cols=27 Identities=19% Similarity=0.381 Sum_probs=25.0
Q ss_pred cCHHHHHHHhcCCchHHHHHHHHhCCe
Q 022787 224 YPLGHLSKVLMMEESDVELFCNAYGLQ 250 (292)
Q Consensus 224 ipl~~l~~~L~f~~~e~~~f~~~~Gl~ 250 (292)
+|+.+.++.||.........|.++|+.
T Consensus 16 lp~~eAA~~Lgv~~T~LKr~CR~~GI~ 42 (52)
T PF02042_consen 16 LPIKEAAKELGVSVTTLKRRCRRLGIP 42 (52)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 999999999999988899999999975
No 21
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=57.37 E-value=42 Score=24.72 Aligned_cols=46 Identities=17% Similarity=0.160 Sum_probs=30.2
Q ss_pred HHHHHHHhhhcCCCCcCHHHHHHHhcCCchHHHHHHHHh-CCeecccCCCccc
Q 022787 209 LALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAY-GLQTCIDEVGNKL 260 (292)
Q Consensus 209 ~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e~~~f~~~~-Gl~~~~d~~g~~~ 260 (292)
-.|+.+++ +.|++++.|+.-+|.+.++.+..++.. +.+. |++|..+
T Consensus 28 ~LLr~LA~----G~PVt~~~LA~a~g~~~e~v~~~L~~~p~tEy--D~~GrIV 74 (77)
T PF12324_consen 28 PLLRLLAK----GQPVTVEQLAAALGWPVEEVRAALAAMPDTEY--DDQGRIV 74 (77)
T ss_dssp HHHHHHTT----TS-B-HHHHHHHHT--HHHHHHHHHH-TTSEE--ETTSEEE
T ss_pred HHHHHHHc----CCCcCHHHHHHHHCCCHHHHHHHHHhCCCceE--cCCCCee
Confidence 35666654 569999999999999988888888765 5555 5677653
No 22
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=55.23 E-value=27 Score=26.52 Aligned_cols=51 Identities=14% Similarity=0.078 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCch---HHHHHHHHhCCeecc
Q 022787 203 IDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEES---DVELFCNAYGLQTCI 253 (292)
Q Consensus 203 ~~~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~---e~~~f~~~~Gl~~~~ 253 (292)
+..++.+.|..|....-....++++.|++.|+++.. ++.++|..-|...++
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEES
T ss_pred CCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecc
Confidence 445667777777541122357999999999999864 478888888987654
No 23
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=54.50 E-value=36 Score=24.67 Aligned_cols=34 Identities=15% Similarity=0.185 Sum_probs=30.6
Q ss_pred hcCCCCcCHHHHHHHhcCCchHHHHHHHHhCCee
Q 022787 218 CYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQT 251 (292)
Q Consensus 218 ~yk~~~ipl~~l~~~L~f~~~e~~~f~~~~Gl~~ 251 (292)
.|+.+.+++...++++|++..+-.++|.++|+.+
T Consensus 29 lY~~g~iS~gkAAelag~s~~eF~~~L~~~gI~~ 62 (76)
T PF03683_consen 29 LYEEGKISLGKAAELAGMSRWEFLELLKERGIPI 62 (76)
T ss_pred HHHcCCCCHHHHHHHhCCCHHHHHHHHHHCCCCC
Confidence 4656689999999999999899999999999995
No 24
>KOG3389 consensus NADH:ubiquinone oxidoreductase, NDUFS4/18 kDa subunit [Energy production and conversion]
Probab=53.30 E-value=8.1 Score=31.86 Aligned_cols=31 Identities=19% Similarity=0.373 Sum_probs=24.3
Q ss_pred CcCHHHHHHHhcCCc-hHHHHHHHHhCCeecc
Q 022787 223 PYPLGHLSKVLMMEE-SDVELFCNAYGLQTCI 253 (292)
Q Consensus 223 ~ipl~~l~~~L~f~~-~e~~~f~~~~Gl~~~~ 253 (292)
.=|++-+--.|.|+. ++|+.||+.+||....
T Consensus 119 aDPlsNvgm~L~F~tkEdA~sFaEkngW~ydv 150 (178)
T KOG3389|consen 119 ADPLSNVGMALAFDTKEDAKSFAEKNGWDYDV 150 (178)
T ss_pred CCcccccceeeeeccHHHHHHHHHHcCCcccc
Confidence 356666666788995 6699999999999854
No 25
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=52.29 E-value=20 Score=25.41 Aligned_cols=32 Identities=13% Similarity=0.223 Sum_probs=25.6
Q ss_pred CcCHHHHHHHhcCC--chHHHHHHHHhCCeeccc
Q 022787 223 PYPLGHLSKVLMME--ESDVELFCNAYGLQTCID 254 (292)
Q Consensus 223 ~ipl~~l~~~L~f~--~~e~~~f~~~~Gl~~~~d 254 (292)
.++.+.+.++||++ .++..+.++..|+.+...
T Consensus 5 ~~~~~~i~~~lG~~i~~~~i~~~L~~lg~~~~~~ 38 (70)
T PF03484_consen 5 TLSLDKINKLLGIDISPEEIIKILKRLGFKVEKI 38 (70)
T ss_dssp EEEHHHHHHHHTS---HHHHHHHHHHTT-EEEE-
T ss_pred EecHHHHHHHhCCCCCHHHHHHHHHHCCCEEEEC
Confidence 47889999999987 367999999999999763
No 26
>PF09759 Atx10homo_assoc: Spinocerebellar ataxia type 10 protein domain; InterPro: IPR019156 This is the conserved C-terminal 100 residues of Ataxin-10. Ataxin-10 belongs to the family of armadillo repeat proteins and in solution it tends to form homotrimeric complexes, which associate via a tip-to-tip association in a horseshoe-shaped contact with the concave sides of the molecules facing each other. This domain may represent the homo-association site since that is located near the C terminus of Ataxin-10. The protein does not contain a signal sequence for secretion or any subcellular compartment confirming its cytoplasmic localisation, specifically to the olivocerebellar region [].
Probab=51.49 E-value=26 Score=27.26 Aligned_cols=68 Identities=22% Similarity=0.182 Sum_probs=44.0
Q ss_pred hHHHHHHHhhhHHHHHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCchHHHHHHHHhCCeecccCCCcccc
Q 022787 192 SYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGNKLL 261 (292)
Q Consensus 192 ~~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e~~~f~~~~Gl~~~~d~~g~~~l 261 (292)
..|..|..+.+-+.+|.+|+-.|..-... .-.-..+..-|--...+-...+++.|+++..|++|++.+
T Consensus 32 liL~~c~iD~~nP~irEwai~aiRnL~e~--n~eNQ~~I~~L~~~~~~~~~~L~~~G~~v~~d~~Gk~~l 99 (102)
T PF09759_consen 32 LILSCCNIDDHNPFIREWAIFAIRNLCEG--NPENQEFIAQLEPQGVADNEELEELGLEVEIDKDGKVRL 99 (102)
T ss_pred HHHHhcCCCcccHHHHHHHHHHHHHHHhC--CHHHHHHHHhccccCCcchHHHHHcCCeEEEcCCCeEee
Confidence 34667788888999999998887653221 222222333332222344567888999999888898866
No 27
>PRK13239 alkylmercury lyase; Provisional
Probab=45.83 E-value=63 Score=28.39 Aligned_cols=50 Identities=20% Similarity=0.141 Sum_probs=39.2
Q ss_pred HHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCchHHHHHHHHhCCeecccCCCccc
Q 022787 206 VRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGNKL 260 (292)
Q Consensus 206 vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e~~~f~~~~Gl~~~~d~~g~~~ 260 (292)
+....|+.+.+ +.+++++.|++.+|.+.+++..-++..+.+.. |++|+.+
T Consensus 23 ~~~~llr~la~----G~pvt~~~lA~~~~~~~~~v~~~L~~l~~~~~-d~~g~iv 72 (206)
T PRK13239 23 LLVPLLRLLAK----GRPVSVTTLAAALGWPVEEVEAVLEAMPDTEY-DEDGRII 72 (206)
T ss_pred HHHHHHHHHHc----CCCCCHHHHHHHhCCCHHHHHHHHHhCCCeEE-CCCCCEE
Confidence 55566667653 55899999999999998999999999876655 5677763
No 28
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=45.58 E-value=28 Score=22.24 Aligned_cols=27 Identities=7% Similarity=0.055 Sum_probs=20.9
Q ss_pred HHHHHHHhcCCchHHHHHHHHhCCeec
Q 022787 226 LGHLSKVLMMEESDVELFCNAYGLQTC 252 (292)
Q Consensus 226 l~~l~~~L~f~~~e~~~f~~~~Gl~~~ 252 (292)
+..++++.|.+++.|..+|+.+||.+.
T Consensus 4 i~~F~~iTg~~~~~A~~~L~~~~wdle 30 (43)
T PF14555_consen 4 IAQFMSITGADEDVAIQYLEANNWDLE 30 (43)
T ss_dssp HHHHHHHH-SSHHHHHHHHHHTTT-HH
T ss_pred HHHHHHHHCcCHHHHHHHHHHcCCCHH
Confidence 456788888877789999999999874
No 29
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=45.20 E-value=6.6 Score=27.11 Aligned_cols=27 Identities=15% Similarity=0.260 Sum_probs=18.6
Q ss_pred HHHHHHHhcCC-chHHHHHHHHhCCeec
Q 022787 226 LGHLSKVLMME-ESDVELFCNAYGLQTC 252 (292)
Q Consensus 226 l~~l~~~L~f~-~~e~~~f~~~~Gl~~~ 252 (292)
-..++++|.-. ++|.+++|+..||.+-
T Consensus 17 P~~I~DLL~SV~~~eV~~YC~~~GWIip 44 (57)
T PF08727_consen 17 PPAIADLLRSVDSPEVREYCEEQGWIIP 44 (57)
T ss_dssp S-TTHHHHHHH--HHHHHHHHHHT--TT
T ss_pred CHHHHHHHHhcCCHHHHHHHHHCCcccc
Confidence 35578888754 5789999999999874
No 30
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=44.39 E-value=30 Score=24.23 Aligned_cols=32 Identities=22% Similarity=0.359 Sum_probs=25.7
Q ss_pred cCCCCcCHHHHHHHhcCC---------chHHHHHHHHhCCeec
Q 022787 219 YKLHPYPLGHLSKVLMME---------ESDVELFCNAYGLQTC 252 (292)
Q Consensus 219 yk~~~ipl~~l~~~L~f~---------~~e~~~f~~~~Gl~~~ 252 (292)
|. ||.+++|..+|..+ ..+..+||...|+.+.
T Consensus 22 Ye--PI~L~el~~~L~~~g~~~~~~~~~~~l~~~lD~~gIt~~ 62 (64)
T PF09494_consen 22 YE--PINLEELHAWLKASGIGFDRKVDPSKLKEWLDSQGITFT 62 (64)
T ss_pred CC--CccHHHHHHHHHHcCCCccceeCHHHHHHHHHHCCceee
Confidence 55 89999999998732 1358999999999874
No 31
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=43.98 E-value=25 Score=23.48 Aligned_cols=29 Identities=14% Similarity=0.164 Sum_probs=23.7
Q ss_pred CcCHHHHHHHhcCCchHHHHHH-HHhCCee
Q 022787 223 PYPLGHLSKVLMMEESDVELFC-NAYGLQT 251 (292)
Q Consensus 223 ~ipl~~l~~~L~f~~~e~~~f~-~~~Gl~~ 251 (292)
++.+.+|++.||.+..+..+.| +..|+.+
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l~~~~Gi~~ 32 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKLFKELGIMV 32 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH-HHHTS--
T ss_pred ceEHHHHHHHHCcCHHHHHHHHHHhCCcCc
Confidence 5788999999999999999999 6699984
No 32
>PF13994 PgaD: PgaD-like protein
Probab=37.90 E-value=49 Score=26.90 Aligned_cols=53 Identities=13% Similarity=0.090 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCchHHHHHHHHhCCeecccCCCcc
Q 022787 203 IDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGNK 259 (292)
Q Consensus 203 ~~~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e~~~f~~~~Gl~~~~d~~g~~ 259 (292)
.++.|.++.+.-.. +.+++.+++++.++.++++..+.-+..-+++.-|++|+.
T Consensus 84 yn~~Rf~~~~rr~~----~~~~~~~elA~~f~l~~~~l~~lr~~k~~~V~~d~~G~I 136 (138)
T PF13994_consen 84 YNRLRFRGRRRRRR----PPPVSDEELARSFGLSPEQLQQLRQAKVLTVHHDDHGRI 136 (138)
T ss_pred HHHHHhcchhhccC----CCCCCHHHHHHHcCCCHHHHHHHHhCCeEEEEeCCCCCc
Confidence 34455555554321 224999999999999987777777777778877888875
No 33
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=37.53 E-value=1.1e+02 Score=21.70 Aligned_cols=47 Identities=11% Similarity=0.227 Sum_probs=27.9
Q ss_pred hHHHHHHHH-HHHHHhhhcCCCCcCHHHHHHHhcCCchH--HHHHHHHhCCeec
Q 022787 202 YIDEVRSLA-LCCIHNCCYKLHPYPLGHLSKVLMMEESD--VELFCNAYGLQTC 252 (292)
Q Consensus 202 ~~~~vR~~a-L~~i~~a~yk~~~ipl~~l~~~L~f~~~e--~~~f~~~~Gl~~~ 252 (292)
|+..+|... ...|.. .. ..|+.+++..+||.+.. ...|-+.+|.+..
T Consensus 27 ~~~~~R~~~a~~~L~~--~~--~~~i~~ia~~~Gf~~~~~f~~~fk~~~g~tP~ 76 (81)
T PF12833_consen 27 YLRELRLQRAKELLRQ--NT--DLSIAEIAEECGFSSQSHFSRAFKRYFGMTPS 76 (81)
T ss_dssp HHHHHHHHHHHHHHHH--HT--T--HHHHHHHTT-SSHHHHHHHHHHHHSS-HH
T ss_pred HHHHHHHHHHHHHHHH--hh--cccHHHHHHHcCCCCHHHHHHHHHHHHCcCHH
Confidence 455566644 444433 22 69999999999999754 5666667788653
No 34
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=35.80 E-value=51 Score=20.13 Aligned_cols=25 Identities=8% Similarity=0.003 Sum_probs=18.3
Q ss_pred HHHHHHHhcCCchHHHHHHHHhCCee
Q 022787 226 LGHLSKVLMMEESDVELFCNAYGLQT 251 (292)
Q Consensus 226 l~~l~~~L~f~~~e~~~f~~~~Gl~~ 251 (292)
+..|.++ ||+.++|++-++..|-.+
T Consensus 6 v~~L~~m-Gf~~~~~~~AL~~~~~nv 30 (37)
T PF00627_consen 6 VQQLMEM-GFSREQAREALRACNGNV 30 (37)
T ss_dssp HHHHHHH-TS-HHHHHHHHHHTTTSH
T ss_pred HHHHHHc-CCCHHHHHHHHHHcCCCH
Confidence 4557777 999889988888887644
No 35
>PF03634 TCP: TCP family transcription factor; InterPro: IPR005333 The TCP transcription factor family was named after: teosinte branched 1 (tb1, Zea mays (Maize)) [], cycloidea (cyc) (Antirrhinum majus) (Garden snapdragon) [] and PCF in rice (Oryza sativa) [, ]. The TCP proteins code for structurally related proteins implicated in the evolution of key morphological traits []. However, the biochemical function of CYC and TB1 proteins remains to be demonstrated. One of the conserved regions is predicted to form a non-canonical basic-Helix-Loop-Helix (bHLP) structure. This domain is also found in two rice DNA-binding proteins, PCF1 and PCF2, where it has been shown to be involved in DNA-binding and dimerization. This family of transcription factors are exclusive to higher plants. They can be divided into two groups, TCP-C and TCP-P, that appear to have separated following an early gene duplication event []. This duplication event may have led to functional divergence and it has been proposed that that the TCP-P subfamily are transcriptional repressors, while the TPC-C subfamily are transcription activators [].
Probab=34.98 E-value=25 Score=28.55 Aligned_cols=17 Identities=18% Similarity=0.229 Sum_probs=12.6
Q ss_pred HHHHHhcCC-chHHHHHH
Q 022787 228 HLSKVLMME-ESDVELFC 244 (292)
Q Consensus 228 ~l~~~L~f~-~~e~~~f~ 244 (292)
+|+++|||| ++.+++||
T Consensus 34 dLQDmLGfDKaSKTveWL 51 (138)
T PF03634_consen 34 DLQDMLGFDKASKTVEWL 51 (138)
T ss_pred HHHHHhcCCCCCchHHHH
Confidence 499999999 56555554
No 36
>PF07643 DUF1598: Protein of unknown function (DUF1598); InterPro: IPR011487 This is a family of Rhodopirellula baltica hypothetical proteins of about 500 amino acids in length.
Probab=34.95 E-value=1.1e+02 Score=22.83 Aligned_cols=64 Identities=17% Similarity=0.146 Sum_probs=37.1
Q ss_pred CHHHHHHHHHHHHHHHcCCCCChhhHHHhhhhhHHHH--HhhhhhhhcCChhhHHHHHHHHHHHHHHHhhhhhcC
Q 022787 13 PLPVLEETLNYLLSLLDSTEHPFEVIHDFVFDRTRSV--RQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRSSC 85 (292)
Q Consensus 13 P~~vL~kT~~yL~~~~~~~~~~~~~~y~Fi~DRlRaI--RQDltvQ~i~~~~~i~v~E~~~Rf~i~~~~~l~~~~ 85 (292)
+++.|++..+|+.+.-.+. .+.. .- ...+.+|.. +||.+|.++..+. ..+|.++.+.|++-...
T Consensus 6 ~~egl~~~qq~~~~~~~~~-~~~~-~~-~~~~~l~~~LG~QdV~V~Gip~~s------h~ArvLVeADyrMKrIg 71 (84)
T PF07643_consen 6 TPEGLKRLQQFLESSNSRS-SPAG-PA-AWVDGLRQALGPQDVTVYGIPADS------HFARVLVEADYRMKRIG 71 (84)
T ss_pred CHHHHHHHHHHHHHHhccc-cccC-HH-HHHHHHHHHhCCceeEEEccCCcc------HHHHHHHHhhhHHHHhc
Confidence 4789999999999865431 1111 11 122344332 4566666664431 45677777899887543
No 37
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=33.36 E-value=2.3e+02 Score=29.66 Aligned_cols=71 Identities=13% Similarity=0.224 Sum_probs=50.8
Q ss_pred HHHHHHHHHHhCcHHHHHHHHHhc------chHHHHHHHhhhHHHHHHHHHHHHHhhhcCC--CCcCHHHHHHHhcCCch
Q 022787 167 FARQALRYFQMGNYRRFLSTVAAE------ASYLQYCIIEPYIDEVRSLALCCIHNCCYKL--HPYPLGHLSKVLMMEES 238 (292)
Q Consensus 167 ~Al~v~~a~~~~Ny~rfFkll~~~------~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~--~~ipl~~l~~~L~f~~~ 238 (292)
+.+...+|+..|||.+-|.-+.+. .|. .--+......+++..+|++..-+ |+. .++++..|++++-++..
T Consensus 656 hVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn-~d~V~~Ml~~rIqEEsLRTYLft-Yss~Y~SvSl~~LA~mFdLp~~ 733 (843)
T KOG1076|consen 656 HVVAASKAMQKGNWQKCFEFIVNNIKVWDLFPN-ADTVLDMLTERIQEESLRTYLFT-YSSVYDSVSLAKLADMFDLPEP 733 (843)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHhhhhHHHhccc-HHHHHHHHHHHHHHHHHHHHHHH-hhhhhhhccHHHHHHHhCCCch
Confidence 566778999999999999843331 222 23456666777899999987653 432 37999999999998854
Q ss_pred H
Q 022787 239 D 239 (292)
Q Consensus 239 e 239 (292)
.
T Consensus 734 ~ 734 (843)
T KOG1076|consen 734 K 734 (843)
T ss_pred h
Confidence 3
No 38
>PRK13503 transcriptional activator RhaS; Provisional
Probab=32.35 E-value=1e+02 Score=27.30 Aligned_cols=46 Identities=13% Similarity=0.216 Sum_probs=35.0
Q ss_pred hHHHHHH-HHHHHHHhhhcCCCCcCHHHHHHHhcCCchH--HHHHHHHhCCeec
Q 022787 202 YIDEVRS-LALCCIHNCCYKLHPYPLGHLSKVLMMEESD--VELFCNAYGLQTC 252 (292)
Q Consensus 202 ~~~~vR~-~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e--~~~f~~~~Gl~~~ 252 (292)
|+..+|. +|.+.+.. ...|+.+++..+||++.- .+.|=+.+|.+..
T Consensus 219 yi~~~Rl~~A~~LL~~-----~~~sI~eIA~~~GF~~~s~F~r~FKk~~G~TP~ 267 (278)
T PRK13503 219 YLNRLRLLKARHLLRH-----SDASVTDIAYRCGFGDSNHFSTLFRREFSWSPR 267 (278)
T ss_pred HHHHHHHHHHHHHHHc-----CCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHH
Confidence 5666777 55665543 158999999999999754 7888899999875
No 39
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=31.97 E-value=84 Score=24.17 Aligned_cols=41 Identities=20% Similarity=0.081 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHhhhcCCCCcC----------HHHHHHHhcCCc----hHHHHHHHH
Q 022787 205 EVRSLALCCIHNCCYKLHPYP----------LGHLSKVLMMEE----SDVELFCNA 246 (292)
Q Consensus 205 ~vR~~aL~~i~~a~yk~~~ip----------l~~l~~~L~f~~----~e~~~f~~~ 246 (292)
.+|.+||..|.. .+..+-++ +..|-+|++|++ +++.+++..
T Consensus 2 EIR~RAL~~I~~-Kl~~~Li~~~dl~~~~~Ll~~LleWFnf~~~~~~~~VL~Ll~~ 56 (98)
T PF14726_consen 2 EIRVRALESIEF-KLEHGLISEEDLVKERLLLKQLLEWFNFPPVPMKEEVLALLLR 56 (98)
T ss_pred hHHHHHHHHHHH-HHHhccccHHHHccHHHHHHHHHHHhCCCCCccHHHHHHHHHH
Confidence 589999999976 34332333 344567999985 234444443
No 40
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=31.39 E-value=1.4e+02 Score=23.63 Aligned_cols=47 Identities=15% Similarity=0.162 Sum_probs=34.5
Q ss_pred hhHHHHHHH-HHHHHHhhhcCCCCcCHHHHHHHhcCCchH--HHHHHHHhCCeec
Q 022787 201 PYIDEVRSL-ALCCIHNCCYKLHPYPLGHLSKVLMMEESD--VELFCNAYGLQTC 252 (292)
Q Consensus 201 ~~~~~vR~~-aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e--~~~f~~~~Gl~~~ 252 (292)
.|+..+|.. |...+.. . ..|+..++..+||.+.. ...|-+.+|.+..
T Consensus 56 ~~l~~~Rl~~A~~~L~~----t-~~~i~eIA~~~Gf~s~s~F~r~Fkk~~G~tP~ 105 (127)
T PRK11511 56 QYIRSRKMTEIAQKLKE----S-NEPILYLAERYGFESQQTLTRTFKNYFDVPPH 105 (127)
T ss_pred HHHHHHHHHHHHHHHHc----C-CCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHH
Confidence 345667874 4555432 1 48999999999999754 6888889999774
No 41
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=31.02 E-value=81 Score=19.55 Aligned_cols=30 Identities=17% Similarity=0.179 Sum_probs=20.4
Q ss_pred CcCHHHHHHHhcCCchH-HHHHHHHhCCeec
Q 022787 223 PYPLGHLSKVLMMEESD-VELFCNAYGLQTC 252 (292)
Q Consensus 223 ~ipl~~l~~~L~f~~~e-~~~f~~~~Gl~~~ 252 (292)
+++++++++.+||+..- ...|=+..|.+..
T Consensus 8 ~~~l~~iA~~~g~S~~~f~r~Fk~~~g~tp~ 38 (42)
T PF00165_consen 8 KLTLEDIAEQAGFSPSYFSRLFKKETGMTPK 38 (42)
T ss_dssp S--HHHHHHHHTS-HHHHHHHHHHHTSS-HH
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHCcCHH
Confidence 69999999999996555 5666667788753
No 42
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=29.94 E-value=1.5e+02 Score=21.15 Aligned_cols=46 Identities=20% Similarity=0.098 Sum_probs=36.2
Q ss_pred HHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCchH---HHHHHHHhCCeecc
Q 022787 206 VRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESD---VELFCNAYGLQTCI 253 (292)
Q Consensus 206 vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e---~~~f~~~~Gl~~~~ 253 (292)
+....|+.|+++-+. .+...+|.+.++.|... ..+.|+..|+.+..
T Consensus 3 ~~~~~Le~I~rsR~~--Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~ 51 (75)
T PF04182_consen 3 IQYCLLERIARSRYN--GITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQ 51 (75)
T ss_pred hHHHHHHHHHhcCCC--CEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEE
Confidence 445788999875444 68889999999988643 68899999998854
No 43
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=29.52 E-value=2e+02 Score=21.20 Aligned_cols=38 Identities=11% Similarity=-0.066 Sum_probs=30.0
Q ss_pred CCcCHHHHHHHhcCCch---HHHHHHHHhCCeecccC-CCcc
Q 022787 222 HPYPLGHLSKVLMMEES---DVELFCNAYGLQTCIDE-VGNK 259 (292)
Q Consensus 222 ~~ipl~~l~~~L~f~~~---e~~~f~~~~Gl~~~~d~-~g~~ 259 (292)
..++-+.|++.||.+.. ..++-++..|+++.... .|-.
T Consensus 18 ~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s~~~kGY~ 59 (79)
T COG1654 18 NFVSGEKLAEELGISRTAVWKHIQQLREEGVDIESVRGKGYL 59 (79)
T ss_pred CcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEecCCCcee
Confidence 37999999999999964 47888999999996542 2544
No 44
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=29.40 E-value=84 Score=23.07 Aligned_cols=53 Identities=21% Similarity=0.223 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCch---H-HHHHHHHhCCeecccCCCcc
Q 022787 205 EVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEES---D-VELFCNAYGLQTCIDEVGNK 259 (292)
Q Consensus 205 ~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~---e-~~~f~~~~Gl~~~~d~~g~~ 259 (292)
.+=.+.|+.|.. .|++.|+-++.|+..|+-+.+ | .+=|+-..|+..-+ ..|.+
T Consensus 8 ~~D~~yL~~l~~-~f~ggPvGl~tlA~~l~ed~~Tie~v~EPyLiq~G~I~RT-~rGR~ 64 (76)
T PF05491_consen 8 ELDRRYLKTLIE-NFKGGPVGLDTLAAALGEDKETIEDVIEPYLIQIGFIQRT-PRGRV 64 (76)
T ss_dssp HHHHHHHHHHHH-CSTTS-B-HHHHHHHTTS-HHHHHHTTHHHHHHTTSEEEE-TTEEE
T ss_pred HHHHHHHHHHHH-HcCCCCeeHHHHHHHHCCCHhHHHHHhhHHHHHhhhHhhC-ccHHH
Confidence 455677888887 688889999999999998743 3 57788899997754 35654
No 45
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=28.93 E-value=2.1e+02 Score=20.05 Aligned_cols=46 Identities=15% Similarity=0.018 Sum_probs=33.6
Q ss_pred HHHHHHHHHHhhhcCCC-CcCHHHHHHHhcCCchHH---HHHHHHhCCeeccc
Q 022787 206 VRSLALCCIHNCCYKLH-PYPLGHLSKVLMMEESDV---ELFCNAYGLQTCID 254 (292)
Q Consensus 206 vR~~aL~~i~~a~yk~~-~ipl~~l~~~L~f~~~e~---~~f~~~~Gl~~~~d 254 (292)
.+.+.|..+... +. .++..+|++.||.+...+ ..-++..|+.....
T Consensus 7 ~~~~IL~~L~~~---g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~ 56 (68)
T smart00550 7 LEEKILEFLENS---GDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQG 56 (68)
T ss_pred HHHHHHHHHHHC---CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 466777887652 22 399999999999997654 44567889987644
No 46
>PF10978 DUF2785: Protein of unknown function (DUF2785); InterPro: IPR021247 Some members in this family are annotated as hypothetical membrane spanning proteins however this cannot be confirmed. The family has no known function.
Probab=28.89 E-value=1.6e+02 Score=24.92 Aligned_cols=87 Identities=17% Similarity=0.274 Sum_probs=49.4
Q ss_pred hcHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHhhcCCCCchhhhHHHHhhhCChhhhcCHhHHHHHHHHHHH
Q 022787 96 LNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRYF 175 (292)
Q Consensus 96 ~n~~ql~qcl~~L~~lY~~~~~~~~~~~ne~EF~aY~iL~~l~~~~~~~~~~l~~~l~~l~~~i~~sp~v~~Al~v~~a~ 175 (292)
.+..+..+.+..+.+.|..... .....|+|-.+..++..+..+.-+ .+.+..|++.++..+-.. +-........
T Consensus 87 ~~~~~~~~lL~~i~~~~~~~~~--~~~~~EdeRLa~~~~~~l~~~~l~-~~~~~~wl~~~~~~l~~~---~~~~~~~~~~ 160 (175)
T PF10978_consen 87 LDRADKIELLAAILEKYKRLST--PFIDGEDERLATALIELLNRNKLY-QEELLSWLKSWRQDLPTQ---RPPYSEADWY 160 (175)
T ss_pred CCHHHHHHHHHHHHHHHcCCCc--ceeCCChhHHHHHHHHHHHcCCCC-HHHHHHHHHHHHHHhhhc---ccccchHHHH
Confidence 4566777778888888876432 234678999998777666554322 334667777653332211 0000112344
Q ss_pred HhCcHHHHHHHHH
Q 022787 176 QMGNYRRFLSTVA 188 (292)
Q Consensus 176 ~~~Ny~rfFkll~ 188 (292)
...|+.+|++.|+
T Consensus 161 ~~~N~~~fL~sLy 173 (175)
T PF10978_consen 161 RFSNIKRFLRSLY 173 (175)
T ss_pred HHHHHHHHHHHHh
Confidence 4567777766543
No 47
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=28.61 E-value=2.7e+02 Score=27.29 Aligned_cols=82 Identities=17% Similarity=0.183 Sum_probs=58.2
Q ss_pred HHHHHHHHhCcHHHHHHHHHhcch------HHHHHHHhhhHHHHHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCc----h
Q 022787 169 RQALRYFQMGNYRRFLSTVAAEAS------YLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEE----S 238 (292)
Q Consensus 169 l~v~~a~~~~Ny~rfFkll~~~~~------~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~----~ 238 (292)
+++..++..+-|.+-+.+|++..| ||... ++..+..||.++|-.... .|. +++++.++.-++.+. .
T Consensus 309 r~il~~fy~sky~~cl~~L~~~k~~llLD~yLaph-Vd~Ly~~IR~r~llqy~~-py~--s~~m~~mA~af~~sv~~le~ 384 (466)
T KOG0686|consen 309 REILFKFYSSKYASCLELLREIKPRLLLDMYLAPH-VDNLYSLIRNRALLQYLS-PYS--SADMSKMAEAFNTSVAILES 384 (466)
T ss_pred HHHHHHHhhhhHHHHHHHHHHhccceeechhcchh-HHHHHHHHHHhhHHHhcC-ccc--cchHHHHHHHhcccHHHHHH
Confidence 457788889999999999875322 33222 344577899999888775 576 799999999999885 3
Q ss_pred HHHHHHHHhCCeeccc
Q 022787 239 DVELFCNAYGLQTCID 254 (292)
Q Consensus 239 e~~~f~~~~Gl~~~~d 254 (292)
+..++..+-.+....|
T Consensus 385 ~l~~LI~~~~i~~rID 400 (466)
T KOG0686|consen 385 ELLELILEGKISGRID 400 (466)
T ss_pred HHHHHHHccchheeec
Confidence 4667766555544334
No 48
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=27.58 E-value=1.7e+02 Score=22.30 Aligned_cols=42 Identities=10% Similarity=-0.004 Sum_probs=33.8
Q ss_pred HHHHHHHhhhcCCCCcCHHHHHHHhcCCchHHHHHHHHhCCeecc
Q 022787 209 LALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCI 253 (292)
Q Consensus 209 ~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e~~~f~~~~Gl~~~~ 253 (292)
.+...+..+ ...+.+.++++.|++...+..++|...|+-...
T Consensus 13 ~~~d~~~~~---~~~~ti~~~AK~L~i~~~~l~~~Lr~~g~l~~~ 54 (111)
T PF03374_consen 13 EFYDAFVDS---DGLYTIREAAKLLGIGRNKLFQWLREKGWLYRR 54 (111)
T ss_pred HHHHHHHcC---CCCccHHHHHHHhCCCHHHHHHHHHhCCceEEC
Confidence 345555432 347999999999999999999999999999863
No 49
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=27.33 E-value=5.5e+02 Score=24.48 Aligned_cols=74 Identities=20% Similarity=0.292 Sum_probs=52.0
Q ss_pred HHHHHHHHHHHHhCcHHHHHHHHHhcchHHHHHH--HhhhHHHHHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCchHHHH
Q 022787 165 MWFARQALRYFQMGNYRRFLSTVAAEASYLQYCI--IEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVEL 242 (292)
Q Consensus 165 v~~Al~v~~a~~~~Ny~rfFkll~~~~~~L~~cl--l~~~~~~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e~~~ 242 (292)
|-..++|+..=...+|+.|..- .-.+++..- =+.-..+||...|..++. - +..||.+++++-|..+++|.+.
T Consensus 240 i~qLL~IF~s~~L~aYveF~~~---N~~Fvqs~gl~~E~~~~KMRLLTlm~LA~--e-s~eisy~~l~k~LqI~edeVE~ 313 (378)
T KOG2753|consen 240 IHQLLKIFVSGKLDAYVEFVAA---NSGFVQSQGLVHEQNMAKMRLLTLMSLAE--E-SNEISYDTLAKELQINEDEVEL 313 (378)
T ss_pred HHHHHHHHHhcchHHHHHHHHh---ChHHHHHhcccHHHHHHHHHHHHHHHHhc--c-CCCCCHHHHHHHhccCHHHHHH
Confidence 5567888888888999998862 334443332 223345689888888864 2 3379999999999999777666
Q ss_pred HH
Q 022787 243 FC 244 (292)
Q Consensus 243 f~ 244 (292)
|.
T Consensus 314 fV 315 (378)
T KOG2753|consen 314 FV 315 (378)
T ss_pred HH
Confidence 63
No 50
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=27.05 E-value=1.1e+02 Score=21.09 Aligned_cols=35 Identities=14% Similarity=0.333 Sum_probs=25.2
Q ss_pred cCHHHHHHHhcCCchHHHHHHHHhCCeecccCCCc
Q 022787 224 YPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGN 258 (292)
Q Consensus 224 ipl~~l~~~L~f~~~e~~~f~~~~Gl~~~~d~~g~ 258 (292)
++++++++.+|.+..-..-+.+..|+....++.|.
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~g~l~~~~~~~g~ 35 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEFNLYIPRTENGR 35 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCCCCCCCCCc
Confidence 46788999999998888888777777643333343
No 51
>TIGR03862 flavo_PP4765 uncharacterized flavoprotein, PP_4765 family. This model describes a sharply distinctive clade of proteins within the larger family of flavoproteins described by Pfam model pfam03486 and TIGRFAMs model TIGR00275. The function is unknown.
Probab=26.31 E-value=66 Score=30.86 Aligned_cols=34 Identities=15% Similarity=0.316 Sum_probs=24.8
Q ss_pred HHHHHHhc-CCchHHHHHHHHhCCeecccCCCccc
Q 022787 227 GHLSKVLM-MEESDVELFCNAYGLQTCIDEVGNKL 260 (292)
Q Consensus 227 ~~l~~~L~-f~~~e~~~f~~~~Gl~~~~d~~g~~~ 260 (292)
.++...|. |+..|+.+|.+++|+.....++|.+|
T Consensus 45 ~fl~~al~~f~~~d~~~fF~~~Gi~~~~e~~grvf 79 (376)
T TIGR03862 45 EWLAPWLEAFDAVALQDWARGLGIETFVGSSGRVF 79 (376)
T ss_pred HHHHHHHHhCCHHHHHHHHHHCCCceEECCCCEEC
Confidence 45555554 67788999999999977666677765
No 52
>PRK13501 transcriptional activator RhaR; Provisional
Probab=26.09 E-value=1.7e+02 Score=26.24 Aligned_cols=48 Identities=17% Similarity=0.351 Sum_probs=36.0
Q ss_pred hhhHHHHHH-HHHHHHHhhhcCCCCcCHHHHHHHhcCCchH--HHHHHHHhCCeec
Q 022787 200 EPYIDEVRS-LALCCIHNCCYKLHPYPLGHLSKVLMMEESD--VELFCNAYGLQTC 252 (292)
Q Consensus 200 ~~~~~~vR~-~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e--~~~f~~~~Gl~~~ 252 (292)
..|+...|. .|.+.+.. ...|+++++..+||++.- .+.|=+..|.+..
T Consensus 222 ~qyi~~~Ri~~A~~LL~~-----t~~sI~eIA~~~GF~~~s~F~r~FKk~~G~TP~ 272 (290)
T PRK13501 222 SHYLRQIRLCHAKCLLRG-----SEHRISDIAARCGFEDSNYFSAVFTREAGMTPR 272 (290)
T ss_pred HHHHHHHHHHHHHHHHHc-----CCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHH
Confidence 346777787 45555543 258999999999999754 6888888899875
No 53
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=24.01 E-value=2.4e+02 Score=19.32 Aligned_cols=29 Identities=14% Similarity=0.234 Sum_probs=25.5
Q ss_pred CcCHHHHHHHhcCCchHHHHHHHHhCCee
Q 022787 223 PYPLGHLSKVLMMEESDVELFCNAYGLQT 251 (292)
Q Consensus 223 ~ipl~~l~~~L~f~~~e~~~f~~~~Gl~~ 251 (292)
.+++..+++.||.+..-...+...+|+.-
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~~r~~W~~ 41 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWKDRYKWDE 41 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHhhCccc
Confidence 48899999999999777899999999864
No 54
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=23.96 E-value=50 Score=31.51 Aligned_cols=44 Identities=16% Similarity=0.288 Sum_probs=31.2
Q ss_pred HHHHHHHHhhhc------CCCCcCHHHHHH-HhcCCchHHHHH---HHHhCCee
Q 022787 208 SLALCCIHNCCY------KLHPYPLGHLSK-VLMMEESDVELF---CNAYGLQT 251 (292)
Q Consensus 208 ~~aL~~i~~a~y------k~~~ipl~~l~~-~L~f~~~e~~~f---~~~~Gl~~ 251 (292)
-+||..++++.| ++.++|+..+.+ +++|+.+||+.| ++.||-.+
T Consensus 246 EqAL~~LvkcnfDteeAlrr~rfnvk~~rd~l~~wsEeEcr~FEegl~~yGKDF 299 (445)
T KOG4329|consen 246 EQALYELVKCNFDTEEALRRLRFNVKTVRDDLSGWSEEECRNFEEGLELYGKDF 299 (445)
T ss_pred HHHHHHHHHcCCcHHHHHHhcCCcceecccccccCCHHHHHHHHHHHHHhcccH
Confidence 468888888755 345678777765 667888999888 66666544
No 55
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=22.38 E-value=2.6e+02 Score=19.00 Aligned_cols=29 Identities=10% Similarity=0.202 Sum_probs=23.3
Q ss_pred CcCHHHHHHHhcC-CchH-HHHHHHHhCCee
Q 022787 223 PYPLGHLSKVLMM-EESD-VELFCNAYGLQT 251 (292)
Q Consensus 223 ~ipl~~l~~~L~f-~~~e-~~~f~~~~Gl~~ 251 (292)
.+++++++..+|| +... ...|-+.+|.+.
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~~g~sp 80 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHCcCh
Confidence 6999999999999 5555 566767778875
No 56
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=22.20 E-value=2.5e+02 Score=18.80 Aligned_cols=44 Identities=18% Similarity=0.116 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCchH---HHHHHHHhCCeec
Q 022787 205 EVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESD---VELFCNAYGLQTC 252 (292)
Q Consensus 205 ~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~e---~~~f~~~~Gl~~~ 252 (292)
..|.+.|+.+.. ..+.++..|++.|+.+... -..-++..|+.-.
T Consensus 10 p~R~~Il~~L~~----~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~ 56 (61)
T PF12840_consen 10 PTRLRILRLLAS----NGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEV 56 (61)
T ss_dssp HHHHHHHHHHHH----CSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHhc----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 478888888832 2379999999999998643 4667888999653
No 57
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=21.59 E-value=2e+02 Score=26.53 Aligned_cols=104 Identities=20% Similarity=0.375 Sum_probs=67.9
Q ss_pred hhHHHHhhhCC--hhhhcCHhHHHHHHHHHHHHhCcHHHHHHHHHh------cchHHHHHHHhhhH---HHHHHHHHHHH
Q 022787 146 ESLSLWFRHVP--SPIIKSKEMWFARQALRYFQMGNYRRFLSTVAA------EASYLQYCIIEPYI---DEVRSLALCCI 214 (292)
Q Consensus 146 ~~l~~~l~~l~--~~i~~sp~v~~Al~v~~a~~~~Ny~rfFkll~~------~~~~L~~cll~~~~---~~vR~~aL~~i 214 (292)
+.|-.++-.|| .++..+..|-.|..+ .|+..|||.-.|++|.. .-+-|+.-=++.|- .++|-+-|-.+
T Consensus 80 erL~rFlwsLp~~~~~~~nEsvLkArA~-vafH~gnf~eLY~iLE~h~Fs~~~h~~LQ~lWl~AhY~EAek~RGR~LgaV 158 (304)
T KOG0775|consen 80 ERLGRFLWSLPVCEELLKNESVLKARAV-VAFHSGNFRELYHILENHKFSPHNHPKLQALWLKAHYKEAEKLRGRPLGAV 158 (304)
T ss_pred HHHHHHHHcCchHHHHhhhHHHHHHHHH-HHHhcccHHHHHHHHHhccCChhhhHHHHHHHHHHHHHHHHHhcCCcCCcc
Confidence 34666677888 667777777767555 78999999999999874 23445554444433 24566667666
Q ss_pred HhhhcC-CCCcCH-------------------HHHHHHhcCCc----hHHHHHHHHhCCeec
Q 022787 215 HNCCYK-LHPYPL-------------------GHLSKVLMMEE----SDVELFCNAYGLQTC 252 (292)
Q Consensus 215 ~~a~yk-~~~ipl-------------------~~l~~~L~f~~----~e~~~f~~~~Gl~~~ 252 (292)
.| |+ ...+|+ +.|.+|..-+. .|=+++.++-||+++
T Consensus 159 ~K--YRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~t 218 (304)
T KOG0775|consen 159 DK--YRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTIT 218 (304)
T ss_pred cc--ceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchh
Confidence 54 53 112332 34677776442 467889999999875
No 58
>PF11360 DUF3110: Protein of unknown function (DUF3110); InterPro: IPR021503 This family of proteins has no known function.
Probab=21.29 E-value=94 Score=23.29 Aligned_cols=31 Identities=29% Similarity=0.550 Sum_probs=19.8
Q ss_pred HhcCCchHHHHHHHHhCCeecccCCC-ccccc
Q 022787 232 VLMMEESDVELFCNAYGLQTCIDEVG-NKLLP 262 (292)
Q Consensus 232 ~L~f~~~e~~~f~~~~Gl~~~~d~~g-~~~l~ 262 (292)
...++.++...||+.+|-...--..| .+++|
T Consensus 52 Ve~id~~~i~~fC~~~gy~~~iv~~g~~l~~P 83 (86)
T PF11360_consen 52 VEEIDPEEIEEFCRSAGYEYEIVPPGRDLLIP 83 (86)
T ss_pred eEEECHHHHHHHHHHCCceEEEECCCCCeeCC
Confidence 33455678999999998765433345 54443
No 59
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=20.72 E-value=1.3e+02 Score=25.75 Aligned_cols=54 Identities=20% Similarity=0.176 Sum_probs=41.6
Q ss_pred CCCcCHHHHHHHhcCCc---hHHHHHHHHhCCeecccCCCccccccCCCcccCCcCcccccc
Q 022787 221 LHPYPLGHLSKVLMMEE---SDVELFCNAYGLQTCIDEVGNKLLPTKQTTFCRPKGGLQNYS 279 (292)
Q Consensus 221 ~~~ipl~~l~~~L~f~~---~e~~~f~~~~Gl~~~~d~~g~~~l~~k~~~f~~~~~~~~~~~ 279 (292)
+.|+.++.+++.||++- +-+..-++..|+.......|. ++..|..|.+-.+..+
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~~G~-----Rk~~F~a~~df~~~f~ 95 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFEKGD-----RKDYFEAEKDFSQIFR 95 (177)
T ss_pred CCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhhhccCc-----chhhhcccchHHHHHH
Confidence 46899999999999994 457888888898776555552 5778888887776544
No 60
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=20.49 E-value=3.5e+02 Score=24.48 Aligned_cols=51 Identities=18% Similarity=0.207 Sum_probs=39.3
Q ss_pred HhhhHHHHHHHHHHHHHhhhcCCCCcCHHHHHHHhcCCch---HHHHHHHHhCCeecc
Q 022787 199 IEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEES---DVELFCNAYGLQTCI 253 (292)
Q Consensus 199 l~~~~~~vR~~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~---e~~~f~~~~Gl~~~~ 253 (292)
++.....+|...|+.+.++ .++.+..+++.||+..+ .-.+-++..|+.-+.
T Consensus 17 ~kalaS~vRv~Il~lL~~k----~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT~ 70 (308)
T COG4189 17 LKALASKVRVAILQLLHRK----GPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHHHHHHh----CCCCHHHHHHHhCCchhhhhhhHHHHHhcCceeee
Confidence 3344556899999999763 37999999999999854 347788999997654
No 61
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=20.20 E-value=2.6e+02 Score=18.11 Aligned_cols=42 Identities=12% Similarity=0.036 Sum_probs=27.0
Q ss_pred HHHHHHHhhhcCCCCcCHHHHHHHhcCCch---HHHHHHHHhCCeecc
Q 022787 209 LALCCIHNCCYKLHPYPLGHLSKVLMMEES---DVELFCNAYGLQTCI 253 (292)
Q Consensus 209 ~aL~~i~~a~yk~~~ipl~~l~~~L~f~~~---e~~~f~~~~Gl~~~~ 253 (292)
+.|..+..+ ..+++.+.|++.|+.+.. .-.+.++..|+.+..
T Consensus 4 ~il~~L~~~---~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~~~I~~ 48 (55)
T PF08279_consen 4 QILKLLLES---KEPITAKELAEELGVSRRTIRRDIKELREWGIPIES 48 (55)
T ss_dssp HHHHHHHHT---TTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT-EEEE
T ss_pred HHHHHHHHc---CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEe
Confidence 345555432 336999999999999863 346667888866643
Done!