Query 023489
Match_columns 281
No_of_seqs 119 out of 452
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 04:25:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023489.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023489hhsearch_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 5.1E-47 1.1E-51 380.5 16.2 233 3-247 168-422 (927)
2 COG5079 SAC3 Nuclear protein e 100.0 3.7E-44 7.9E-49 340.5 16.0 219 19-250 149-386 (646)
3 PF03399 SAC3_GANP: SAC3/GANP/ 100.0 5E-43 1.1E-47 305.9 17.9 178 22-224 26-204 (204)
4 KOG1861 Leucine permease trans 100.0 3.6E-42 7.8E-47 324.8 16.7 217 5-254 302-519 (540)
5 PF10075 PCI_Csn8: COP9 signal 98.9 1E-08 2.2E-13 85.1 10.3 129 114-250 3-133 (143)
6 KOG3151 26S proteasome regulat 98.1 0.00031 6.7E-09 62.8 16.6 164 52-240 55-221 (260)
7 PF01399 PCI: PCI domain; Int 96.1 0.061 1.3E-06 41.0 9.1 72 158-233 4-81 (105)
8 KOG3252 Uncharacterized conser 91.6 0.94 2E-05 39.5 7.6 102 143-251 87-189 (217)
9 KOG4414 COP9 signalosome, subu 84.8 6.5 0.00014 33.2 8.0 97 142-241 63-161 (197)
10 KOG1464 COP9 signalosome, subu 84.3 23 0.0005 33.2 12.1 146 83-239 240-391 (440)
11 smart00753 PAM PCI/PINT associ 83.5 3.2 6.9E-05 30.8 5.3 55 190-247 5-63 (88)
12 smart00088 PINT motif in prote 83.5 3.2 6.9E-05 30.8 5.3 55 190-247 5-63 (88)
13 KOG0687 26S proteasome regulat 83.0 36 0.00077 32.6 12.9 96 146-244 241-353 (393)
14 KOG2581 26S proteasome regulat 72.6 19 0.00042 35.3 8.1 89 142-233 301-398 (493)
15 smart00874 B5 tRNA synthetase 63.8 12 0.00026 26.6 3.8 33 212-244 5-39 (71)
16 KOG0775 Transcription factor S 60.3 36 0.00078 31.5 7.0 105 134-241 79-218 (304)
17 KOG2908 26S proteasome regulat 60.3 68 0.0015 30.8 9.0 86 154-240 234-323 (380)
18 COG5187 RPN7 26S proteasome re 56.2 31 0.00067 32.6 5.9 97 144-243 250-366 (412)
19 PF03484 B5: tRNA synthetase B 54.4 18 0.0004 25.9 3.5 32 212-243 5-38 (70)
20 PF13986 DUF4224: Domain of un 52.8 35 0.00076 22.9 4.3 39 213-251 3-42 (47)
21 PF04800 ETC_C1_NDUFA4: ETC co 51.6 10 0.00022 29.8 1.8 24 221-244 52-76 (101)
22 KOG2753 Uncharacterized conser 48.2 2.3E+02 0.005 27.2 10.4 74 154-233 240-315 (378)
23 PF02042 RWP-RK: RWP-RK domain 47.6 27 0.00059 24.1 3.2 28 212-239 15-42 (52)
24 PF09759 Atx10homo_assoc: Spin 47.3 30 0.00065 27.2 3.8 68 182-251 33-100 (102)
25 PF03634 TCP: TCP family trans 43.5 15 0.00033 30.0 1.7 17 217-233 34-51 (138)
26 PF09494 Slx4: Slx4 endonuclea 38.7 41 0.00089 23.8 3.2 31 211-241 23-62 (64)
27 PF03683 UPF0175: Uncharacteri 38.0 80 0.0017 23.1 4.7 34 207-240 29-62 (76)
28 KOG1076 Translation initiation 36.7 1.7E+02 0.0037 30.8 8.2 70 156-227 656-733 (843)
29 PRK13503 transcriptional activ 36.7 3E+02 0.0065 24.3 10.8 61 169-241 204-267 (278)
30 PF13994 PgaD: PgaD-like prote 36.2 60 0.0013 26.6 4.2 54 191-248 83-136 (138)
31 PRK13501 transcriptional activ 35.3 1.7E+02 0.0037 26.3 7.5 61 169-241 209-272 (290)
32 PF07643 DUF1598: Protein of u 31.5 22 0.00048 27.0 0.8 29 39-73 42-70 (84)
33 PRK11511 DNA-binding transcrip 30.0 2.8E+02 0.0061 21.9 7.6 61 168-240 41-104 (127)
34 PRK13239 alkylmercury lyase; P 28.3 1.7E+02 0.0037 25.9 6.0 51 193-248 21-71 (206)
35 KOG3389 NADH:ubiquinone oxidor 28.0 30 0.00065 29.0 1.1 32 212-243 119-151 (178)
36 PF12324 HTH_15: Helix-turn-he 27.2 2.2E+02 0.0049 21.2 5.5 45 198-248 28-73 (77)
37 cd04764 HTH_MlrA-like_sg1 Heli 26.2 1E+02 0.0022 21.4 3.5 34 213-246 1-34 (67)
38 PF10978 DUF2785: Protein of u 25.7 2E+02 0.0043 24.5 5.8 87 84-176 86-172 (175)
39 KOG2688 Transcription-associat 25.1 4.6E+02 0.0099 25.7 8.7 103 158-260 275-391 (394)
40 PF12833 HTH_18: Helix-turn-he 25.0 2.4E+02 0.0051 19.9 5.4 47 191-240 27-75 (81)
41 PF04760 IF2_N: Translation in 24.0 72 0.0016 21.4 2.2 29 212-240 3-32 (54)
42 PF00627 UBA: UBA/TS-N domain; 23.2 1.1E+02 0.0023 18.9 2.8 23 215-238 6-28 (37)
43 PHA02755 hypothetical protein; 23.0 2E+02 0.0043 21.7 4.5 47 143-189 13-68 (96)
44 PRK10219 DNA-binding transcrip 22.4 3.2E+02 0.0069 20.6 6.0 63 166-240 35-100 (107)
45 PF08784 RPA_C: Replication pr 22.3 1.9E+02 0.0041 21.9 4.6 51 192-242 45-98 (102)
46 KOG2891 Surface glycoprotein [ 21.0 58 0.0013 30.4 1.6 38 226-270 13-50 (445)
47 KOG2141 Protein involved in hi 20.7 27 0.00059 36.5 -0.6 31 18-49 681-711 (822)
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=5.1e-47 Score=380.52 Aligned_cols=233 Identities=31% Similarity=0.518 Sum_probs=205.6
Q ss_pred cccccchHHHHHHHhccCCCCccccccccccchhhhhhhhhHhccCChhHHHHHHHHHHHHHHhhhhhhccCCCCCCChh
Q 023489 3 ILAIHLQPLLLKSFAERCRPRKCGHQMCGLSQTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRSSCSSSSISPL 82 (281)
Q Consensus 3 ~~~~~~~~~ll~~~~~~~~~~~~~Y~F~i~DRlRaIRQDltvQ~i~~~~~i~vlE~~aRf~i~s~~~L~~~~~~~~f~~~ 82 (281)
||-.++=+++-+.+...+.++..+|+| +||||||||||+|+||+.+..||.++|+|+||||++.|+||+.+ +.| |
T Consensus 168 VL~~T~dYLl~~v~~~~~~sl~~~y~F-vwDRtRAVR~D~t~Q~~~d~~Av~llE~i~RfhI~~~h~Lce~~--~~F--d 242 (927)
T KOG1860|consen 168 VLVKTVDYLLGKVLCDKDISLREMYDF-VWDRTRAVRQDFTIQNYSDQEAVELLERIARFHILFRHRLCEEP--EQF--D 242 (927)
T ss_pred HHHHHHHHHHHHhhccccccHHHHHHH-HHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHhccCc--ccC--C
Confidence 444455444445566667799999999 99999999999999999999999999999999999999999987 357 6
Q ss_pred hhhcHHHHHHHHHHHHHHHHhcccCCCCCCCHHHHHHHHHHHhccCCCCchhhhHHHHhhhCChhhhcChhHHHHHHHHH
Q 023489 83 HYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALR 162 (281)
Q Consensus 83 ~~~n~eql~qcl~~L~~lY~~~~~~g~~~~ne~EF~aY~iL~~l~~~~~~~~~~l~~~l~~l~~~i~~~p~v~~Al~i~~ 162 (281)
.++|+|||++|+.+|.++|+|.++.|+.||||+||+||++|++|++++. ..+ .+.+|+++++++.|++|+.+++
T Consensus 243 a~~nlEQL~K~l~sL~elYdD~r~~g~~cpnE~EFR~Y~vLl~Lgd~~~-~~~-----iq~~~~evr~~~~Vk~al~~~~ 316 (927)
T KOG1860|consen 243 AQQNLEQLQKCLQSLGELYDDLRKGGIPCPNEPEFRGYYVLLSLGDPQV-VRD-----IQAWPDEVRQDSEVKLALCLRR 316 (927)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHhcCCchH-HHH-----HHhcCcccccchhHHHHHHHHH
Confidence 8999999999999999999999999999999999999999999999874 222 4578999999999999999999
Q ss_pred HHHhCcHHHHHH------------------HHHh-CCchHHHHHHHHhHHHHHHHHHHHHHhhcCCC--CCcCHHHHHHH
Q 023489 163 YFQMGNYRRFLS------------------TVAA-EASYLQYCIIEPYIDEVRSLALCCIHNCCYKL--HPYPLGHLSKV 221 (281)
Q Consensus 163 a~~~~Ny~rFF~------------------L~~~-~~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~--~~~pl~~L~~~ 221 (281)
|++.|||.+||+ +..+ ..++|++|+++.+|+.+|..|+++|.++ |+. .++|+.++.++
T Consensus 317 a~~~nn~~~~~r~~~~~t~a~~~l~~~~~~l~q~p~~~~L~~~v~~~~f~~ir~~al~~~~~~-~~~~~~~vp~~~l~~~ 395 (927)
T KOG1860|consen 317 AFQSNNFRRFFRLSSLRTEALQNLYTRFFKLMQSPALPYLMGCVLELFFPDIRWAALRAMSHA-YNSKHVPVPLGKLDRI 395 (927)
T ss_pred HhccCCeeeeeeccchhHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHHHHH-HhccCCCcchhHHHHH
Confidence 999999988874 4433 4788999999999999999999999997 754 68999999999
Q ss_pred HcCC-chHHHHHHHHhCCeeeecCCCc
Q 023489 222 LMME-ESDVELFCNAYGLQTCIDEVGN 247 (281)
Q Consensus 222 L~fd-d~e~~~fc~~~Gl~~~~d~~g~ 247 (281)
|+|+ .++...+|..|||+++.|..++
T Consensus 396 l~f~~~e~~~~~~~~y~Leis~~~~~~ 422 (927)
T KOG1860|consen 396 LLFDGEEELKVVCNYYGLEISVDDKIV 422 (927)
T ss_pred HhcCChhhhHhhhhheeeEeecccccc
Confidence 9999 5789999999999998765444
No 2
>COG5079 SAC3 Nuclear protein export factor [Intracellular trafficking and secretion / Cell division and chromosome partitioning]
Probab=100.00 E-value=3.7e-44 Score=340.50 Aligned_cols=219 Identities=29% Similarity=0.407 Sum_probs=197.4
Q ss_pred cCCCCccccccccccchhhhhhhhhHhccCChhHHHHHHHHHHHHHHhhhhhhccCCCCCCChhhhhcHHHHHHHHHHHH
Q 023489 19 RCRPRKCGHQMCGLSQTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRSSCSSSSISPLHYLNLEQLTKALTSLY 98 (281)
Q Consensus 19 ~~~~~~~~Y~F~i~DRlRaIRQDltvQ~i~~~~~i~vlE~~aRf~i~s~~~L~~~~~~~~f~~~~~~n~eql~qcl~~L~ 98 (281)
..+++...|.| +|||+||||||+|+||..+..||+|+|++|||||++.|.|++.+ .|+ .+|++|||.+.|.+|.
T Consensus 149 ~~d~l~e~~~F-v~drtRavrqDftiQN~~g~dAV~c~EriaRfhIl~lh~L~~~p---~Fs--~qqeleQL~ksL~sL~ 222 (646)
T COG5079 149 AGDQLIEMHRF-VRDRTRAVRQDFTIQNEKGKDAVECHERIARFHILFLHLLHDHP---HFS--KQQELEQLKKSLASLI 222 (646)
T ss_pred cCcchHHHHHH-HHhhhHHHHhhceeecccCchHHHHHHHHHHHHHHHHHHHhcCc---ccc--HHhHHHHHHHHHHHHH
Confidence 46788999999 99999999999999999999999999999999999999999974 586 7899999999999999
Q ss_pred HHHHhcccCCCCCCCHHHHHHHHHHHhccCCCCchhhhHHHHhhhCChhhhcChhHHHHHHHHHHHHhCc----------
Q 023489 99 NLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRYFQMGN---------- 168 (281)
Q Consensus 99 ~lY~~~~~~g~~~~ne~EF~aY~iL~~l~~~~~~~~~~l~~~l~~l~~~i~~~p~v~~Al~i~~a~~~~N---------- 168 (281)
++|++++..+..||||+||+||.||.+|+|+.- +.. .+.+|..++.++.|+.|+...+-.+.||
T Consensus 223 elYdd~r~~~~~cpneaEFraYaiL~slgDp~y--v~~----iq~wp~~if~d~~vq~alkl~~laq~nn~r~~~~rnte 296 (646)
T COG5079 223 ELYDDGRAGKKECPNEAEFRAYAILASLGDPRY--VAG----IQGWPGGIFCDLPVQIALKLMQLAQSNNFRLLGRRNTE 296 (646)
T ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHhCCchh--hhc----cccCCccccccchHHHHHHHHHHhhccCeeeccccchh
Confidence 999999998889999999999999999999874 221 3567999999999999999988776665
Q ss_pred -----HHHHHHHHHh-CCchHHHHHHHHhHHHHHHHHHHHHHhhcCCC--CCcCHHHHHHHHcCCc-hHHHHHHHHhCCe
Q 023489 169 -----YRRFLSTVAA-EASYLQYCIIEPYIDEVRSLALCCIHNCCYKL--HPYPLGHLSKVLMMEE-SDVELFCNAYGLQ 239 (281)
Q Consensus 169 -----y~rFF~L~~~-~~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~--~~~pl~~L~~~L~fdd-~e~~~fc~~~Gl~ 239 (281)
|.|||+++++ .++||++|+++.|+..+|..||+.|.++ +.. .++|..++..+|.|++ +|+++||+.||++
T Consensus 297 ac~nlytrFfkl~qSpsv~~lmg~lle~h~~sir~~aLkAm~k~-~~sahk~ipf~~l~~il~f~~~~e~~efckyy~le 375 (646)
T COG5079 297 ACFNLYTRFFKLIQSPSVQYLMGCLLEKHNISIRGGALKAMEKE-IESAHKNIPFVDLSGILDFEEKGEGEEFCKYYGLE 375 (646)
T ss_pred hhhHHHHHHHHHHhCccHHHHHHHHHHHhhHHHHHHHHHHHHHH-HHHhhcCCCeehhhhhccccccchhHHHhhhccee
Confidence 8999999987 7999999999999999999999999997 422 4799999999999996 6899999999999
Q ss_pred eeecCCCcccc
Q 023489 240 TCIDEVGNKLL 250 (281)
Q Consensus 240 ~~~d~~g~~~~ 250 (281)
+..+.+|+..+
T Consensus 376 i~~ed~~~l~i 386 (646)
T COG5079 376 IRIEDSVKLPI 386 (646)
T ss_pred eecccccccch
Confidence 98766676543
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=5e-43 Score=305.86 Aligned_cols=178 Identities=35% Similarity=0.537 Sum_probs=148.1
Q ss_pred CCccccccccccchhhhhhhhhHhccCChhHHHHHHHHHHHHHHhhhhhhccCCCCCCChhhhhcHHHHHHHHHHHHHHH
Q 023489 22 PRKCGHQMCGLSQTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRSSCSSSSISPLHYLNLEQLTKALTSLYNLY 101 (281)
Q Consensus 22 ~~~~~Y~F~i~DRlRaIRQDltvQ~i~~~~~i~vlE~~aRf~i~s~~~L~~~~~~~~f~~~~~~n~eql~qcl~~L~~lY 101 (281)
++.++|+| ||||+||||||++|||+.++++|+|||.+|||+|++ .|.+||++|+++|+++|
T Consensus 26 ~~~~~y~f-i~drlRsiRqDl~vQ~~~~~~~i~v~E~~ar~~i~~------------------~d~~qf~~c~~~L~~lY 86 (204)
T PF03399_consen 26 PFKDDYNF-IWDRLRSIRQDLTVQNIENDFAIKVYERIARFAIES------------------GDLEQFNQCLSQLKELY 86 (204)
T ss_dssp CCCCHHHH-HHHHHHHHHHHHHHTT--SHHHHHHHHHHHHHHHHH------------------HHHHHHHHHHHHHHHHH
T ss_pred hhhhhhHH-HHHHhHHHHhhHHHHhcCCHHHHHHHHHHHHHHhhc------------------CCHHHHHHHHHHHHHHH
Confidence 88889999 999999999999999999999999999999999976 25889999999999999
Q ss_pred HhcccCCCCCCCHHHHHHHHHHHhccCCCCchhhhHHHHhhhCChhhhcChhHHHHHHHHHHHHhCcHHHHHHHHH-hCC
Q 023489 102 EANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRYFQMGNYRRFLSTVA-AEA 180 (281)
Q Consensus 102 ~~~~~~g~~~~ne~EF~aY~iL~~l~~~~~~~~~~l~~~l~~l~~~i~~~p~v~~Al~i~~a~~~~Ny~rFF~L~~-~~~ 180 (281)
++.+. +.+++|++||.||+||+++.+.+. .+ +...+..+|++++++|.|++|++|..|+.+|||++||++++ +++
T Consensus 87 ~~~~~-~~~~~~~~ef~~y~lL~~l~~~~~--~~-~~~~l~~l~~~~~~~~~i~~al~l~~a~~~gny~~ff~l~~~~~~ 162 (204)
T PF03399_consen 87 DDLRD-LPPSPNEAEFIAYYLLYLLCQNNI--PD-FHMELELLPSEILSSPYIQFALELCRALMEGNYVRFFRLYRSKSA 162 (204)
T ss_dssp HHHHH-T---TTHHHHHHHHHHHTT-T-----TH-HHHHHTTS-HHHHTSHHHHHHHHHHHHH--TTHHHHHHHHT-TTS
T ss_pred Hhhcc-CCCCCCHHHHHHHHHHHHHHcccc--hH-HHHHHHHCchhhhcCHHHHHHHHHHHHHHcCCHHHHHHHHhccCC
Confidence 99743 567899999999999999954422 22 33346678999999999999999999999999999999982 279
Q ss_pred chHHHHHHHHhHHHHHHHHHHHHHhhcCCCCCcCHHHHHHHHcC
Q 023489 181 SYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMM 224 (281)
Q Consensus 181 ~~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~~pl~~L~~~L~f 224 (281)
|++.+|+++.+++.||..||++|++| |++ ++|++.+++||+|
T Consensus 163 ~~l~~~l~~~~~~~iR~~al~~i~~a-y~~-~i~l~~l~~~L~F 204 (204)
T PF03399_consen 163 PYLFACLMERFFNRIRLRALQSISKA-YRS-SIPLSFLAELLGF 204 (204)
T ss_dssp -HHHHHHHGGGHHHHHHHHHHHHHHH-S-T--EEHHHHHHHTT-
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHH-cCC-CCCHHHHHHHcCC
Confidence 99999999999999999999999996 875 6999999999998
No 4
>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]
Probab=100.00 E-value=3.6e-42 Score=324.75 Aligned_cols=217 Identities=18% Similarity=0.287 Sum_probs=186.3
Q ss_pred cccchHHHHHHHhccCCCCccccccccccchhhhhhhhhHhccCChhHHHHHHHHHHHHHHhhhhhhccCCCCCCChhhh
Q 023489 5 AIHLQPLLLKSFAERCRPRKCGHQMCGLSQTRSVRQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRSSCSSSSISPLHY 84 (281)
Q Consensus 5 ~~~~~~~ll~~~~~~~~~~~~~Y~F~i~DRlRaIRQDltvQ~i~~~~~i~vlE~~aRf~i~s~~~L~~~~~~~~f~~~~~ 84 (281)
+..|+.+-|-+++.++..- .-|.| ++|||||||||||||+|+|+|||+|||+|||++++.
T Consensus 302 P~~VL~ksL~~vkdk~k~~-~~Y~y-~CdQ~KSiRQDLTVQ~IrneFTveVYEtHARIALEk------------------ 361 (540)
T KOG1861|consen 302 PLEVLKKSLCLVKDKWKAK-ANYAY-LCDQFKSIRQDLTVQRIRNEFTVEVYETHARIALEK------------------ 361 (540)
T ss_pred CHHHHHHHHHHHHHHHHhh-ccHHH-HHHHHHHHhhhhhhheeccceeeeeehhhhHHHHhc------------------
Confidence 4456666676777765544 67999 999999999999999999999999999999999842
Q ss_pred hcHHHHHHHHHHHHHHHHhcccCCCCCCCHHHHHHHHHHHhccCCCCchhhhHHHHhhhCChhhhcChhHHHHHHHHHHH
Q 023489 85 LNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRYF 164 (281)
Q Consensus 85 ~n~eql~qcl~~L~~lY~~~~~~g~~~~ne~EF~aY~iL~~l~~~~~~~~~~l~~~l~~l~~~i~~~p~v~~Al~i~~a~ 164 (281)
.+.++||||+++|+.+|.+. +++. -.||.||+|||.|-..+. .++ ...++.|++++.++|.|.+||+++.|+
T Consensus 362 GD~~EfNQCQtQLk~LY~eg----ipg~-~~EF~AYriLY~i~tkN~--~di-~sll~~lt~E~ked~~V~hAL~vR~A~ 433 (540)
T KOG1861|consen 362 GDLEEFNQCQTQLKALYSEG----IPGA-YLEFTAYRILYYIFTKNY--PDI-LSLLRDLTEEDKEDEAVAHALEVRSAV 433 (540)
T ss_pred CCHHHHHHHHHHHHHHHccC----CCCc-hhhHHHHHHHHHHHhcCc--hHH-HHHHHhccHhhccCHHHHHHHHHHHHH
Confidence 47889999999999999553 2333 799999999999966654 243 345889999999999999999999999
Q ss_pred HhCcHHHHHHHHHhCCchHHHHHHHHhHHHHHHHHHHHHHhhcCCCCCcCHHHHHHHHcCCc-hHHHHHHHHhCCeeeec
Q 023489 165 QMGNYRRFLSTVAAEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEE-SDVELFCNAYGLQTCID 243 (281)
Q Consensus 165 ~~~Ny~rFF~L~~~~~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~~pl~~L~~~L~fdd-~e~~~fc~~~Gl~~~~d 243 (281)
..|||++||+|++ .+|.+..|+|+.|+++.|..||.+|+|| |++ .+|+++|++.|.|++ ++|..|++.+|++- +
T Consensus 434 ~~GNY~kFFrLY~-~AP~M~~yLmdlF~erER~~Al~ii~Ks-yrP-~i~~~fi~~~laf~~~e~c~~~l~~~~~~~--~ 508 (540)
T KOG1861|consen 434 TLGNYHKFFRLYL-TAPNMSGYLMDLFLERERKKALTIICKS-YRP-TITVDFIASELAFDSMEDCVNFLNEQNLTY--D 508 (540)
T ss_pred HhccHHHHHHHHh-hcccchhHHHHHHHHHHHHHHHHHHHHH-cCC-CccHHHHhhhhhhchHHHHHHHHhccCccc--c
Confidence 9999999999997 7999999999999999999999999996 996 699999999999996 67999999999765 5
Q ss_pred CCCccccccCc
Q 023489 244 EVGNKLLPTKQ 254 (281)
Q Consensus 244 ~~g~~~~~~k~ 254 (281)
..|..++..+-
T Consensus 509 ~~g~~~~~~~~ 519 (540)
T KOG1861|consen 509 SLGPQILDKNA 519 (540)
T ss_pred ccCCccccccc
Confidence 66766665343
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=98.91 E-value=1e-08 Score=85.13 Aligned_cols=129 Identities=19% Similarity=0.280 Sum_probs=91.7
Q ss_pred HHHHHHHHHHHhccCCCCchhhhHHHHhhhCChhhhcC-hhHHHHHHHHHHHHhCcHHHHHHHHHhC-CchHHHHHHHHh
Q 023489 114 EAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKS-KEMWFARQALRYFQMGNYRRFLSTVAAE-ASYLQYCIIEPY 191 (281)
Q Consensus 114 e~EF~aY~iL~~l~~~~~~~~~~l~~~l~~l~~~i~~~-p~v~~Al~i~~a~~~~Ny~rFF~L~~~~-~~~L~~cll~~~ 191 (281)
.+++.+-.++..|-..+. .+ ....+..+|+++.++ |.++....+.+++.+++|..|+..+++. -+--..-++..+
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 467888877777754442 23 233356899999994 9999999999999999999999988642 122334556778
Q ss_pred HHHHHHHHHHHHHhhcCCCCCcCHHHHHHHHcCCchHHHHHHHHhCCeeeecCCCcccc
Q 023489 192 IDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGNKLL 250 (281)
Q Consensus 192 ~~~vR~~aL~~i~~a~yk~~~~pl~~L~~~L~fdd~e~~~fc~~~Gl~~~~d~~g~~~~ 250 (281)
.+.+|...+..+.+| |. +++++.++++||++++|+.++|+..|=++ |++|..+.
T Consensus 80 ~~~iR~~i~~~i~~a-Y~--sIs~~~la~~Lg~~~~el~~~~~~~gW~~--d~~~~~~~ 133 (143)
T PF10075_consen 80 EDTIRERIAHLISKA-YS--SISLSDLAEMLGLSEEELEKFIKSRGWTV--DGDGVLFP 133 (143)
T ss_dssp HHHHHHHHHHHHHHH--S--EE-HHHHHHHTTS-HHHHHHHHHHHT-EE-------EE-
T ss_pred HHHHHHHHHHHHHHH-Hh--HcCHHHHHHHhCCCHHHHHHHHHHcCCEE--CCCccEEe
Confidence 899999999999997 86 69999999999999889999999999988 45566544
No 6
>KOG3151 consensus 26S proteasome regulatory complex, subunit RPN12/PSMD8 [Posttranslational modification, protein turnover, chaperones]
Probab=98.08 E-value=0.00031 Score=62.75 Aligned_cols=164 Identities=15% Similarity=0.261 Sum_probs=129.3
Q ss_pred HHHHHHHHHHHHHHhhhhhhccCCCCCCChhhhhcHHHHHHHHHHHHHHHHhcccCCCCCCCHHHHHHHHHHHhccCCCC
Q 023489 52 AINMFEKIVKFHVISHHKLRSSCSSSSISPLHYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQ 131 (281)
Q Consensus 52 ~i~vlE~~aRf~i~s~~~L~~~~~~~~f~~~~~~n~eql~qcl~~L~~lY~~~~~~g~~~~ne~EF~aY~iL~~l~~~~~ 131 (281)
|-+|||--|=..|.. -|.+.|..-+.||+..|-|....=..++++.=+.+..+|+.+..+.
T Consensus 55 aR~ilEi~vl~SI~t------------------~D~~sFerY~~Qlk~YY~d~~~~l~~S~~~~~l~GLnLL~LLsqNR- 115 (260)
T KOG3151|consen 55 ARDILEIGVLLSILT------------------KDFESFERYMNQLKPYYFDYNEKLSESEKKHKLLGLNLLYLLSQNR- 115 (260)
T ss_pred HHHHHHHHHHHHHHh------------------ccHHHHHHHHHHhcchhcccccccCcchhhhHHHHHHHHHHHHhcc-
Confidence 678999888666642 2445688999999999988765434678889999999999886554
Q ss_pred chhhhHHHHhhhCChhhhcC-hhHHHHHHHHHHHHhCcHHHHHHHHHhCCch-HHHHHHHHhHHHHHHHHHHHHHhhcCC
Q 023489 132 PVGESLSLWFRHVPSPIIKS-KEMWFARQALRYFQMGNYRRFLSTVAAEASY-LQYCIIEPYIDEVRSLALCCIHNCCYK 209 (281)
Q Consensus 132 ~~~~~l~~~l~~l~~~i~~~-p~v~~Al~i~~a~~~~Ny~rFF~L~~~~~~~-L~~cll~~~~~~vR~~aL~~i~~a~yk 209 (281)
+.+ +-..+..||..++.+ |.|+.++++=+.++.|-|-+.|...+ ..|. .-.-.|......+|..-=..+-|| |.
T Consensus 116 -iae-FHteLe~lp~~~l~~~~~I~~~v~LEq~~MEGaYnKv~~a~~-s~p~~~y~~FmdIl~~tiRdEIA~c~EKs-Yd 191 (260)
T KOG3151|consen 116 -IAE-FHTELELLPKKILQHNPYISHPVSLEQSLMEGAYNKVLSAKQ-SIPSEEYTYFMDILLDTIRDEIAGCIEKS-YD 191 (260)
T ss_pred -HHH-HHHHHHhccHHHhhccchhhhHHHHHHHHHhhHHHHHHHHHh-cCCcHHHHHHHHHHHHHHHHHHHHHHHHH-Hh
Confidence 223 223377899988776 99999999999999999999998765 4554 334567777888898877777785 85
Q ss_pred CCCcCHHHHHHHHcCC-chHHHHHHHHhCCee
Q 023489 210 LHPYPLGHLSKVLMME-ESDVELFCNAYGLQT 240 (281)
Q Consensus 210 ~~~~pl~~L~~~L~fd-d~e~~~fc~~~Gl~~ 240 (281)
.+|++..+.+|+|+ ++|...|....+-.+
T Consensus 192 --~l~~s~a~~~L~f~~~~e~~~~~~~r~W~l 221 (260)
T KOG3151|consen 192 --KLSASDATQMLLFNNDKELKKFATERQWPL 221 (260)
T ss_pred --hcCHHHHHHHHhcCChHHHHHHHHhcCCcc
Confidence 69999999999999 678999999998655
No 7
>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=96.08 E-value=0.061 Score=41.00 Aligned_cols=72 Identities=21% Similarity=0.385 Sum_probs=54.3
Q ss_pred HHHHHHHHhCcHHHHHHHHHhC------CchHHHHHHHHhHHHHHHHHHHHHHhhcCCCCCcCHHHHHHHHcCCchHHHH
Q 023489 158 RQALRYFQMGNYRRFLSTVAAE------ASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVEL 231 (281)
Q Consensus 158 l~i~~a~~~~Ny~rFF~L~~~~------~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~~pl~~L~~~L~fdd~e~~~ 231 (281)
.++..|+..||+..|...++.- .+++.. .+......+|..+|..+++ .|+ ++|++.+++.|+++.++++.
T Consensus 4 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~-~~~~l~~~i~~~~l~~l~~-~y~--~i~~~~ia~~l~~~~~~vE~ 79 (105)
T PF01399_consen 4 SELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAE-YVEQLKEKIRRRNLRQLSK-PYS--SISISEIAKALQLSEEEVES 79 (105)
T ss_dssp HHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHH-HHHHHHHHHHHHHHHHHHH-C-S--EEEHHHHHHHHTCCHHHHHH
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHH-HHHHHHHHHHHHHHHHHHH-Hhc--ccchHHHHHHhccchHHHHH
Confidence 4578899999999999988742 233333 5566788999999999999 476 69999999999999765544
Q ss_pred HH
Q 023489 232 FC 233 (281)
Q Consensus 232 fc 233 (281)
++
T Consensus 80 ~l 81 (105)
T PF01399_consen 80 IL 81 (105)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 8
>KOG3252 consensus Uncharacterized conserved protein [Function unknown]
Probab=91.64 E-value=0.94 Score=39.46 Aligned_cols=102 Identities=18% Similarity=0.237 Sum_probs=79.4
Q ss_pred hCChhhhcChhHHHHHHHHHHHHhCcHHHHHHHHHhCCchHHHHHHHHhHHHHHHHHHHHHHhhcCCCCCcCHHHHHHHH
Q 023489 143 HVPSPIIKSKEMWFARQALRYFQMGNYRRFLSTVAAEASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVL 222 (281)
Q Consensus 143 ~l~~~i~~~p~v~~Al~i~~a~~~~Ny~rFF~L~~~~~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~~pl~~L~~~L 222 (281)
-+++....+..++.-+.+...+.++||..|+.-.. +-+.+..- +--|=..||.-|=..+.-+ |. .+|-..|+++|
T Consensus 87 li~~~~~~ee~~r~ii~L~~~LEt~~Fq~FW~~~~-~N~~mle~-itGFedsvr~yachvv~iT-yQ--kI~k~lLaell 161 (217)
T KOG3252|consen 87 LIDERVQMEEPFRSIIDLGDYLETCRFQQFWQEAD-ENRDMLEG-ITGFEDSVRKYACHVVGIT-YQ--KIDKWLLAELL 161 (217)
T ss_pred hcCHHHhcccchhHHHhHHHHHhhchHHHHhhhhc-cchHHhcC-CCcHHHHHHHHHHHheech-Hh--hchHHHHHHhh
Confidence 36777788889999999999999999999998653 33332221 2235567888877777764 74 79999999999
Q ss_pred cCC-chHHHHHHHHhCCeeeecCCCccccc
Q 023489 223 MME-ESDVELFCNAYGLQTCIDEVGNKLLP 251 (281)
Q Consensus 223 ~fd-d~e~~~fc~~~Gl~~~~d~~g~~~~~ 251 (281)
|-- |++.+.+.+.+|-.. +++|..++.
T Consensus 162 G~~sDs~le~~~~~~GW~a--~e~G~ifv~ 189 (217)
T KOG3252|consen 162 GGLSDSQLEVWMTKYGWIA--DESGQIFVA 189 (217)
T ss_pred CcccHHHHHHHHHHcccee--cCCceEEEe
Confidence 986 789999999999977 788987775
No 9
>KOG4414 consensus COP9 signalosome, subunit CSN8 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=84.77 E-value=6.5 Score=33.16 Aligned_cols=97 Identities=16% Similarity=0.155 Sum_probs=78.5
Q ss_pred hhCChhhhc-ChhHHHHHHHHHHHHhCcHHHHHHHHHh-CCchHHHHHHHHhHHHHHHHHHHHHHhhcCCCCCcCHHHHH
Q 023489 142 RHVPSPIIK-SKEMWFARQALRYFQMGNYRRFLSTVAA-EASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLS 219 (281)
Q Consensus 142 ~~l~~~i~~-~p~v~~Al~i~~a~~~~Ny~rFF~L~~~-~~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~~pl~~L~ 219 (281)
.++|+.|.+ .|++--|..|-.-+.+.+|...+.-++. .=+--..-+|..+-..-|.++...+..| |. ++-.++++
T Consensus 63 KRIP~AIKe~k~El~aaWgiGQkiWq~Df~GiYeaI~~~dWSeeak~imaAf~D~~~kR~FaLl~qA-Ys--sI~~~D~A 139 (197)
T KOG4414|consen 63 KRIPPAIKEAKPELGAAWGIGQKIWQHDFAGIYEAINAHDWSEEAKDIMAAFRDATRKRAFALLLQA-YS--SIIADDFA 139 (197)
T ss_pred HhCCHHHhhcCchhhhhhhhhHHHHhcccchHHHHHhhhcchHHHHHHHHHHHHHHHHHHHHHHHHH-HH--HHHHHHHH
Confidence 578999876 8899999999999999999999988863 2222334455556677799999999986 75 68899999
Q ss_pred HHHcCCchHHHHHHHHhCCeee
Q 023489 220 KVLMMEESDVELFCNAYGLQTC 241 (281)
Q Consensus 220 ~~L~fdd~e~~~fc~~~Gl~~~ 241 (281)
-.||+.++|+....-+.|-++.
T Consensus 140 ~FlGl~~ddAtk~ilEnGWqaD 161 (197)
T KOG4414|consen 140 AFLGLPEDDATKGILENGWQAD 161 (197)
T ss_pred HHhCCCHHHHHHHHHHcccchh
Confidence 9999999999888888898773
No 10
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=84.27 E-value=23 Score=33.17 Aligned_cols=146 Identities=16% Similarity=0.236 Sum_probs=99.1
Q ss_pred hhhcHHHHHHHHHHHHHHHHhcccCCCCCCCHHHHHHHHHHHhccCCCCchhhhHHHHhhhCChhhhcChhHHHHHHHHH
Q 023489 83 HYLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALR 162 (281)
Q Consensus 83 ~~~n~eql~qcl~~L~~lY~~~~~~g~~~~ne~EF~aY~iL~~l~~~~~~~~~~l~~~l~~l~~~i~~~p~v~~Al~i~~ 162 (281)
-|+..+++.+.-+...+.++--...| +|.+.--.-|-+|.+|--... + +.+. - +--+....+|++----++..
T Consensus 240 MHlreg~fe~AhTDFFEAFKNYDEsG--spRRttCLKYLVLANMLmkS~-i-NPFD--s-QEAKPyKNdPEIlAMTnlv~ 312 (440)
T KOG1464|consen 240 MHLREGEFEKAHTDFFEAFKNYDESG--SPRRTTCLKYLVLANMLMKSG-I-NPFD--S-QEAKPYKNDPEILAMTNLVA 312 (440)
T ss_pred cccccchHHHHHhHHHHHHhcccccC--CcchhHHHHHHHHHHHHHHcC-C-CCCc--c-cccCCCCCCHHHHHHHHHHH
Confidence 45677778888887777665443334 677788888988888622111 0 0000 0 11123456888877788899
Q ss_pred HHHhCcHHHHHHHHHhC------CchHHHHHHHHhHHHHHHHHHHHHHhhcCCCCCcCHHHHHHHHcCCchHHHHHHHHh
Q 023489 163 YFQMGNYRRFLSTVAAE------ASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAY 236 (281)
Q Consensus 163 a~~~~Ny~rFF~L~~~~------~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~~pl~~L~~~L~fdd~e~~~fc~~~ 236 (281)
|++.++...|=+.+++. .||+--. ++-.+..+|.+.|-.+.+- |. .+-+.++++.|..+..|.++++-.+
T Consensus 313 aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh-~EdLl~niRTQVLlkLIkP-Yt--~i~Ipfis~~Lnv~~~dV~~LLV~~ 388 (440)
T KOG1464|consen 313 AYQNNDIIEFERILKSNRSNIMDDPFIREH-IEDLLRNIRTQVLLKLIKP-YT--NIGIPFISKELNVPEADVESLLVSC 388 (440)
T ss_pred HHhcccHHHHHHHHHhhhccccccHHHHHH-HHHHHHHHHHHHHHHHhcc-cc--ccCchhhHhhcCCCHHHHHHHHHHH
Confidence 99999999999999863 4454333 4456788999999888884 76 4666679999999987776666665
Q ss_pred CCe
Q 023489 237 GLQ 239 (281)
Q Consensus 237 Gl~ 239 (281)
=|.
T Consensus 389 ILD 391 (440)
T KOG1464|consen 389 ILD 391 (440)
T ss_pred Hhc
Confidence 443
No 11
>smart00753 PAM PCI/PINT associated module.
Probab=83.49 E-value=3.2 Score=30.77 Aligned_cols=55 Identities=22% Similarity=0.259 Sum_probs=38.9
Q ss_pred HhHHHHHHHHHHHHHhhcCCCCCcCHHHHHHHHcCCchHHH----HHHHHhCCeeeecCCCc
Q 023489 190 PYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVE----LFCNAYGLQTCIDEVGN 247 (281)
Q Consensus 190 ~~~~~vR~~aL~~i~~a~yk~~~~pl~~L~~~L~fdd~e~~----~fc~~~Gl~~~~d~~g~ 247 (281)
.....+|..++..+++. |+ .++++.+++.++++.++++ +....-.+....|....
T Consensus 5 ~l~~~~~~~~l~~l~~~-y~--~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~ 63 (88)
T smart00753 5 RLQRKIRLTNLLQLSEP-YS--SISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNG 63 (88)
T ss_pred HHHHHHHHHHHHHHhHH-hc--eeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCC
Confidence 45688999999999994 76 6999999999999965544 33344344444454333
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=83.49 E-value=3.2 Score=30.77 Aligned_cols=55 Identities=22% Similarity=0.259 Sum_probs=38.9
Q ss_pred HhHHHHHHHHHHHHHhhcCCCCCcCHHHHHHHHcCCchHHH----HHHHHhCCeeeecCCCc
Q 023489 190 PYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVE----LFCNAYGLQTCIDEVGN 247 (281)
Q Consensus 190 ~~~~~vR~~aL~~i~~a~yk~~~~pl~~L~~~L~fdd~e~~----~fc~~~Gl~~~~d~~g~ 247 (281)
.....+|..++..+++. |+ .++++.+++.++++.++++ +....-.+....|....
T Consensus 5 ~l~~~~~~~~l~~l~~~-y~--~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~ 63 (88)
T smart00088 5 RLQRKIRLTNLLQLSEP-YS--SISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNG 63 (88)
T ss_pred HHHHHHHHHHHHHHhHH-hc--eeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCC
Confidence 45688999999999994 76 6999999999999965544 33344344444454333
No 13
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=83.02 E-value=36 Score=32.57 Aligned_cols=96 Identities=21% Similarity=0.281 Sum_probs=68.1
Q ss_pred hhhhcChhHHH-------HHHHHHHHHhCcHHHHHHHHHh------CCchHHHHHHHHhHHHHHHHHHHHHHhhcCCCCC
Q 023489 146 SPIIKSKEMWF-------ARQALRYFQMGNYRRFLSTVAA------EASYLQYCIIEPYIDEVRSLALCCIHNCCYKLHP 212 (281)
Q Consensus 146 ~~i~~~p~v~~-------Al~i~~a~~~~Ny~rFF~L~~~------~~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~ 212 (281)
..|.++|+|.- ..+...++...||..||.-+.. +......--..-|..+||.++-..+-- +|| +
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 44566776653 3445567889999999998842 112222223345788999999999988 498 5
Q ss_pred cCHHHHHHHHcCC----chHHHHHHHHhCCeeeecC
Q 023489 213 YPLGHLSKVLMME----ESDVELFCNAYGLQTCIDE 244 (281)
Q Consensus 213 ~pl~~L~~~L~fd----d~e~~~fc~~~Gl~~~~d~ 244 (281)
+.++.+++-+|.+ |-|+-.|.-+-.|-...|.
T Consensus 318 l~l~~MA~aFgVSVefiDreL~rFI~~grL~ckIDr 353 (393)
T KOG0687|consen 318 LTLESMAKAFGVSVEFIDRELGRFIAAGRLHCKIDR 353 (393)
T ss_pred HHHHHHHHHhCchHHHHHhHHHHhhccCceeeeeec
Confidence 8999999999998 3578888877666665554
No 14
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=72.61 E-value=19 Score=35.27 Aligned_cols=89 Identities=15% Similarity=0.194 Sum_probs=54.8
Q ss_pred hhCC-hhhhcChhHHHH----HHHHHHHHhCcHHHHHHHHHhCCchHHHHHHHHhHHHHH----HHHHHHHHhhcCCCCC
Q 023489 142 RHVP-SPIIKSKEMWFA----RQALRYFQMGNYRRFLSTVAAEASYLQYCIIEPYIDEVR----SLALCCIHNCCYKLHP 212 (281)
Q Consensus 142 ~~l~-~~i~~~p~v~~A----l~i~~a~~~~Ny~rFF~L~~~~~~~L~~cll~~~~~~vR----~~aL~~i~~a~yk~~~ 212 (281)
..+| ..++..|.++-+ +.+.+|+..||-.+|=.-+.+-.+-+++==....+-++| +.+++.|+-+ |. +
T Consensus 301 geiPers~F~Qp~~~ksL~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISls-YS--R 377 (493)
T KOG2581|consen 301 GEIPERSVFRQPGMRKSLRPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISLS-YS--R 377 (493)
T ss_pred CCCcchhhhcCccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheeee-ee--e
Confidence 4455 356677766555 456689999999999876643122122111111223333 4566777764 75 6
Q ss_pred cCHHHHHHHHcCCchHHHHHH
Q 023489 213 YPLGHLSKVLMMEESDVELFC 233 (281)
Q Consensus 213 ~pl~~L~~~L~fdd~e~~~fc 233 (281)
+++.+++..|+.+++|-.+|.
T Consensus 378 ISl~DIA~kL~l~Seed~Eyi 398 (493)
T KOG2581|consen 378 ISLQDIAKKLGLNSEEDAEYI 398 (493)
T ss_pred ccHHHHHHHhcCCCchhHHHH
Confidence 999999999999976544443
No 15
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=63.85 E-value=12 Score=26.65 Aligned_cols=33 Identities=9% Similarity=0.280 Sum_probs=28.4
Q ss_pred CcCHHHHHHHHcCC--chHHHHHHHHhCCeeeecC
Q 023489 212 PYPLGHLSKVLMME--ESDVELFCNAYGLQTCIDE 244 (281)
Q Consensus 212 ~~pl~~L~~~L~fd--d~e~~~fc~~~Gl~~~~d~ 244 (281)
.++.+.+.++||.+ +++..+.++..|+.+..++
T Consensus 5 ~~~~~~i~~llG~~i~~~ei~~~L~~lg~~~~~~~ 39 (71)
T smart00874 5 TLRRERINRLLGLDLSAEEIEEILKRLGFEVEVSG 39 (71)
T ss_pred EecHHHHHHHHCCCCCHHHHHHHHHHCCCeEEecC
Confidence 57899999999998 4689999999999997543
No 16
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=60.33 E-value=36 Score=31.55 Aligned_cols=105 Identities=20% Similarity=0.369 Sum_probs=70.3
Q ss_pred hhhHHHHhhhCC--hhhhcChhHHHHHHHHHHHHhCcHHHHHHHHHhC------CchHHHHHHHHhH---HHHHHHHHHH
Q 023489 134 GESLSLWFRHVP--SPIIKSKEMWFARQALRYFQMGNYRRFLSTVAAE------ASYLQYCIIEPYI---DEVRSLALCC 202 (281)
Q Consensus 134 ~~~l~~~l~~l~--~~i~~~p~v~~Al~i~~a~~~~Ny~rFF~L~~~~------~~~L~~cll~~~~---~~vR~~aL~~ 202 (281)
.+.|..|+..|| .++..+..|--|..+ .||..|||...|+++.+. -+-|+.-=++.|. .++|-+-|-.
T Consensus 79 ~erL~rFlwsLp~~~~~~~nEsvLkArA~-vafH~gnf~eLY~iLE~h~Fs~~~h~~LQ~lWl~AhY~EAek~RGR~Lga 157 (304)
T KOG0775|consen 79 IERLGRFLWSLPVCEELLKNESVLKARAV-VAFHSGNFRELYHILENHKFSPHNHPKLQALWLKAHYKEAEKLRGRPLGA 157 (304)
T ss_pred HHHHHHHHHcCchHHHHhhhHHHHHHHHH-HHHhcccHHHHHHHHHhccCChhhhHHHHHHHHHHHHHHHHHhcCCcCCc
Confidence 456888899999 567777777767654 589999999999999641 2335544333322 3355555655
Q ss_pred HHhhcCCC-CCcCH-------------------HHHHHHHcCCc----hHHHHHHHHhCCeee
Q 023489 203 IHNCCYKL-HPYPL-------------------GHLSKVLMMEE----SDVELFCNAYGLQTC 241 (281)
Q Consensus 203 i~~a~yk~-~~~pl-------------------~~L~~~L~fdd----~e~~~fc~~~Gl~~~ 241 (281)
+-| ||- .++|+ ..|.+|-.-+. +|=.++.++-||+++
T Consensus 158 V~K--YRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~t 218 (304)
T KOG0775|consen 158 VDK--YRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTIT 218 (304)
T ss_pred ccc--ceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchh
Confidence 554 542 23333 36778877652 578999999999886
No 17
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=60.30 E-value=68 Score=30.81 Aligned_cols=86 Identities=20% Similarity=0.222 Sum_probs=60.2
Q ss_pred HHHHHHHHHHHHhCcHHHHHHHHHh--CCchHHHHHHHHhHHHHHHHHHHHHHhhc-CCCCCcCHHHHHHHHcCCchHHH
Q 023489 154 MWFARQALRYFQMGNYRRFLSTVAA--EASYLQYCIIEPYIDEVRSLALCCIHNCC-YKLHPYPLGHLSKVLMMEESDVE 230 (281)
Q Consensus 154 v~~Al~i~~a~~~~Ny~rFF~L~~~--~~~~L~~cll~~~~~~vR~~aL~~i~~a~-yk~~~~pl~~L~~~L~fdd~e~~ 230 (281)
.+.-.++..|+..||..+|+++.+. +-|-|.+-. .....++|.-||--|+-.- .+..++|.+.+++....+..|++
T Consensus 234 ~eWL~dll~Afn~Gdl~~f~~l~~~~~~~p~L~~~e-~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip~~eVE 312 (380)
T KOG2908|consen 234 REWLKDLLIAFNSGDLKRFESLKGVWGKQPDLASNE-DFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIPNKEVE 312 (380)
T ss_pred HHHHHHHHHHhccCCHHHHHHHHHHhccCchHHHHH-HHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCCHHHHH
Confidence 3566789999999999999998864 455655433 2245778888887777531 12247999999999999965543
Q ss_pred -HHHHHhCCee
Q 023489 231 -LFCNAYGLQT 240 (281)
Q Consensus 231 -~fc~~~Gl~~ 240 (281)
-..++.++-.
T Consensus 313 ~LVMKAlslgL 323 (380)
T KOG2908|consen 313 LLVMKALSLGL 323 (380)
T ss_pred HHHHHHHhccc
Confidence 3456666643
No 18
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=56.18 E-value=31 Score=32.59 Aligned_cols=97 Identities=16% Similarity=0.205 Sum_probs=65.6
Q ss_pred CChhhhcChhH----------HHHHHHHHHHHhCcHHHHHHHHHh-CCchHHHHH-----HHHhHHHHHHHHHHHHHhhc
Q 023489 144 VPSPIIKSKEM----------WFARQALRYFQMGNYRRFLSTVAA-EASYLQYCI-----IEPYIDEVRSLALCCIHNCC 207 (281)
Q Consensus 144 l~~~i~~~p~v----------~~Al~i~~a~~~~Ny~rFF~L~~~-~~~~L~~cl-----l~~~~~~vR~~aL~~i~~a~ 207 (281)
+...|..+|+| +.--++..++...||..||.-+.. .+..|+.|. ...|+.+||.++.-.+-- +
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 34456677754 222345567778899999876542 233333332 355788999999988888 4
Q ss_pred CCCCCcCHHHHHHHHcCC----chHHHHHHHHhCCeeeec
Q 023489 208 YKLHPYPLGHLSKVLMME----ESDVELFCNAYGLQTCID 243 (281)
Q Consensus 208 yk~~~~pl~~L~~~L~fd----d~e~~~fc~~~Gl~~~~d 243 (281)
|+ .+.++.++.-+|.+ |-|+-+|.-.-.|....|
T Consensus 329 Yr--~lsl~sMA~tFgVSV~yvdrDLg~FIp~~~LncvID 366 (412)
T COG5187 329 YR--LLSLESMAQTFGVSVEYVDRDLGEFIPEGRLNCVID 366 (412)
T ss_pred HH--HhhHHHHHHHhCccHHHHhhhHHhhCCCCceeeeee
Confidence 98 58999999999997 246778877666655544
No 19
>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=54.42 E-value=18 Score=25.92 Aligned_cols=32 Identities=13% Similarity=0.230 Sum_probs=25.5
Q ss_pred CcCHHHHHHHHcCC-c-hHHHHHHHHhCCeeeec
Q 023489 212 PYPLGHLSKVLMME-E-SDVELFCNAYGLQTCID 243 (281)
Q Consensus 212 ~~pl~~L~~~L~fd-d-~e~~~fc~~~Gl~~~~d 243 (281)
.++.+.+.++||.+ + ++..+.++..|+.+...
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 47889999999998 3 68999999999999873
No 20
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=52.79 E-value=35 Score=22.85 Aligned_cols=39 Identities=10% Similarity=0.123 Sum_probs=31.9
Q ss_pred cCHHHHHHHHcCCc-hHHHHHHHHhCCeeeecCCCccccc
Q 023489 213 YPLGHLSKVLMMEE-SDVELFCNAYGLQTCIDEVGNKLLP 251 (281)
Q Consensus 213 ~pl~~L~~~L~fdd-~e~~~fc~~~Gl~~~~d~~g~~~~~ 251 (281)
+.-+.|.++-|+.- +.-.++++..|+.+..+.+|.+.+.
T Consensus 3 LT~~El~elTG~k~~~~Q~~~L~~~Gi~~~~~~~G~p~V~ 42 (47)
T PF13986_consen 3 LTDEELQELTGYKRPSKQIRWLRRNGIPFVVRADGRPIVT 42 (47)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHHHCCCeeEECCCCCEEee
Confidence 45678899999884 5567899999999999999987664
No 21
>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=51.59 E-value=10 Score=29.84 Aligned_cols=24 Identities=17% Similarity=0.307 Sum_probs=18.5
Q ss_pred HHcCCc-hHHHHHHHHhCCeeeecC
Q 023489 221 VLMMEE-SDVELFCNAYGLQTCIDE 244 (281)
Q Consensus 221 ~L~fdd-~e~~~fc~~~Gl~~~~d~ 244 (281)
.|.|++ ++|+.||+.+|+.....+
T Consensus 52 ~l~F~skE~Ai~yaer~G~~Y~V~~ 76 (101)
T PF04800_consen 52 RLKFDSKEDAIAYAERNGWDYEVEE 76 (101)
T ss_dssp EEEESSHHHHHHHHHHCT-EEEEE-
T ss_pred EeeeCCHHHHHHHHHHcCCeEEEeC
Confidence 577886 679999999999997643
No 22
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=48.19 E-value=2.3e+02 Score=27.23 Aligned_cols=74 Identities=20% Similarity=0.326 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHHhCcHHHHHHHHHhCCchHHHH--HHHHhHHHHHHHHHHHHHhhcCCCCCcCHHHHHHHHcCCchHHHH
Q 023489 154 MWFARQALRYFQMGNYRRFLSTVAAEASYLQYC--IIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVEL 231 (281)
Q Consensus 154 v~~Al~i~~a~~~~Ny~rFF~L~~~~~~~L~~c--ll~~~~~~vR~~aL~~i~~a~yk~~~~pl~~L~~~L~fdd~e~~~ 231 (281)
|--.++|+..=....|+.|..- ...|++.- .=+....+||...|..++. - +..+|.+.+++-|..++.|.+.
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 4557888888888899999852 33443321 1223457899998888875 2 3479999999999999766655
Q ss_pred HH
Q 023489 232 FC 233 (281)
Q Consensus 232 fc 233 (281)
|.
T Consensus 314 fV 315 (378)
T KOG2753|consen 314 FV 315 (378)
T ss_pred HH
Confidence 54
No 23
>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=47.62 E-value=27 Score=24.07 Aligned_cols=28 Identities=18% Similarity=0.355 Sum_probs=25.4
Q ss_pred CcCHHHHHHHHcCCchHHHHHHHHhCCe
Q 023489 212 PYPLGHLSKVLMMEESDVELFCNAYGLQ 239 (281)
Q Consensus 212 ~~pl~~L~~~L~fdd~e~~~fc~~~Gl~ 239 (281)
.+|+..-++.||+.....+.-|+.+|+.
T Consensus 15 hlp~~eAA~~Lgv~~T~LKr~CR~~GI~ 42 (52)
T PF02042_consen 15 HLPIKEAAKELGVSVTTLKRRCRRLGIP 42 (52)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 4899999999999988899999999984
No 24
>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=47.32 E-value=30 Score=27.21 Aligned_cols=68 Identities=22% Similarity=0.189 Sum_probs=45.8
Q ss_pred hHHHHHHHHhHHHHHHHHHHHHHhhcCCCCCcCHHHHHHHHcCCchHHHHHHHHhCCeeeecCCCccccc
Q 023489 182 YLQYCIIEPYIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGNKLLP 251 (281)
Q Consensus 182 ~L~~cll~~~~~~vR~~aL~~i~~a~yk~~~~pl~~L~~~L~fdd~e~~~fc~~~Gl~~~~d~~g~~~~~ 251 (281)
.|..|.++.+-+-+|..|+-.+....-. .-.-..+..-|--....-.+-++..|+.+..|++|.+.+.
T Consensus 33 iL~~c~iD~~nP~irEwai~aiRnL~e~--n~eNQ~~I~~L~~~~~~~~~~L~~~G~~v~~d~~Gk~~l~ 100 (102)
T PF09759_consen 33 ILSCCNIDDHNPFIREWAIFAIRNLCEG--NPENQEFIAQLEPQGVADNEELEELGLEVEIDKDGKVRLK 100 (102)
T ss_pred HHHhcCCCcccHHHHHHHHHHHHHHHhC--CHHHHHHHHhccccCCcchHHHHHcCCeEEEcCCCeEeee
Confidence 3667888999999999999988874221 1222333333333323345778889999999888987664
No 25
>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=43.52 E-value=15 Score=30.03 Aligned_cols=17 Identities=18% Similarity=0.229 Sum_probs=12.9
Q ss_pred HHHHHHcCC-chHHHHHH
Q 023489 217 HLSKVLMME-ESDVELFC 233 (281)
Q Consensus 217 ~L~~~L~fd-d~e~~~fc 233 (281)
.|+++|||| ++.+.+|+
T Consensus 34 dLQDmLGfDKaSKTveWL 51 (138)
T PF03634_consen 34 DLQDMLGFDKASKTVEWL 51 (138)
T ss_pred HHHHHhcCCCCCchHHHH
Confidence 699999999 56655554
No 26
>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=38.71 E-value=41 Score=23.80 Aligned_cols=31 Identities=19% Similarity=0.278 Sum_probs=24.6
Q ss_pred CCcCHHHHHHHHcCC---------chHHHHHHHHhCCeee
Q 023489 211 HPYPLGHLSKVLMME---------ESDVELFCNAYGLQTC 241 (281)
Q Consensus 211 ~~~pl~~L~~~L~fd---------d~e~~~fc~~~Gl~~~ 241 (281)
.|++++.|..+|... ..+..+||...|+.+.
T Consensus 23 ePI~L~el~~~L~~~g~~~~~~~~~~~l~~~lD~~gIt~~ 62 (64)
T PF09494_consen 23 EPINLEELHAWLKASGIGFDRKVDPSKLKEWLDSQGITFT 62 (64)
T ss_pred CCccHHHHHHHHHHcCCCccceeCHHHHHHHHHHCCceee
Confidence 489999999998732 1358999999999875
No 27
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=38.04 E-value=80 Score=23.10 Aligned_cols=34 Identities=15% Similarity=0.185 Sum_probs=30.7
Q ss_pred cCCCCCcCHHHHHHHHcCCchHHHHHHHHhCCee
Q 023489 207 CYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQT 240 (281)
Q Consensus 207 ~yk~~~~pl~~L~~~L~fdd~e~~~fc~~~Gl~~ 240 (281)
-|+...+++..-++++|++-.+..+++..+|+++
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 3666789999999999999889999999999994
No 28
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=36.71 E-value=1.7e+02 Score=30.83 Aligned_cols=70 Identities=13% Similarity=0.225 Sum_probs=53.1
Q ss_pred HHHHHHHHHHhCcHHHHHHHHHhC------CchHHHHHHHHhHHHHHHHHHHHHHhhcCCC--CCcCHHHHHHHHcCCch
Q 023489 156 FARQALRYFQMGNYRRFLSTVAAE------ASYLQYCIIEPYIDEVRSLALCCIHNCCYKL--HPYPLGHLSKVLMMEES 227 (281)
Q Consensus 156 ~Al~i~~a~~~~Ny~rFF~L~~~~------~~~L~~cll~~~~~~vR~~aL~~i~~a~yk~--~~~pl~~L~~~L~fdd~ 227 (281)
+.+...+|...|||.+-|..+... .|- .--+..+...+|+-.+|++.--+ |.+ .+++++.|++++-++..
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 567778899999999999855421 122 34567778899999999998875 543 47999999999988753
No 29
>PRK13503 transcriptional activator RhaS; Provisional
Probab=36.66 E-value=3e+02 Score=24.29 Aligned_cols=61 Identities=15% Similarity=0.210 Sum_probs=41.9
Q ss_pred HHHHHHHHHhCCchHHHHHHHHhHHHHHHH-HHHHHHhhcCCCCCcCHHHHHHHHcCCchH--HHHHHHHhCCeee
Q 023489 169 YRRFLSTVAAEASYLQYCIIEPYIDEVRSL-ALCCIHNCCYKLHPYPLGHLSKVLMMEESD--VELFCNAYGLQTC 241 (281)
Q Consensus 169 y~rFF~L~~~~~~~L~~cll~~~~~~vR~~-aL~~i~~a~yk~~~~pl~~L~~~L~fdd~e--~~~fc~~~Gl~~~ 241 (281)
..|.||-.- ..|+.. |+.++|.. |.+.+..+ ..|+..++..+||++.- ...|=+.+|.+-.
T Consensus 204 l~r~Fk~~~-G~S~~~------yi~~~Rl~~A~~LL~~~-----~~sI~eIA~~~GF~~~s~F~r~FKk~~G~TP~ 267 (278)
T PRK13503 204 LHRQLKQQT-GLTPQR------YLNRLRLLKARHLLRHS-----DASVTDIAYRCGFGDSNHFSTLFRREFSWSPR 267 (278)
T ss_pred HHHHHHHHh-CcCHHH------HHHHHHHHHHHHHHHcC-----CCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHH
Confidence 445554331 455543 78888884 45555442 58999999999999754 6889999998653
No 30
>PF13994 PgaD: PgaD-like protein
Probab=36.20 E-value=60 Score=26.57 Aligned_cols=54 Identities=13% Similarity=0.075 Sum_probs=41.1
Q ss_pred hHHHHHHHHHHHHHhhcCCCCCcCHHHHHHHHcCCchHHHHHHHHhCCeeeecCCCcc
Q 023489 191 YIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGNK 248 (281)
Q Consensus 191 ~~~~vR~~aL~~i~~a~yk~~~~pl~~L~~~L~fdd~e~~~fc~~~Gl~~~~d~~g~~ 248 (281)
..++.|.++.+.-.. +.+++.+++++.++.++++..+.=+..-+++..|++|..
T Consensus 83 ~yn~~Rf~~~~rr~~----~~~~~~~elA~~f~l~~~~l~~lr~~k~~~V~~d~~G~I 136 (138)
T PF13994_consen 83 KYNRLRFRGRRRRRR----PPPVSDEELARSFGLSPEQLQQLRQAKVLTVHHDDHGRI 136 (138)
T ss_pred HHHHHHhcchhhccC----CCCCCHHHHHHHcCCCHHHHHHHHhCCeEEEEeCCCCCc
Confidence 345666665555443 124999999999999988888888888888888999975
No 31
>PRK13501 transcriptional activator RhaR; Provisional
Probab=35.26 E-value=1.7e+02 Score=26.33 Aligned_cols=61 Identities=13% Similarity=0.287 Sum_probs=42.4
Q ss_pred HHHHHHHHHhCCchHHHHHHHHhHHHHHHHH-HHHHHhhcCCCCCcCHHHHHHHHcCCchH--HHHHHHHhCCeee
Q 023489 169 YRRFLSTVAAEASYLQYCIIEPYIDEVRSLA-LCCIHNCCYKLHPYPLGHLSKVLMMEESD--VELFCNAYGLQTC 241 (281)
Q Consensus 169 y~rFF~L~~~~~~~L~~cll~~~~~~vR~~a-L~~i~~a~yk~~~~pl~~L~~~L~fdd~e--~~~fc~~~Gl~~~ 241 (281)
..|.||-. ...++. .|+.+.|... ...+.. ...|++.++..+||+|.- ...|=+.+|++-.
T Consensus 209 l~r~Fk~~-~G~T~~------qyi~~~Ri~~A~~LL~~-----t~~sI~eIA~~~GF~~~s~F~r~FKk~~G~TP~ 272 (290)
T PRK13501 209 LKQLFRQQ-TGMSIS------HYLRQIRLCHAKCLLRG-----SEHRISDIAARCGFEDSNYFSAVFTREAGMTPR 272 (290)
T ss_pred HHHHHHHH-HCcCHH------HHHHHHHHHHHHHHHHc-----CCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHH
Confidence 35566543 234444 3888889854 444443 258999999999999754 6888899998663
No 32
>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=31.52 E-value=22 Score=26.98 Aligned_cols=29 Identities=17% Similarity=0.272 Sum_probs=20.2
Q ss_pred hhhhhHhccCChhHHHHHHHHHHHHHHhhhhhhcc
Q 023489 39 RQDLIMQNIVNDKAINMFEKIVKFHVISHHKLRSS 73 (281)
Q Consensus 39 RQDltvQ~i~~~~~i~vlE~~aRf~i~s~~~L~~~ 73 (281)
+||.+|.++-.+. ..||..+.+.|+|--.
T Consensus 42 ~QdV~V~Gip~~s------h~ArvLVeADyrMKrI 70 (84)
T PF07643_consen 42 PQDVTVYGIPADS------HFARVLVEADYRMKRI 70 (84)
T ss_pred CceeEEEccCCcc------HHHHHHHHhhhHHHHh
Confidence 4555555555554 6789999999988654
No 33
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=30.00 E-value=2.8e+02 Score=21.95 Aligned_cols=61 Identities=15% Similarity=0.177 Sum_probs=42.3
Q ss_pred cHHHHHHHHHhCCchHHHHHHHHhHHHHHHH-HHHHHHhhcCCCCCcCHHHHHHHHcCCchH--HHHHHHHhCCee
Q 023489 168 NYRRFLSTVAAEASYLQYCIIEPYIDEVRSL-ALCCIHNCCYKLHPYPLGHLSKVLMMEESD--VELFCNAYGLQT 240 (281)
Q Consensus 168 Ny~rFF~L~~~~~~~L~~cll~~~~~~vR~~-aL~~i~~a~yk~~~~pl~~L~~~L~fdd~e--~~~fc~~~Gl~~ 240 (281)
-..|.|+-.- ..|+. .|+..+|.. |...+..+ ..|+..++..+||.+.. ...|-+.+|.+-
T Consensus 41 ~l~r~Fk~~~-G~s~~------~~l~~~Rl~~A~~~L~~t-----~~~i~eIA~~~Gf~s~s~F~r~Fkk~~G~tP 104 (127)
T PRK11511 41 HLQRMFKKET-GHSLG------QYIRSRKMTEIAQKLKES-----NEPILYLAERYGFESQQTLTRTFKNYFDVPP 104 (127)
T ss_pred HHHHHHHHHH-CcCHH------HHHHHHHHHHHHHHHHcC-----CCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence 3456666442 45554 377888885 44444432 48999999999999754 688999999865
No 34
>PRK13239 alkylmercury lyase; Provisional
Probab=28.28 E-value=1.7e+02 Score=25.90 Aligned_cols=51 Identities=20% Similarity=0.117 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHhhcCCCCCcCHHHHHHHHcCCchHHHHHHHHhCCeeeecCCCcc
Q 023489 193 DEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVGNK 248 (281)
Q Consensus 193 ~~vR~~aL~~i~~a~yk~~~~pl~~L~~~L~fdd~e~~~fc~~~Gl~~~~d~~g~~ 248 (281)
..+....|+.+++ +.+++.+.|++.++.+.+++..-++..+.... |++|.+
T Consensus 21 ~~~~~~llr~la~----G~pvt~~~lA~~~~~~~~~v~~~L~~l~~~~~-d~~g~i 71 (206)
T PRK13239 21 ATLLVPLLRLLAK----GRPVSVTTLAAALGWPVEEVEAVLEAMPDTEY-DEDGRI 71 (206)
T ss_pred hHHHHHHHHHHHc----CCCCCHHHHHHHhCCCHHHHHHHHHhCCCeEE-CCCCCE
Confidence 3456666777765 35899999999999998899999999887765 677876
No 35
>KOG3389 consensus NADH:ubiquinone oxidoreductase, NDUFS4/18 kDa subunit [Energy production and conversion]
Probab=28.00 E-value=30 Score=29.02 Aligned_cols=32 Identities=19% Similarity=0.390 Sum_probs=26.0
Q ss_pred CcCHHHHHHHHcCCc-hHHHHHHHHhCCeeeec
Q 023489 212 PYPLGHLSKVLMMEE-SDVELFCNAYGLQTCID 243 (281)
Q Consensus 212 ~~pl~~L~~~L~fdd-~e~~~fc~~~Gl~~~~d 243 (281)
.=|++-+.-.|.|+. ++|..||+.+|-.....
T Consensus 119 aDPlsNvgm~L~F~tkEdA~sFaEkngW~ydve 151 (178)
T KOG3389|consen 119 ADPLSNVGMALAFDTKEDAKSFAEKNGWDYDVE 151 (178)
T ss_pred CCcccccceeeeeccHHHHHHHHHHcCCccccc
Confidence 347777778899995 67999999999988653
No 36
>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=27.17 E-value=2.2e+02 Score=21.22 Aligned_cols=45 Identities=18% Similarity=0.150 Sum_probs=28.1
Q ss_pred HHHHHHHhhcCCCCCcCHHHHHHHHcCCchHHHHHHHHh-CCeeeecCCCcc
Q 023489 198 LALCCIHNCCYKLHPYPLGHLSKVLMMEESDVELFCNAY-GLQTCIDEVGNK 248 (281)
Q Consensus 198 ~aL~~i~~a~yk~~~~pl~~L~~~L~fdd~e~~~fc~~~-Gl~~~~d~~g~~ 248 (281)
-.|+.+++ +.|++.+.|+.-+|.+-++....++.. +.+. |++|.+
T Consensus 28 ~LLr~LA~----G~PVt~~~LA~a~g~~~e~v~~~L~~~p~tEy--D~~GrI 73 (77)
T PF12324_consen 28 PLLRLLAK----GQPVTVEQLAAALGWPVEEVRAALAAMPDTEY--DDQGRI 73 (77)
T ss_dssp HHHHHHTT----TS-B-HHHHHHHHT--HHHHHHHHHH-TTSEE--ETTSEE
T ss_pred HHHHHHHc----CCCcCHHHHHHHHCCCHHHHHHHHHhCCCceE--cCCCCe
Confidence 35666665 358999999999999987877776654 3333 667765
No 37
>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=26.22 E-value=1e+02 Score=21.35 Aligned_cols=34 Identities=15% Similarity=0.339 Sum_probs=25.9
Q ss_pred cCHHHHHHHHcCCchHHHHHHHHhCCeeeecCCC
Q 023489 213 YPLGHLSKVLMMEESDVELFCNAYGLQTCIDEVG 246 (281)
Q Consensus 213 ~pl~~L~~~L~fdd~e~~~fc~~~Gl~~~~d~~g 246 (281)
++++.+++.+|.+...+.-|.+..|+.+..++.|
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~g~l~~~~~~~g 34 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEFNLYIPRTENG 34 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCCCCCCCCC
Confidence 4678899999999888888888878775433334
No 38
>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=25.66 E-value=2e+02 Score=24.52 Aligned_cols=87 Identities=17% Similarity=0.279 Sum_probs=51.2
Q ss_pred hhcHHHHHHHHHHHHHHHHhcccCCCCCCCHHHHHHHHHHHhccCCCCchhhhHHHHhhhCChhhhcChhHHHHHHHHHH
Q 023489 84 YLNLEQLTKALTSLYNLYEANRSSKPIHEKEAEFRSFYVLLHLDSNGQPVGESLSLWFRHVPSPIIKSKEMWFARQALRY 163 (281)
Q Consensus 84 ~~n~eql~qcl~~L~~lY~~~~~~g~~~~ne~EF~aY~iL~~l~~~~~~~~~~l~~~l~~l~~~i~~~p~v~~Al~i~~a 163 (281)
+.........+..+.+.|..... ...-.|+|-.|..+...+..+.- -.+.+..|+..++..+-.. +-.......
T Consensus 86 ~~~~~~~~~lL~~i~~~~~~~~~--~~~~~EdeRLa~~~~~~l~~~~l-~~~~~~~wl~~~~~~l~~~---~~~~~~~~~ 159 (175)
T PF10978_consen 86 ELDRADKIELLAAILEKYKRLST--PFIDGEDERLATALIELLNRNKL-YQEELLSWLKSWRQDLPTQ---RPPYSEADW 159 (175)
T ss_pred CCCHHHHHHHHHHHHHHHcCCCc--ceeCCChhHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHHhhhc---ccccchHHH
Confidence 34566677788888888876542 24557899999977777765532 1334556665553332110 001111335
Q ss_pred HHhCcHHHHHHHH
Q 023489 164 FQMGNYRRFLSTV 176 (281)
Q Consensus 164 ~~~~Ny~rFF~L~ 176 (281)
+...|+.+|++-+
T Consensus 160 ~~~~N~~~fL~sL 172 (175)
T PF10978_consen 160 YRFSNIKRFLRSL 172 (175)
T ss_pred HHHHHHHHHHHHH
Confidence 5677888888755
No 39
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=25.09 E-value=4.6e+02 Score=25.66 Aligned_cols=103 Identities=17% Similarity=0.175 Sum_probs=58.7
Q ss_pred HHHHHHHHhCcHHHHHHHHHhCCchHHHHHHHHhHHHHHHHHHHHHHhh----cCCCCCcCHHHHHHHHcCCc--h-H-H
Q 023489 158 RQALRYFQMGNYRRFLSTVAAEASYLQYCIIEPYIDEVRSLALCCIHNC----CYKLHPYPLGHLSKVLMMEE--S-D-V 229 (281)
Q Consensus 158 l~i~~a~~~~Ny~rFF~L~~~~~~~L~~cll~~~~~~vR~~aL~~i~~a----~yk~~~~pl~~L~~~L~fdd--~-e-~ 229 (281)
..+.+|+..||+..|=.-+++.-.++.+|=+..-+.+.|.-..+-+-+- ..+...+|++.+...|.+.. + + -
T Consensus 275 ~~lv~aVr~Gnl~~f~~al~~~E~~f~~~gi~l~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~~~~~~~~~~d 354 (394)
T KOG2688|consen 275 SPLVQAVRSGNLRLFDLALADNERFFIRSGIYLTLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQFSGVTDVDLD 354 (394)
T ss_pred HHHHHHHHhccHHHHHHHHhhhHHHHHHhccHHHhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhcCCCCCchh
Confidence 3456899999999988777653344444333333333444443333321 12556899999999999964 1 1 1
Q ss_pred HHHHHHhCCee------eecCCCccccccCcccccCC
Q 023489 230 ELFCNAYGLQT------CIDEVGNKLLPTKQTTFCRP 260 (281)
Q Consensus 230 ~~fc~~~Gl~~------~~d~~g~~~~~~k~s~f~~p 260 (281)
+-.|.--|+.- +.+..-+..|..|+++|..-
T Consensus 355 eveciLa~lI~~G~ikgYish~~~~~V~sK~~pfp~~ 391 (394)
T KOG2688|consen 355 EVECILANLIDLGRIKGYISHQLQTLVFSKKDPFPHL 391 (394)
T ss_pred hHHHHHHhhhhhccccchhchhhheEEEecCCCCCCC
Confidence 23333333322 22344455666788888654
No 40
>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=24.99 E-value=2.4e+02 Score=19.94 Aligned_cols=47 Identities=11% Similarity=0.183 Sum_probs=30.2
Q ss_pred hHHHHHHHHHHHHHhhcCCCCCcCHHHHHHHHcCCchH--HHHHHHHhCCee
Q 023489 191 YIDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEESD--VELFCNAYGLQT 240 (281)
Q Consensus 191 ~~~~vR~~aL~~i~~a~yk~~~~pl~~L~~~L~fdd~e--~~~fc~~~Gl~~ 240 (281)
|+..+|......+-.. . ..+|+..++..+||.+.. ...|-+.+|.+.
T Consensus 27 ~~~~~R~~~a~~~L~~-~--~~~~i~~ia~~~Gf~~~~~f~~~fk~~~g~tP 75 (81)
T PF12833_consen 27 YLRELRLQRAKELLRQ-N--TDLSIAEIAEECGFSSQSHFSRAFKRYFGMTP 75 (81)
T ss_dssp HHHHHHHHHHHHHHHH-H--TT--HHHHHHHTT-SSHHHHHHHHHHHHSS-H
T ss_pred HHHHHHHHHHHHHHHH-h--hcccHHHHHHHcCCCCHHHHHHHHHHHHCcCH
Confidence 6677777655554321 1 269999999999999754 578888888754
No 41
>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=23.96 E-value=72 Score=21.43 Aligned_cols=29 Identities=14% Similarity=0.164 Sum_probs=23.3
Q ss_pred CcCHHHHHHHHcCCchHHHHHH-HHhCCee
Q 023489 212 PYPLGHLSKVLMMEESDVELFC-NAYGLQT 240 (281)
Q Consensus 212 ~~pl~~L~~~L~fdd~e~~~fc-~~~Gl~~ 240 (281)
++.+..|++.||.+..+....| +..|+.+
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 4678899999999999999999 6699983
No 42
>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=23.20 E-value=1.1e+02 Score=18.89 Aligned_cols=23 Identities=9% Similarity=-0.008 Sum_probs=15.8
Q ss_pred HHHHHHHHcCCchHHHHHHHHhCC
Q 023489 215 LGHLSKVLMMEESDVELFCNAYGL 238 (281)
Q Consensus 215 l~~L~~~L~fdd~e~~~fc~~~Gl 238 (281)
+..|.++ ||+.+++..-++..|=
T Consensus 6 v~~L~~m-Gf~~~~~~~AL~~~~~ 28 (37)
T PF00627_consen 6 VQQLMEM-GFSREQAREALRACNG 28 (37)
T ss_dssp HHHHHHH-TS-HHHHHHHHHHTTT
T ss_pred HHHHHHc-CCCHHHHHHHHHHcCC
Confidence 4556666 9997788877777764
No 43
>PHA02755 hypothetical protein; Provisional
Probab=22.99 E-value=2e+02 Score=21.71 Aligned_cols=47 Identities=21% Similarity=0.282 Sum_probs=33.9
Q ss_pred hCChhhhcChh---------HHHHHHHHHHHHhCcHHHHHHHHHhCCchHHHHHHH
Q 023489 143 HVPSPIIKSKE---------MWFARQALRYFQMGNYRRFLSTVAAEASYLQYCIIE 189 (281)
Q Consensus 143 ~l~~~i~~~p~---------v~~Al~i~~a~~~~Ny~rFF~L~~~~~~~L~~cll~ 189 (281)
+.|..+..+|. ++.|+.|+.|+..-+...|=..+-...--|+.|++.
T Consensus 13 sypdavqgsp~~e~aee~ykmkyalgic~alke~dpk~fee~fgage~~lq~c~~~ 68 (96)
T PHA02755 13 SYPDAVQGSPAAEAAEEKYKMKYALGICQALKEADPKAFEETFGAGEADLQKCALA 68 (96)
T ss_pred cCcccccCChHHHHHHHHHHHHHHHHHHHHHHHhChHHHHHHhcccchhHHHHHHH
Confidence 45666666664 688999999999999888776553234557888753
No 44
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=22.37 E-value=3.2e+02 Score=20.59 Aligned_cols=63 Identities=16% Similarity=0.175 Sum_probs=39.4
Q ss_pred hCcHHHHHHHHHhCCchHHHHHHHHhHHHHHHHH-HHHHHhhcCCCCCcCHHHHHHHHcCCch-H-HHHHHHHhCCee
Q 023489 166 MGNYRRFLSTVAAEASYLQYCIIEPYIDEVRSLA-LCCIHNCCYKLHPYPLGHLSKVLMMEES-D-VELFCNAYGLQT 240 (281)
Q Consensus 166 ~~Ny~rFF~L~~~~~~~L~~cll~~~~~~vR~~a-L~~i~~a~yk~~~~pl~~L~~~L~fdd~-e-~~~fc~~~Gl~~ 240 (281)
.....|.|+-.- ..++. .|+..+|... ...+.. ...|+..++.-+||++. . ...|=+.+|.+-
T Consensus 35 ~~~l~r~f~~~~-g~s~~------~~i~~~Rl~~a~~~L~~-----~~~~i~~iA~~~Gf~~~s~f~~~Fk~~~G~tP 100 (107)
T PRK10219 35 KWYLQRMFRTVT-HQTLG------DYIRQRRLLLAAVELRT-----TERPIFDIAMDLGYVSQQTFSRVFRRQFDRTP 100 (107)
T ss_pred HHHHHHHHHHHH-CcCHH------HHHHHHHHHHHHHHHHc-----cCCCHHHHHHHHCCCCHHHHHHHHHHHHCcCH
Confidence 334455555432 33433 3677777643 444443 24799999999999974 4 467777778754
No 45
>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=22.32 E-value=1.9e+02 Score=21.93 Aligned_cols=51 Identities=14% Similarity=0.078 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHhhcCCCCCcCHHHHHHHHcCCch---HHHHHHHHhCCeeee
Q 023489 192 IDEVRSLALCCIHNCCYKLHPYPLGHLSKVLMMEES---DVELFCNAYGLQTCI 242 (281)
Q Consensus 192 ~~~vR~~aL~~i~~a~yk~~~~pl~~L~~~L~fdd~---e~~~fc~~~Gl~~~~ 242 (281)
+..++.+-|..+....-...-++++.|++.|+++.. ++.+++..-|...++
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 455566666666652122356999999999999853 588888888887754
No 46
>KOG2891 consensus Surface glycoprotein [General function prediction only]
Probab=20.99 E-value=58 Score=30.38 Aligned_cols=38 Identities=24% Similarity=0.216 Sum_probs=27.4
Q ss_pred chHHHHHHHHhCCeeeecCCCccccccCcccccCCcCcccccccc
Q 023489 226 ESDVELFCNAYGLQTCIDEVGNKLLPTKQTTFCRPKGGLQNYSFL 270 (281)
Q Consensus 226 d~e~~~fc~~~Gl~~~~d~~g~~~~~~k~s~f~~p~~~~~~~~~~ 270 (281)
-+||++||.++||-+.+-. . -+.+..-|..++||.+++
T Consensus 13 gseaedf~kaq~lylkpia-----~--ikisv~lpql~ipgksis 50 (445)
T KOG2891|consen 13 GSEAEDFCKAQGLYLKPIA-----K--IKISVALPQLKIPGKSIS 50 (445)
T ss_pred hhHHHhhhhhcceeeccce-----e--EEEEEecccccCCCcccc
Confidence 4799999999999885421 1 144667788888877664
No 47
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=20.69 E-value=27 Score=36.46 Aligned_cols=31 Identities=23% Similarity=0.155 Sum_probs=24.5
Q ss_pred ccCCCCccccccccccchhhhhhhhhHhccCC
Q 023489 18 ERCRPRKCGHQMCGLSQTRSVRQDLIMQNIVN 49 (281)
Q Consensus 18 ~~~~~~~~~Y~F~i~DRlRaIRQDltvQ~i~~ 49 (281)
.-.++|.-.+.||+|||+|-+-+ +..+++.|
T Consensus 681 e~~~~~~~tfQF~~WD~f~ele~-ls~~ri~n 711 (822)
T KOG2141|consen 681 EFNKNLKKTFQFALWDRFKELEQ-LSLFRISN 711 (822)
T ss_pred HHhhhhHHHHHHHHHHHHHHhhh-cchhhHhH
Confidence 34667788899999999999876 77777665
Done!