Query 026639
Match_columns 235
No_of_seqs 185 out of 319
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 10:40:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026639.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026639hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4325 Uncharacterized conser 100.0 3.9E-43 8.5E-48 299.3 16.6 197 10-228 3-210 (212)
2 PF09282 Mago-bind: Mago bindi 99.7 5.1E-18 1.1E-22 105.4 0.9 27 25-51 1-27 (27)
3 KOG2315 Predicted translation 99.1 1.1E-10 2.3E-15 114.5 6.5 51 177-227 515-566 (566)
4 COG5354 Uncharacterized protei 97.1 0.00086 1.9E-08 66.4 5.4 51 175-225 507-558 (561)
5 PF14282 FlxA: FlxA-like prote 87.2 6.8 0.00015 31.1 9.0 54 177-232 16-70 (106)
6 PF14193 DUF4315: Domain of un 58.6 21 0.00046 27.7 4.5 37 177-213 19-57 (83)
7 TIGR03091 SASP_sspK small, aci 54.0 5.7 0.00012 25.9 0.6 10 31-40 12-21 (32)
8 PF14257 DUF4349: Domain of un 52.5 61 0.0013 28.9 7.1 53 176-232 135-188 (262)
9 PF13234 rRNA_proc-arch: rRNA- 48.9 45 0.00097 29.8 5.7 53 179-231 208-267 (268)
10 PF10153 DUF2361: Uncharacteri 44.9 48 0.001 27.1 4.8 36 185-229 2-37 (114)
11 PF03980 Nnf1: Nnf1 ; InterPr 37.2 1.6E+02 0.0035 22.8 6.6 50 181-230 28-90 (109)
12 PF08176 SspK: Small acid-solu 36.4 16 0.00034 25.8 0.6 10 31-40 27-36 (47)
13 PF13243 Prenyltrans_1: Prenyl 35.6 12 0.00027 28.0 0.0 15 26-40 5-19 (109)
14 PF15188 CCDC-167: Coiled-coil 34.6 2E+02 0.0043 22.5 6.5 37 179-215 4-44 (85)
15 PF07106 TBPIP: Tat binding pr 34.0 1.7E+02 0.0038 24.3 6.7 57 176-234 75-137 (169)
16 PF14723 SSFA2_C: Sperm-specif 33.6 1.9E+02 0.0042 25.6 7.0 54 177-232 106-171 (179)
17 PRK03081 sspK acid-soluble spo 31.4 21 0.00046 25.4 0.6 10 31-40 26-35 (50)
18 PF13864 Enkurin: Calmodulin-b 30.0 1.4E+02 0.0029 23.1 5.0 57 174-233 38-94 (98)
19 PF03942 DTW: DTW domain; Int 27.4 15 0.00031 31.6 -0.9 12 35-46 120-131 (203)
20 PF05121 GvpK: Gas vesicle pro 26.0 2.4E+02 0.0052 22.3 5.7 51 177-227 13-66 (88)
21 PF10458 Val_tRNA-synt_C: Valy 26.0 2.2E+02 0.0047 20.5 5.2 55 178-232 2-65 (66)
22 COG3148 Uncharacterized conser 25.9 17 0.00037 33.2 -0.8 12 34-45 134-145 (231)
23 COG4550 Predicted membrane pro 25.4 2.9E+02 0.0062 23.1 6.3 21 176-196 5-25 (120)
24 PF12017 Tnp_P_element: Transp 23.8 1.2E+02 0.0027 27.5 4.3 37 177-214 29-65 (236)
25 PF11221 Med21: Subunit 21 of 22.3 4.2E+02 0.0091 21.9 6.9 46 181-229 74-120 (144)
26 PF03962 Mnd1: Mnd1 family; I 22.1 4.9E+02 0.011 22.6 7.5 27 206-232 103-129 (188)
27 KOG2150 CCR4-NOT transcription 20.1 2.7E+02 0.0059 28.8 6.2 49 177-228 9-57 (575)
No 1
>KOG4325 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.9e-43 Score=299.32 Aligned_cols=197 Identities=46% Similarity=0.624 Sum_probs=159.7
Q ss_pred HHhhhhhhccccccCCCeeccCccCCCCCcccceecCCCCCCccchhhhhcchHHHHHhhhccCCCCCCCCCcCCCC---
Q 026639 10 EELKRMAELSKTLKEGERILAPTRRPDGTLRKPIRIRAGYVPQDEVAIYQSKGALLRKELTALQEAPPGYDPELDAK--- 86 (235)
Q Consensus 10 ~~~~~~~~~~~~~~~g~~~i~~s~R~DGt~Rk~~rvr~gy~p~eev~~y~~~~~~~~~~~~~~~~~PPG~~p~~~~k--- 86 (235)
+..+.||+.+.....|++||.+||||||||||+||||+||+|+|||++|+|++..|++.++. .+||||+|++.++
T Consensus 3 aaGkpaAeesgnlkegek~ia~TqRPDGT~RK~~RikeGYtPedEVp~YenK~~kffKek~e--q~PPGlePdaaa~~kp 80 (212)
T KOG4325|consen 3 AAGKPAAEESGNLKEGEKIIAPTQRPDGTLRKPIRIKEGYTPEDEVPKYENKGSKFFKEKAE--QGPPGLEPDAAAKPKP 80 (212)
T ss_pred ccccchhhhhccccccceeeccccCCCCccccceeccCCCCchhhhhhhhhhhhHHHhhhhh--cCCCCCCCCCCCCCCC
Confidence 46789999999999999999999999999999999999999999999999999999999882 4999999985532
Q ss_pred --------ccchhhhhhhHHHHHHHHHHHHhhcchhhhhcccccchhhhhhhhhccCCCCcchhhhhhhhhccccCCCCc
Q 026639 87 --------PKTKSVKRNERKKEKRQQQAALEKGKIVEKLVDGEIKTEEVVSAENLSHGSASTDSLTSQMNELSVSANPVV 158 (235)
Q Consensus 87 --------~~skaakKN~KRKEKrkkq~a~~k~~~~~~~~dg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~ 158 (235)
.+++++|+|.||++++++|+. ++.. .+++ ..+.++..|.-..+.|..++++.+..+
T Consensus 81 k~~eggEpglsktakRnlKkeek~qaqaE--K~ea---eea~-----------S~sldsqkVnleasa~~~~apqgn~aa 144 (212)
T KOG4325|consen 81 KAAEGGEPGLSKTAKRNLKKEEKLQAQAE--KAEA---EEAG-----------SASLDSQKVNLEASAMEALAPQGNNAA 144 (212)
T ss_pred CcccCCCccchhHHHhhhhHHHHHHHHHH--hhcc---hhhh-----------ccccCccccchhhhhhhccCcccCccc
Confidence 368889999999999886653 3331 1111 112334456667777877777777766
Q ss_pred CCCCCCCCCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHhcHHHHHHHHHHHHHh
Q 026639 159 ENPLSDAKDPGDAGAPGQDIDKRIRAIKKKIRLSEAQQQKAGQQELKPEQLEKLSKLEGWRNELKLLEEK 228 (235)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~e~~KkiRnLkKKLRqIE~Lk~k~~G~~L~~eQleKl~k~~el~~EL~~Le~~ 228 (235)
|+.. +........++.+||||||+||||+.|+|++++..+.|+++|++|+.+..+|+.|++.||..
T Consensus 145 ~~aA----~d~~dsaa~edkaKkIkaLKKKiR~tEalQQkiaagdln~~qkEkfeKLaerRa~eeaLED~ 210 (212)
T KOG4325|consen 145 CGAA----PDPGDSAAGEDKAKKIKALKKKIRLTEALQQKIAAGDLNPEQKEKFEKLAERRAEEEALEDK 210 (212)
T ss_pred ccCC----CCCCcccchhhHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHHHhhhh
Confidence 5532 11122234679999999999999999999999999999999999999999999999999864
No 2
>PF09282 Mago-bind: Mago binding; InterPro: IPR015362 Members of this family adopt a structure consisting of a small globular all-beta-domain, with a three-stranded beta-sheet and a contiguous beta-hairpin. They bind to Mago alpha-helices via extensive electrostatic interactions and at a beta2-beta3 loop via hydrophobic interactions []. ; GO: 0005515 protein binding; PDB: 1RK8_C.
Probab=99.69 E-value=5.1e-18 Score=105.40 Aligned_cols=27 Identities=63% Similarity=1.195 Sum_probs=14.0
Q ss_pred CCeeccCccCCCCCcccceecCCCCCC
Q 026639 25 GERILAPTRRPDGTLRKPIRIRAGYVP 51 (235)
Q Consensus 25 g~~~i~~s~R~DGt~Rk~~rvr~gy~p 51 (235)
|++|||+||||||||||+||||+||+|
T Consensus 1 Ger~I~~s~RpDGt~RK~irvr~GY~P 27 (27)
T PF09282_consen 1 GERIIPASQRPDGTWRKEIRVRPGYTP 27 (27)
T ss_dssp --EEE--EE-TTS-EE--EE--TT---
T ss_pred CccCcCcccCCCCCcccceeccCCcCC
Confidence 799999999999999999999999998
No 3
>KOG2315 consensus Predicted translation initiation factor related to eIF-3a [Translation, ribosomal structure and biogenesis]
Probab=99.10 E-value=1.1e-10 Score=114.48 Aligned_cols=51 Identities=35% Similarity=0.418 Sum_probs=48.3
Q ss_pred chHHHHHHHHHHHHHHHHHH-HHhccCCCCHHHHHHHhcHHHHHHHHHHHHH
Q 026639 177 DIDKRIRAIKKKIRLSEAQQ-QKAGQQELKPEQLEKLSKLEGWRNELKLLEE 227 (235)
Q Consensus 177 e~~KkiRnLkKKLRqIE~Lk-~k~~G~~L~~eQleKl~k~~el~~EL~~Le~ 227 (235)
+.+||||+|.||||.||.|| +...|+.|+++||+||.++..|+.||+.|++
T Consensus 515 ~~ekKir~L~kkLraIe~LK~r~a~Ge~Le~nQl~kIq~E~~~l~ELk~L~~ 566 (566)
T KOG2315|consen 515 EEEKKIRSLLKKLRAIEALKERMANGEQLEVNQLNKIQKEPKLLSELKKLGW 566 (566)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcccccCHHHHHHHhhhHHHHHHHHhhcC
Confidence 88999999999999999999 6668999999999999999999999999963
No 4
>COG5354 Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only]
Probab=97.05 E-value=0.00086 Score=66.44 Aligned_cols=51 Identities=31% Similarity=0.342 Sum_probs=45.8
Q ss_pred CCchHHHHHHHHHHHHHHHHHH-HHhccCCCCHHHHHHHhcHHHHHHHHHHH
Q 026639 175 GQDIDKRIRAIKKKIRLSEAQQ-QKAGQQELKPEQLEKLSKLEGWRNELKLL 225 (235)
Q Consensus 175 ~~e~~KkiRnLkKKLRqIE~Lk-~k~~G~~L~~eQleKl~k~~el~~EL~~L 225 (235)
....+.|||.|-||||.|+.|+ +...|++|+..|+-||..+.+++.||+.|
T Consensus 507 e~s~e~ki~sl~~~lRaIe~lker~~~~eele~~qv~kietee~VlsElk~l 558 (561)
T COG5354 507 EYSDEDKIRSLLKKLRAIEALKERMRSGEELEVIQVNKIETEEEVLSELKEL 558 (561)
T ss_pred ccCHHHHHHHHHHHhhhhhcchhhcccccchhhhhhhhhhhHHHHHHHhhhc
Confidence 3344559999999999999999 66689999999999999999999999988
No 5
>PF14282 FlxA: FlxA-like protein
Probab=87.24 E-value=6.8 Score=31.10 Aligned_cols=54 Identities=22% Similarity=0.367 Sum_probs=38.0
Q ss_pred chHHHHHHHHHHHHHHHHHHHHh-ccCCCCHHHHHHHhcHHHHHHHHHHHHHhhhhh
Q 026639 177 DIDKRIRAIKKKIRLSEAQQQKA-GQQELKPEQLEKLSKLEGWRNELKLLEEKKADL 232 (235)
Q Consensus 177 e~~KkiRnLkKKLRqIE~Lk~k~-~G~~L~~eQleKl~k~~el~~EL~~Le~~~a~l 232 (235)
..+..|..|++.|..+.+-=..+ ....|++++.. .+...|..+|..|+.+++.|
T Consensus 16 ~~~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~--~q~q~Lq~QI~~LqaQI~ql 70 (106)
T PF14282_consen 16 SSDSQIEQLQKQIKQLQEQLQELSQDSDLDAEQKQ--QQIQLLQAQIQQLQAQIAQL 70 (106)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHcccCCCHHHHH--HHHHHHHHHHHHHHHHHHHH
Confidence 34788888887776665433333 44778877654 45788999999999887765
No 6
>PF14193 DUF4315: Domain of unknown function (DUF4315)
Probab=58.62 E-value=21 Score=27.66 Aligned_cols=37 Identities=16% Similarity=0.369 Sum_probs=31.5
Q ss_pred chHHHHHHHHHHHHHHHHHH--HHhccCCCCHHHHHHHh
Q 026639 177 DIDKRIRAIKKKIRLSEAQQ--QKAGQQELKPEQLEKLS 213 (235)
Q Consensus 177 e~~KkiRnLkKKLRqIE~Lk--~k~~G~~L~~eQleKl~ 213 (235)
+.+.|+|.|..++++.|.++ +.+.+-.|+|+||.-+-
T Consensus 19 e~Q~rlK~Le~qk~E~EN~EIv~~VR~~~mtp~eL~~~L 57 (83)
T PF14193_consen 19 ELQARLKELEAQKTEAENLEIVQMVRSMKMTPEELAAFL 57 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 56789999999999999999 66689999999997653
No 7
>TIGR03091 SASP_sspK small, acid-soluble spore protein K. This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. It is a minor SASP (small, acid-soluble spore protein) designated SspK.
Probab=53.96 E-value=5.7 Score=25.90 Aligned_cols=10 Identities=50% Similarity=1.122 Sum_probs=8.8
Q ss_pred CccCCCCCcc
Q 026639 31 PTRRPDGTLR 40 (235)
Q Consensus 31 ~s~R~DGt~R 40 (235)
+|.|||||+.
T Consensus 12 aSKR~dGtin 21 (32)
T TIGR03091 12 ASKRPDGTIN 21 (32)
T ss_pred hhcCCCCCcc
Confidence 7999999975
No 8
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=52.52 E-value=61 Score=28.86 Aligned_cols=53 Identities=23% Similarity=0.295 Sum_probs=38.4
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHhc-HHHHHHHHHHHHHhhhhh
Q 026639 176 QDIDKRIRAIKKKIRLSEAQQQKAGQQELKPEQLEKLSK-LEGWRNELKLLEEKKADL 232 (235)
Q Consensus 176 ~e~~KkiRnLkKKLRqIE~Lk~k~~G~~L~~eQleKl~k-~~el~~EL~~Le~~~a~l 232 (235)
.|.+.||++|++....+.+|-.+.. +.+.+-+|.+ ...++.||+.|+.++.-|
T Consensus 135 ~D~~arl~~l~~~~~rl~~ll~ka~----~~~d~l~ie~~L~~v~~eIe~~~~~~~~l 188 (262)
T PF14257_consen 135 VDLEARLKNLEAEEERLLELLEKAK----TVEDLLEIERELSRVRSEIEQLEGQLKYL 188 (262)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcC----CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3788999999998888888765433 4555555543 467888999998876655
No 9
>PF13234 rRNA_proc-arch: rRNA-processing arch domain; PDB: 4A4K_E 4A4Z_A 2XGJ_B 3L9O_A.
Probab=48.88 E-value=45 Score=29.80 Aligned_cols=53 Identities=19% Similarity=0.311 Sum_probs=39.3
Q ss_pred HHHHH--HHHHHHHHHHHHHHHhccCCCC-----HHHHHHHhcHHHHHHHHHHHHHhhhh
Q 026639 179 DKRIR--AIKKKIRLSEAQQQKAGQQELK-----PEQLEKLSKLEGWRNELKLLEEKKAD 231 (235)
Q Consensus 179 ~KkiR--nLkKKLRqIE~Lk~k~~G~~L~-----~eQleKl~k~~el~~EL~~Le~~~a~ 231 (235)
+=+|+ .+.+-++.|+.|+.++.+..|- .+++..+.++..|.+||+.|..++..
T Consensus 208 DmkI~d~~~~e~~~k~~~Le~rl~~~~~~~~~~~~~~~~~~~~k~~l~~~i~~Lk~~l~~ 267 (268)
T PF13234_consen 208 DMKIKDPEFVELVKKIEALEKRLSSHPLHKCPDFEEHYALYHEKAELQEEIKALKRQLSD 267 (268)
T ss_dssp HH----HHHHHHHHHHHHHHHHHHHSCHCCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hCCCCcHHHHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34554 6777888889998766554442 47889999999999999999988754
No 10
>PF10153 DUF2361: Uncharacterised conserved protein (DUF2361); InterPro: IPR019310 This entry represents the rRNA-processing protein EFG1 family. EFG1 is involved in rRNA processing.
Probab=44.90 E-value=48 Score=27.14 Aligned_cols=36 Identities=25% Similarity=0.285 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHHHhccCCCCHHHHHHHhcHHHHHHHHHHHHHhh
Q 026639 185 IKKKIRLSEAQQQKAGQQELKPEQLEKLSKLEGWRNELKLLEEKK 229 (235)
Q Consensus 185 LkKKLRqIE~Lk~k~~G~~L~~eQleKl~k~~el~~EL~~Le~~~ 229 (235)
|+++||+|+-|=.+. .|.++- ..+.+.+|+.|+.++
T Consensus 2 lK~riRdieRLL~r~---~Lp~~v------R~~~Er~L~~L~~~l 37 (114)
T PF10153_consen 2 LKKRIRDIERLLKRK---DLPADV------RVEKERELEALKREL 37 (114)
T ss_pred HHHHHHHHHHHHcCC---CCCHHH------HHHHHHHHHHHHHHH
Confidence 678888888875322 777654 334444555555443
No 11
>PF03980 Nnf1: Nnf1 ; InterPro: IPR007128 NNF1 is an essential yeast gene required for proper spindle orientation, nucleolar and nuclear envelope structure and mRNA export [].
Probab=37.23 E-value=1.6e+02 Score=22.78 Aligned_cols=50 Identities=16% Similarity=0.142 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHH-----HHhccCC--------CCHHHHHHHhcHHHHHHHHHHHHHhhh
Q 026639 181 RIRAIKKKIRLSEAQQ-----QKAGQQE--------LKPEQLEKLSKLEGWRNELKLLEEKKA 230 (235)
Q Consensus 181 kiRnLkKKLRqIE~Lk-----~k~~G~~--------L~~eQleKl~k~~el~~EL~~Le~~~a 230 (235)
+=|+|..||-.++.|- ++..|.. |+|+++-...--..+..+++.|...+.
T Consensus 28 ~Er~v~~kLneLd~Li~eA~~r~~~~~~~~~~~~~~l~P~~~i~a~l~~~~~~~~~~L~~~l~ 90 (109)
T PF03980_consen 28 EERDVVEKLNELDKLIEEAKERKNSGEREKPVWRHSLTPEEDIRAHLAPYKKKEREQLNARLQ 90 (109)
T ss_pred HHhhHHHHHHHHHHHHHHHHHhHhccccCCCCCCCCCChHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 4589999999998885 2223443 778776554445555555555554433
No 12
>PF08176 SspK: Small acid-soluble spore protein K family; InterPro: IPR012611 This family consists of the small acid-soluble spore proteins (SASP) belonging to the K type (sspK). The sspK are unique to the spores of Bacillus subtilis and are expressed only in the forespore compartment of sporulating cells of this organism. The sspK gene is monocistronic and transcription is primarily by the RNA polymerase with the forespore-specific sigma factor, sigma-G. Mutation deleting sspK results in loss of SspK from the spore but had no discernible effect on sporulation, spore properties or spore germination [].; GO: 0030436 asexual sporulation, 0042601 endospore-forming forespore
Probab=36.39 E-value=16 Score=25.84 Aligned_cols=10 Identities=40% Similarity=0.880 Sum_probs=8.7
Q ss_pred CccCCCCCcc
Q 026639 31 PTRRPDGTLR 40 (235)
Q Consensus 31 ~s~R~DGt~R 40 (235)
+|.|||||+.
T Consensus 27 aSKR~dGtiN 36 (47)
T PF08176_consen 27 ASKRADGTIN 36 (47)
T ss_pred hhcCCCCCcc
Confidence 5999999975
No 13
>PF13243 Prenyltrans_1: Prenyltransferase-like; PDB: 3SDR_A 3SAE_A 3SDV_A 3SDT_A 3SDQ_A 3SDU_A.
Probab=35.62 E-value=12 Score=27.96 Aligned_cols=15 Identities=27% Similarity=0.497 Sum_probs=0.0
Q ss_pred CeeccCccCCCCCcc
Q 026639 26 ERILAPTRRPDGTLR 40 (235)
Q Consensus 26 ~~~i~~s~R~DGt~R 40 (235)
-.+|-..|+|||+|.
T Consensus 5 ~~~l~~~Q~~dG~W~ 19 (109)
T PF13243_consen 5 AEWLLSQQNPDGSWG 19 (109)
T ss_dssp ---------------
T ss_pred ccccccccccccccc
Confidence 357889999999994
No 14
>PF15188 CCDC-167: Coiled-coil domain-containing protein 167
Probab=34.59 E-value=2e+02 Score=22.54 Aligned_cols=37 Identities=30% Similarity=0.415 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHH----HHHHHHHhccCCCCHHHHHHHhcH
Q 026639 179 DKRIRAIKKKIRL----SEAQQQKAGQQELKPEQLEKLSKL 215 (235)
Q Consensus 179 ~KkiRnLkKKLRq----IE~Lk~k~~G~~L~~eQleKl~k~ 215 (235)
.+.|..|..||.+ +|.+..+..+..|+|++..-+.++
T Consensus 4 ~~eId~lEekl~~cr~~le~ve~rL~~~eLs~e~R~~lE~E 44 (85)
T PF15188_consen 4 AKEIDGLEEKLAQCRRRLEAVESRLRRRELSPEARRSLEKE 44 (85)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHcccCCChHHHHHHHHH
Confidence 4566666666654 455567788999999887666544
No 15
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=34.00 E-value=1.7e+02 Score=24.32 Aligned_cols=57 Identities=21% Similarity=0.336 Sum_probs=37.8
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHh------ccCCCCHHHHHHHhcHHHHHHHHHHHHHhhhhhhc
Q 026639 176 QDIDKRIRAIKKKIRLSEAQQQKA------GQQELKPEQLEKLSKLEGWRNELKLLEEKKADLEA 234 (235)
Q Consensus 176 ~e~~KkiRnLkKKLRqIE~Lk~k~------~G~~L~~eQleKl~k~~el~~EL~~Le~~~a~l~~ 234 (235)
.+.+..|..|+..|.+++.--+.. -...+..++|... ...|..|+..|+..|..|..
T Consensus 75 ~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~--i~~l~~e~~~l~~kL~~l~~ 137 (169)
T PF07106_consen 75 AELDAEIKELREELAELKKEVKSLEAELASLSSEPTNEELREE--IEELEEEIEELEEKLEKLRS 137 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHH--HHHHHHHHHHHHHHHHHHHh
Confidence 355677888888877765433111 1335556776554 77888899999988877653
No 16
>PF14723 SSFA2_C: Sperm-specific antigen 2 C-terminus
Probab=33.58 E-value=1.9e+02 Score=25.62 Aligned_cols=54 Identities=20% Similarity=0.206 Sum_probs=40.1
Q ss_pred chHHHHHHHHHHHHHHHHHHHHhcc------CCCC------HHHHHHHhcHHHHHHHHHHHHHhhhhh
Q 026639 177 DIDKRIRAIKKKIRLSEAQQQKAGQ------QELK------PEQLEKLSKLEGWRNELKLLEEKKADL 232 (235)
Q Consensus 177 e~~KkiRnLkKKLRqIE~Lk~k~~G------~~L~------~eQleKl~k~~el~~EL~~Le~~~a~l 232 (235)
|.+-.-+.|+.==+|.++|+..+-+ ..|+ .+||.-| +++++.||.+||.+|..-
T Consensus 106 Elq~mr~~ln~FR~qm~dlE~~l~~QQalvy~hMSeeER~EaeQLQsL--R~avRqElqELE~QL~DR 171 (179)
T PF14723_consen 106 ELQQMRRSLNSFREQMMDLELHLMRQQALVYRHMSEEEREEAEQLQSL--RSAVRQELQELEFQLEDR 171 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHH
Confidence 6677777888777888888844322 2344 3788888 899999999999987653
No 17
>PRK03081 sspK acid-soluble spore protein K; Provisional
Probab=31.44 E-value=21 Score=25.43 Aligned_cols=10 Identities=40% Similarity=1.039 Sum_probs=8.8
Q ss_pred CccCCCCCcc
Q 026639 31 PTRRPDGTLR 40 (235)
Q Consensus 31 ~s~R~DGt~R 40 (235)
+|.|||||+.
T Consensus 26 ASKR~dGtiN 35 (50)
T PRK03081 26 ASKRPNGTIN 35 (50)
T ss_pred hhcCCCCCcc
Confidence 7999999975
No 18
>PF13864 Enkurin: Calmodulin-binding
Probab=30.00 E-value=1.4e+02 Score=23.11 Aligned_cols=57 Identities=19% Similarity=0.225 Sum_probs=40.6
Q ss_pred CCCchHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHhcHHHHHHHHHHHHHhhhhhh
Q 026639 174 PGQDIDKRIRAIKKKIRLSEAQQQKAGQQELKPEQLEKLSKLEGWRNELKLLEEKKADLE 233 (235)
Q Consensus 174 ~~~e~~KkiRnLkKKLRqIE~Lk~k~~G~~L~~eQleKl~k~~el~~EL~~Le~~~a~l~ 233 (235)
+..+...-+..|+++..++.. ...+=.+.-+=+-+..++..|+.+|.+|+..+.-++
T Consensus 38 ~eeER~~lL~~Lk~~~~el~~---ey~~lp~~~DT~~~~~rK~~lE~~L~qlE~dI~~ls 94 (98)
T PF13864_consen 38 SEEERQELLEGLKKNWDELNK---EYQKLPFSIDTLRKKRRKEELEKELKQLEKDIKKLS 94 (98)
T ss_pred CHHHHHHHHHHHHHHHHHHHH---HHHhCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 345677788999988876643 222223334566788899999999999998876554
No 19
>PF03942 DTW: DTW domain; InterPro: IPR005636 This presumed domain is found in bacterial and eukaryotic proteins. Its function is unknown. The domain contains multiple conserved motifs including a DTXW motif that this domain has been named after.
Probab=27.36 E-value=15 Score=31.63 Aligned_cols=12 Identities=33% Similarity=0.498 Sum_probs=10.2
Q ss_pred CCCCcccceecC
Q 026639 35 PDGTLRKPIRIR 46 (235)
Q Consensus 35 ~DGt~Rk~~rvr 46 (235)
-||||++++++-
T Consensus 120 iDgTW~qA~km~ 131 (203)
T PF03942_consen 120 IDGTWRQAKKML 131 (203)
T ss_pred ECCchHHHHHHH
Confidence 699999998873
No 20
>PF05121 GvpK: Gas vesicle protein K ; InterPro: IPR007805 Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in liquid to access oxygen and/or light. Proteins containing this domain are involved in the formation of gas vesicles [].; GO: 0031412 gas vesicle organization
Probab=26.03 E-value=2.4e+02 Score=22.34 Aligned_cols=51 Identities=20% Similarity=0.294 Sum_probs=33.4
Q ss_pred chHHHHHHHHHHHHHHHHHH--HHhccCCCCHHHHHHHhc-HHHHHHHHHHHHH
Q 026639 177 DIDKRIRAIKKKIRLSEAQQ--QKAGQQELKPEQLEKLSK-LEGWRNELKLLEE 227 (235)
Q Consensus 177 e~~KkiRnLkKKLRqIE~Lk--~k~~G~~L~~eQleKl~k-~~el~~EL~~Le~ 227 (235)
...+=+=.+=.=|||.=+.+ ++..++.|+++|++.+.. -..|...+..|..
T Consensus 13 gL~~LVLtvVELLRqlmErQAiRRme~G~Lse~qiErlG~tLm~Le~~~~~l~~ 66 (88)
T PF05121_consen 13 GLARLVLTVVELLRQLMERQAIRRMEAGSLSEEQIERLGETLMKLEEAMEELCE 66 (88)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444555677777776 777999999999998864 3344555555543
No 21
>PF10458 Val_tRNA-synt_C: Valyl tRNA synthetase tRNA binding arm; InterPro: IPR019499 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the C-terminal domain of Valyl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IVS_B 1GAX_B.
Probab=26.03 E-value=2.2e+02 Score=20.46 Aligned_cols=55 Identities=27% Similarity=0.407 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHHH----HHHHHHHHhcc-CCCC--H-HHH-HHHhcHHHHHHHHHHHHHhhhhh
Q 026639 178 IDKRIRAIKKKIR----LSEAQQQKAGQ-QELK--P-EQL-EKLSKLEGWRNELKLLEEKKADL 232 (235)
Q Consensus 178 ~~KkiRnLkKKLR----qIE~Lk~k~~G-~~L~--~-eQl-eKl~k~~el~~EL~~Le~~~a~l 232 (235)
+++-|..|.|+|. +|+.+..+... .-+. | +-+ .--.+..++..+|..|...++.|
T Consensus 2 ~~~E~~rL~Kel~kl~~~i~~~~~kL~n~~F~~kAP~eVve~er~kl~~~~~~~~~l~~~l~~L 65 (66)
T PF10458_consen 2 VEAEIERLEKELEKLEKEIERLEKKLSNENFVEKAPEEVVEKEREKLEELEEELEKLEEALEQL 65 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHHHHS-CCHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4555666666664 45555555543 3332 3 222 22344678888888888877665
No 22
>COG3148 Uncharacterized conserved protein [Function unknown]
Probab=25.89 E-value=17 Score=33.20 Aligned_cols=12 Identities=33% Similarity=0.490 Sum_probs=9.9
Q ss_pred CCCCCcccceec
Q 026639 34 RPDGTLRKPIRI 45 (235)
Q Consensus 34 R~DGt~Rk~~rv 45 (235)
=.|||||+++|+
T Consensus 134 llDgTW~eArKM 145 (231)
T COG3148 134 LLDGTWREARKM 145 (231)
T ss_pred EecCccHHHHHH
Confidence 369999998875
No 23
>COG4550 Predicted membrane protein [Function unknown]
Probab=25.41 E-value=2.9e+02 Score=23.10 Aligned_cols=21 Identities=29% Similarity=0.387 Sum_probs=19.1
Q ss_pred CchHHHHHHHHHHHHHHHHHH
Q 026639 176 QDIDKRIRAIKKKIRLSEAQQ 196 (235)
Q Consensus 176 ~e~~KkiRnLkKKLRqIE~Lk 196 (235)
.+..++.++|..||++.++.+
T Consensus 5 ~di~~~a~~la~~ik~teeV~ 25 (120)
T COG4550 5 DDILKQADNLANKIKETEEVK 25 (120)
T ss_pred HHHHHHHHHHHHHHHhhHHHH
Confidence 477899999999999999988
No 24
>PF12017 Tnp_P_element: Transposase protein; InterPro: IPR021896 Protein in this family are transposases found in insects. This region is about 230 amino acids in length and is found associated with PF05485 from PFAM.
Probab=23.85 E-value=1.2e+02 Score=27.50 Aligned_cols=37 Identities=16% Similarity=0.381 Sum_probs=24.2
Q ss_pred chHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHhc
Q 026639 177 DIDKRIRAIKKKIRLSEAQQQKAGQQELKPEQLEKLSK 214 (235)
Q Consensus 177 e~~KkiRnLkKKLRqIE~Lk~k~~G~~L~~eQleKl~k 214 (235)
..++.++.|+++|..++.|+... ...+.++|+..|..
T Consensus 29 ~le~~l~~Lk~~l~~~~~l~~~L-~~~Fs~~Qi~~lk~ 65 (236)
T PF12017_consen 29 RLEKELKKLKQKLEKYQKLENSL-KQIFSEDQIRNLKN 65 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHhCcHHHHHHHhc
Confidence 34566677777777767666443 34577889887753
No 25
>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.
Probab=22.33 E-value=4.2e+02 Score=21.85 Aligned_cols=46 Identities=22% Similarity=0.169 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHHhccCCCCH-HHHHHHhcHHHHHHHHHHHHHhh
Q 026639 181 RIRAIKKKIRLSEAQQQKAGQQELKP-EQLEKLSKLEGWRNELKLLEEKK 229 (235)
Q Consensus 181 kiRnLkKKLRqIE~Lk~k~~G~~L~~-eQleKl~k~~el~~EL~~Le~~~ 229 (235)
=.+.|=.|-|||+.|=...-|...++ +|++.| .+|..|++..+..+
T Consensus 74 lA~dIi~kakqIe~LIdsLPg~~~see~Q~~~i---~~L~~E~~~~~~el 120 (144)
T PF11221_consen 74 LATDIIRKAKQIEYLIDSLPGIEVSEEEQLKRI---KELEEENEEAEEEL 120 (144)
T ss_dssp HHHHHHHHHHHHHHHHHHSTTSSS-HHHHHHHH---HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHH---HHHHHHHHHHHHHH
Confidence 34567788899999987777766564 676554 55666666666543
No 26
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=22.14 E-value=4.9e+02 Score=22.62 Aligned_cols=27 Identities=33% Similarity=0.400 Sum_probs=20.4
Q ss_pred HHHHHHHhcHHHHHHHHHHHHHhhhhh
Q 026639 206 PEQLEKLSKLEGWRNELKLLEEKKADL 232 (235)
Q Consensus 206 ~eQleKl~k~~el~~EL~~Le~~~a~l 232 (235)
.+-...|.+..+|..+++.|...+..+
T Consensus 103 ~eR~~~l~~l~~l~~~~~~l~~el~~~ 129 (188)
T PF03962_consen 103 EEREELLEELEELKKELKELKKELEKY 129 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455567888888888888888877643
No 27
>KOG2150 consensus CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=20.07 E-value=2.7e+02 Score=28.84 Aligned_cols=49 Identities=20% Similarity=0.334 Sum_probs=33.6
Q ss_pred chHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHhcHHHHHHHHHHHHHh
Q 026639 177 DIDKRIRAIKKKIRLSEAQQQKAGQQELKPEQLEKLSKLEGWRNELKLLEEK 228 (235)
Q Consensus 177 e~~KkiRnLkKKLRqIE~Lk~k~~G~~L~~eQleKl~k~~el~~EL~~Le~~ 228 (235)
++++=++.+.-.|..-+++=++...-. +.+|.+|+ +..|.+||+.|...
T Consensus 9 eIdr~lkKv~Egve~Fd~i~ek~~~~~-n~sqkeK~--e~DLKkEIKKLQRl 57 (575)
T KOG2150|consen 9 EIDRCLKKVDEGVEIFDEIYEKLHSAN-NVSQKEKL--ESDLKKEIKKLQRL 57 (575)
T ss_pred HHHHHHHHhhhhHHHHHHHHHHHHhcC-ChhHHHHH--HHHHHHHHHHHHHH
Confidence 445555555555555555545553333 78999999 89999999999864
Done!