Query 038235
Match_columns 514
No_of_seqs 154 out of 197
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 08:58:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038235.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038235hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2627 Nuclear protein ES2 [G 100.0 3E-106 7E-111 828.0 33.6 458 7-504 1-479 (488)
2 PF09751 Es2: Nuclear protein 100.0 4.6E-96 1E-100 775.2 31.0 378 46-454 1-414 (414)
3 PF14711 Nitr_red_bet_C: Respi 37.7 46 0.001 28.6 3.8 36 67-102 20-56 (83)
4 PF08473 VGCC_alpha2: Neuronal 35.9 14 0.00031 32.3 0.4 15 365-379 45-59 (94)
5 PF12178 INCENP_N: Chromosome 32.0 43 0.00094 24.8 2.3 24 76-99 13-36 (38)
6 PF07834 RanGAP1_C: RanGAP1 C- 29.0 24 0.00051 34.6 0.7 32 52-88 131-162 (183)
7 PF12583 TPPII_N: Tripeptidyl 25.1 42 0.0009 31.4 1.6 20 69-90 106-125 (139)
8 PF07729 FCD: FCD domain; Int 17.9 1.9E+02 0.0041 23.9 4.1 26 76-101 98-123 (125)
9 PF13060 DUF3921: Protein of u 17.0 85 0.0018 24.6 1.5 12 76-87 36-47 (58)
10 PRK02733 photosystem I reactio 16.8 87 0.0019 23.7 1.5 16 57-73 22-37 (42)
No 1
>KOG2627 consensus Nuclear protein ES2 [General function prediction only]
Probab=100.00 E-value=3e-106 Score=828.00 Aligned_cols=458 Identities=40% Similarity=0.589 Sum_probs=360.6
Q ss_pred CCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCCcccchhhHHHHHHhhhhhccCCCchhhhhHHHHHHHHh
Q 038235 7 NSPRHLASPSPSPSQSSFPESYLTNVNNSASATQKVPPKKRAKVLDEDTYVSAIESIIERDYFPDLSKLRDRYEWLQATR 86 (514)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kk~~VLdED~Y~eaLs~II~RDFFPdL~klraQ~EYLdAle 86 (514)
|||+.+.++|++.+....+.+ .+....+.+....+++|++|||||+|||+|++||||||||||.|||+|+|||||++
T Consensus 1 ~s~~~~t~~s~a~~~~~~~~s---~~~~~~s~~~~~~~k~k~rvL~Ee~YIEgl~kIIqrDyFPDl~KLrAq~dyLeAe~ 77 (488)
T KOG2627|consen 1 HSPRQITPGSPAMSLAKKINS---DPKQKVSPVNKVQTKKKPRVLDEEKYIEGLSKIIQRDYFPDLEKLRAQKDYLEAEE 77 (488)
T ss_pred CCCCCCCCCchhhhhhhhhcc---cchhhcccccccccccCcccCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHh
Confidence 899999999999999888866 56666677788889999999999999999999999999999999999999999999
Q ss_pred cCChHHHHHHHHHHHHhhcccccccCCCCCCCCCCCCCCcccCCCCCCCC--CCCcCCCCCCCCccCCC-CCccCCCCCC
Q 038235 87 TGDPVQIRDAQLKIMERRGKKVISLNSDGKIRTQTETPGSTFARNFTPFD--EFDVNITTPKVGVELSG-EGVCRDGTDE 163 (514)
Q Consensus 87 s~D~~~ir~a~~k~~~r~~~~~~~~~~~~~~~~~~~TP~s~~~~~~tp~~--eTp~~~~~~~~~~~~~~-~~~~~~~~~~ 163 (514)
+||+++|++||+||+++++.+.... .+.+.+ .|+.+++-...++.. .+|.. .+....++-.. ..+..+.+.+
T Consensus 78 ~~D~~qireiq~k~~~~~~~~t~~~---~~~r~~-~~s~sT~E~~~~~~~~~n~p~P-rs~~~s~pfa~ee~dkedl~~d 152 (488)
T KOG2627|consen 78 NGDFDQIREIQDKFLSYLIKKTSED---DPLRKT-LTSLSTFEIPKAQLDGENKPTP-RSRSVSRPFAGEEVDKEDLDED 152 (488)
T ss_pred cCCHHHHHHHHHHHHHhhccccCCC---CCcccC-CCCccccccccccccccCCCCC-CCcccccccccccccccccccc
Confidence 9999999999999998775433222 111111 122222222222221 11100 00011111001 1111222337
Q ss_pred CCCCCCHHHHhhhcCCchhHHHHHHHHHHHHHHHHhhHHhhhccccccccchHhhhhhccccCCCCCCCCCCCCccCcCC
Q 038235 164 VDVSMRLDEFLRKHTSEDNDSFSKILEKVNRKRKERYQFLLEGEKRDNNNLIEDVKKDRITDGYGTSYQPPSTLEGWKYT 243 (514)
Q Consensus 164 ~d~~lSLD~F~akYTSEDNaSF~eIlek~n~KrreKyaWl~~~ek~~~~~lie~~kr~~i~~~~~~~d~rpa~~d~Wkyk 243 (514)
++.+||||.|++|||||||+||+||||.+++|+++||+|||.+|+++.+++|+..+.++|.+++..+|+ ++.+++|+|+
T Consensus 153 ~~~~lSLd~fl~rYTSEDNaSFqEimE~~~~k~r~k~~~ly~~Eke~~k~~~e~~~~~ai~~~~~~~d~-~~sietW~Y~ 231 (488)
T KOG2627|consen 153 IDLNLSLDNFLRRYTSEDNASFQEIMEVASRKRREKHAWLYGAEKEQPKQTIEALNLDAIKHQAWESDQ-PKSIETWNYT 231 (488)
T ss_pred chhhhhHHHHHHhhcccchhhHHHHHHHHHHHHHhhhhhhhhhhhcchhhhhhhhhhhhhhhhhccCCC-cccccccccc
Confidence 789999999999999999999999999999999999999999999998888998899999999998887 8999999999
Q ss_pred CCCcccccCCCCCCCCCCHHHHHHHhhcCCCceeccCCCCCCCCCCCCCCCCCcccccccccCCCCCCCccccccccccc
Q 038235 244 AKNLLMYHPADCGEAPLTEEEQAVRLKGLTKEINKTNTRFHGKIMDSRPNDDGTVEVLYTPVAGTTPGPVFDRDGDKMKK 323 (514)
Q Consensus 244 akNsLMf~Pd~~~~~~~t~~e~~e~~~~~pk~I~~~NTR~~~~~~~~~~~~~~~~~~~~~~~a~~sp~~~~~rd~~~~k~ 323 (514)
|+|+|||+|+|+...+ ++.|.++ .+++|+|+||||+.+.+++++.... .....+...+|.|.++
T Consensus 232 akNslMY~Peg~~~t~-~e~q~a~----r~~qi~~~nTRfpd~~k~~~~d~~~--------i~a~~~~~~sg~d~~~--- 295 (488)
T KOG2627|consen 232 AKNSLMYTPEGVHSTP-TEAQLAV----RLQQIKKNNTRFPDKTKDSRPDSTE--------INADVPQHLSGSDRDK--- 295 (488)
T ss_pred ccceeeecCCCCccch-HHHHHHH----HHHhhhhcccccCCcccccccchhh--------hhccccccccCCcccc---
Confidence 9999999999976655 5555444 3579999999999998887765222 2223444456655431
Q ss_pred chhhhhhcCCCCccccCCCcccCccccccCCCCCCCCCCCCccccccccCcccccCCCCCcccCCCCCCCCCccCCCCCh
Q 038235 324 YDLEDMRKTPNRFYVESGKKAENGYSFVKTPSPAPGADESPFITWGEIEGTPLRLETEDTPIDIGGSGDGPHFKIPSAPT 403 (514)
Q Consensus 324 ~d~~~~~~tp~~~~~~s~~p~vnGY~fV~TPsp~PGvd~SPlMTWGeIegTP~rLd~~dtp~~~~~~~~gp~FkIpe~~~ 403 (514)
|+++.+|+||||+||.||+|+|||++||+||||||||||||||+.|||+.++ +.||.|+|||.++
T Consensus 296 -------------~v~~e~~~~ngf~fvrtPSP~Pg~~~SP~mTWGEIdGTP~Rld~~dtp~~~~--t~gP~F~IpE~pr 360 (488)
T KOG2627|consen 296 -------------YVESELPAANGFSFVRTPSPAPGVPESPNMTWGEIDGTPLRLDGFDTPVGSG--TSGPYFNIPERPR 360 (488)
T ss_pred -------------cccccccccCCcccccCCCCCCCCCCCcccccccccCceeeecCCCCccccC--CCCCcccCCCCch
Confidence 4567799999999999999999999999999999999999999999999865 8999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHhhccc-CCCCCCCCCCCC-CCCCCCCCCCHHHHHHHHHHhccCCcchhHHhhhcccC-----
Q 038235 404 RDVMAHELSREASRKLKERSKMF-QKPPLPSPYRAG-SASPSGKLLSPAAQKFMRNAMAKSSSSVDDALRASYRG----- 476 (514)
Q Consensus 404 RE~La~~La~~as~k~R~k~~~~-~~~~~~sp~r~~-~~sP~~~~LSPAAqRL~~k~~~~~~~~~D~~LRaSY~~----- 476 (514)
||+|||.|++.|++|+|+|++++ ..+..+.+++++ ..++.+.+||||||||+.+++++++.-++..+++||.+
T Consensus 361 RE~la~sla~~isak~R~kkq~al~~a~~~~~sp~~~s~s~~l~~lSPAAQkL~tk~l~~~~sp~~rs~~as~p~~s~r~ 440 (488)
T KOG2627|consen 361 RERLAASLARDISAKSRNKKQTALDSASTALNSPSTPSVSRKLANLSPAAQKLVTKKLGKSSSPAHRSSPASSPGTSLRT 440 (488)
T ss_pred HHHHHHHHHHHHHHHHhHhHHHHHhccccccCCCCccCcchhhcccCHHHHHHHHHHhhcccCccccCCCCCCCCccccc
Confidence 99999999999999999999954 344444344443 55777889999999999999999887777777777766
Q ss_pred CCC--CCCCCCC-----Cc---ccccccCCCCCC-CCCC
Q 038235 477 SSP--VTGTPKG-----GR---SVSRLGRDVSLS-SRSP 504 (514)
Q Consensus 477 ~tp--~~~tp~~-----~~---~~~~~~~~~~~~-~~~~ 504 (514)
.|| |..||++ ++ +++|||-|+.-+ +++|
T Consensus 441 ~tP~~G~~TP~s~~~pgtp~~~~i~r~g~~~t~s~~~~P 479 (488)
T KOG2627|consen 441 STPSKGSWTPTSAQTPGTPIESSISRFGKDRTDSTLPTP 479 (488)
T ss_pred cCCcCCCCCCCCcCCCCCcccccccccccccccccccCc
Confidence 477 7888888 45 788999887655 5566
No 2
>PF09751 Es2: Nuclear protein Es2; InterPro: IPR019148 This entry represents a family of proteins of approximately 500 residues with alternating regions of low complexity and conservation where the domain similarities are strong. Apart from a predicted coiled-coil domain, no other known functional domains have been characterised. May be involved in pre-mRNA splicing and has been associated with the spliceosome C complex. The protein appears to be expressed in the nucleus, particularly in the pons sub-region of the brain. It is clearly necessary for normal development of the nervous system [].
Probab=100.00 E-value=4.6e-96 Score=775.17 Aligned_cols=378 Identities=40% Similarity=0.596 Sum_probs=264.7
Q ss_pred CCCcccchhhHHHHHHhhhhhccCCCchhhhhHHHHHHHHhcCChHHHHHHHHHHHHhhccccc----ccCCCCCCCCCC
Q 038235 46 KRAKVLDEDTYVSAIESIIERDYFPDLSKLRDRYEWLQATRTGDPVQIRDAQLKIMERRGKKVI----SLNSDGKIRTQT 121 (514)
Q Consensus 46 kk~~VLdED~Y~eaLs~II~RDFFPdL~klraQ~EYLdAles~D~~~ir~a~~k~~~r~~~~~~----~~~~~~~~~~~~ 121 (514)
++++|||||+||++||+||||||||||+|||+|+||||||++||++||++|+++|.+.++.... ++ ++..
T Consensus 1 r~~~vL~Ed~Y~~~l~~II~RDfFPdL~~l~~q~eyLeA~es~D~~~ir~~~~k~~~~~~~~~~~~~~tp---~~~~--- 74 (414)
T PF09751_consen 1 RKQKVLDEDEYTEALSKIIQRDFFPDLPKLRAQNEYLEALESNDPERIREAQRKLSSRMRKSSRRSSPTP---GRFR--- 74 (414)
T ss_pred CCCccccHHHHHHHHHHHHHhhhCCChHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhccCCCCcCCCCC---CccC---
Confidence 5789999999999999999999999999999999999999999999999999999875532221 11 1111
Q ss_pred CCCCcccCCCCCCCC--------CCCcCCCCCCCCccCCCC----C----ccCCCCCCCCCCCCHHHHhhhcCCchhHHH
Q 038235 122 ETPGSTFARNFTPFD--------EFDVNITTPKVGVELSGE----G----VCRDGTDEVDVSMRLDEFLRKHTSEDNDSF 185 (514)
Q Consensus 122 ~TP~s~~~~~~tp~~--------eTp~~~~~~~~~~~~~~~----~----~~~~~~~~~d~~lSLD~F~akYTSEDNaSF 185 (514)
||........++.. .||.. ..++++.+.. . ........++++||||+||+|||||||+||
T Consensus 75 -tp~~~~~~~~~~~~~~~~~~~~~tp~~---~~~dtp~s~~~~~~~~~~~~~~~~~~~~~~~lSLD~F~akYTSEDNaSF 150 (414)
T PF09751_consen 75 -TPSSSSGTPSTPPPSTPSTPGDNTPSG---WGGDTPMSSASSATSDDEEGKGKKKKNYDTNLSLDAFQAKYTSEDNASF 150 (414)
T ss_pred -CCcccccCCCCCCCCCCCCCCCCCCcc---cCCCCCCCccccccccccccccccccccccCCCHHHHHhhccchhHHHH
Confidence 22100000001111 11110 0111111111 0 011223356899999999999999999999
Q ss_pred HHHHHHHHHHHHHhhHHhhhccccccccchHhh---hhhccccCCC----CCCCCCCCCccCcCCCCCcccccCCCCCCC
Q 038235 186 SKILEKVNRKRKERYQFLLEGEKRDNNNLIEDV---KKDRITDGYG----TSYQPPSTLEGWKYTAKNLLMYHPADCGEA 258 (514)
Q Consensus 186 ~eIlek~n~KrreKyaWl~~~ek~~~~~lie~~---kr~~i~~~~~----~~d~rpa~~d~WkykakNsLMf~Pd~~~~~ 258 (514)
++|||++|+|+++||+|||+.+..++ +.|+.. ......++.+ ..+.+|+.+|+|+|+++|+|||+|++++..
T Consensus 151 ~eIle~~n~krreKyaWl~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~i~~rp~~~d~W~~k~rN~LMf~P~~~~~~ 229 (414)
T PF09751_consen 151 EEILEKQNQKRREKYAWLYDNEKESN-RRLAQQLALPSIEEQDKAGIRSLAIEDRPAAPDTWKYKARNSLMFPPDGVEDT 229 (414)
T ss_pred HHHHHHHHHHHHHHhHHHHhcccccH-HHHHHHhhcchhhhhhccccchhhhhcCCCCCccccccccccccccCCCCccc
Confidence 99999999999999999999544443 444321 1111222222 234688999999999999999999998766
Q ss_pred CCCHHHHHHHhhcCCCceeccCCCCCC---CCCCCCCCCCCcccccccccCCCCCCCcccccccccccchhhhhhcCCCC
Q 038235 259 PLTEEEQAVRLKGLTKEINKTNTRFHG---KIMDSRPNDDGTVEVLYTPVAGTTPGPVFDRDGDKMKKYDLEDMRKTPNR 335 (514)
Q Consensus 259 ~~t~~e~~e~~~~~pk~I~~~NTR~~~---~~~~~~~~~~~~~~~~~~~~a~~sp~~~~~rd~~~~k~~d~~~~~~tp~~ 335 (514)
.....+.......+||+|+|+||||+. ......+. +++.+.+.+++++..+-... ..
T Consensus 230 ~~e~~~~~~~~~~~pk~I~~~NTR~p~~~~~~~~~~~~---------------s~s~s~i~~a~~~~~~~~~~-----~~ 289 (414)
T PF09751_consen 230 PHETIEQKARAPSPPKEIVHANTRFPESTPDESNSFPP---------------SPSRSAIDDAIAGRPRPKDS-----EV 289 (414)
T ss_pred ccchhhhhhhcccCcccccccccCCccccccccCCCCC---------------CcCHHHHHHHHhcCCccCcc-----cc
Confidence 333223222222368999999999952 11111111 11222222222222110000 00
Q ss_pred ccccCC----CcccCccccccCCCCCCCCCCCCccccccccCcccccCCCCCcccCCCCCCCCCccCCCCChhHHHHHHH
Q 038235 336 FYVESG----KKAENGYSFVKTPSPAPGADESPFITWGEIEGTPLRLETEDTPIDIGGSGDGPHFKIPSAPTRDVMAHEL 411 (514)
Q Consensus 336 ~~~~s~----~p~vnGY~fV~TPsp~PGvd~SPlMTWGeIegTP~rLd~~dtp~~~~~~~~gp~FkIpe~~~RE~La~~L 411 (514)
.+.++. +|+||||+||+||+|+|||++|||||||+|+|||||||++|||+.+++.+.||+|+||++++||+|||+|
T Consensus 290 ~~~g~egk~~tP~vnGy~fV~tpsp~Pg~~~sPlmTWG~i~~TP~~Ld~~~tp~~~~~~~~~p~FkI~e~~~RE~la~~L 369 (414)
T PF09751_consen 290 AATGSEGKELTPRVNGYSFVDTPSPAPGVDESPLMTWGEIEGTPLRLDGSDTPLDIGGDSTGPPFKIPEPSKREKLAHRL 369 (414)
T ss_pred ccccccccccCCCCCCccccCCCCCCCCCCCCCccccccccCCccccccCCCccccccCCCCCcccCCCCCHHHHHHHHH
Confidence 000112 7999999999999999999999999999999999999999999998777899999999999999999999
Q ss_pred HHHHH-HHHHHhhcccC-CCCCCCCCCCCCCCCCCCCCCHHHHHH
Q 038235 412 SREAS-RKLKERSKMFQ-KPPLPSPYRAGSASPSGKLLSPAAQKF 454 (514)
Q Consensus 412 a~~as-~k~R~k~~~~~-~~~~~sp~r~~~~sP~~~~LSPAAqRL 454 (514)
+++|+ +|+|+|+.++. +....||.++++++|++.+||||||||
T Consensus 370 ~~k~a~~k~r~k~~~~~~~~~~~sp~~~~~s~~~~~~LSPAAqrL 414 (414)
T PF09751_consen 370 ADKAARKKRREKARGATAKRNSSSPVPRFPSSPRLSSLSPAAQRL 414 (414)
T ss_pred HHHHHHhhhHhhhhhhccCCCCCCCCCCCCCCCCcccCCHHHhcC
Confidence 99999 88888886555 445567778888899988999999998
No 3
>PF14711 Nitr_red_bet_C: Respiratory nitrate reductase beta C-terminal; PDB: 3IR7_B 1Y5N_B 1R27_D 3EGW_B 1Y5I_B 1Q16_B 1Y4Z_B 1Y5L_B 3IR6_B 3IR5_B ....
Probab=37.72 E-value=46 Score=28.56 Aligned_cols=36 Identities=28% Similarity=0.472 Sum_probs=28.1
Q ss_pred ccCCCchhhhhHHHHHHHHh-cCChHHHHHHHHHHHH
Q 038235 67 DYFPDLSKLRDRYEWLQATR-TGDPVQIRDAQLKIME 102 (514)
Q Consensus 67 DFFPdL~klraQ~EYLdAle-s~D~~~ir~a~~k~~~ 102 (514)
++||+|.+||.=.+||--|= .||.+-|+.+-.|+..
T Consensus 20 ~~~p~id~lRIPi~YLAnLftAGd~~~V~~~L~rL~A 56 (83)
T PF14711_consen 20 GIFPAIDSLRIPIEYLANLFTAGDEEPVRRALKRLLA 56 (83)
T ss_dssp BTS--GGGBSS-HHHHHHHHSTT-HHHHHHHHHHHHH
T ss_pred cccchHHHhcccHHHHHHHHccCChHHHHHHHHHHHH
Confidence 89999999999999998765 5799999999888864
No 4
>PF08473 VGCC_alpha2: Neuronal voltage-dependent calcium channel alpha 2acd; InterPro: IPR013680 Ca2+ ions are unique in that they not only carry charge but they are also the most widely used of diffusible second messengers. Voltage-dependent Ca2+ channels (VDCC) are a family of molecules that allow cells to couple electrical activity to intracellular Ca2+ signalling. The opening and closing of these channels by depolarizing stimuli, such as action potentials, allows Ca2+ ions to enter neurons down a steep electrochemical gradient, producing transient intracellular Ca2+ signals. Many of the processes that occur in neurons, including transmitter release, gene transcription and metabolism are controlled by Ca2+ influx occurring simultaneously at different cellular locales. The pore is formed by the alpha-1 subunit which incorporates the conduction pore, the voltage sensor and gating apparatus, and the known sites of channel regulation by second messengers, drugs, and toxins []. The activity of this pore is modulated by 4 tightly-coupled subunits: an intracellular beta subunit; a transmembrane gamma subunit; and a disulphide-linked complex of alpha-2 and delta subunits, which are proteolytically cleaved from the same gene product. Properties of the protein including gating voltage-dependence, G protein modulation and kinase susceptibility can be influenced by these subunits. Voltage-gated calcium channels are classified as T, L, N, P, Q and R, and are distinguished by their sensitivity to pharmacological blocks, single-channel conductance kinetics, and voltage-dependence. On the basis of their voltage activation properties, the voltage-gated calcium classes can be further divided into two broad groups: the low (T-type) and high (L, N, P, Q and R-type) threshold-activated channels. This eukaryotic domain has been found in the neuronal voltage-dependent calcium channel (VGCC) alpha 2a, 2c, and 2d subunits. It is also found in other calcium channel alpha-2/delta subunits to the N terminus of a Cache domain (IPR004010 from INTERPRO).
Probab=35.94 E-value=14 Score=32.28 Aligned_cols=15 Identities=40% Similarity=0.651 Sum_probs=12.9
Q ss_pred ccccccccCcccccC
Q 038235 365 FITWGEIEGTPLRLE 379 (514)
Q Consensus 365 lMTWGeIegTP~rLd 379 (514)
--||+.|+||||.|-
T Consensus 45 tYtw~PI~gT~ySLa 59 (94)
T PF08473_consen 45 TYTWTPINGTDYSLA 59 (94)
T ss_pred eEEEeccCCCcceeE
Confidence 359999999999984
No 5
>PF12178 INCENP_N: Chromosome passenger complex (CPC) protein INCENP N terminal; InterPro: IPR022006 This domain family is found in eukaryotes, and is approximately 40 amino acids in length. INCENP is a regulatory protein in the chromosome passenger complex. It is involved in regulation of the catalytic protein Aurora B. It performs this function in association with two other proteins - Survivin and Borealin. These proteins form a tight three-helical bundle. The N-terminal domain is the domain involved in formation of this three helical bundle. ; PDB: 2QFA_C.
Probab=31.98 E-value=43 Score=24.77 Aligned_cols=24 Identities=21% Similarity=0.209 Sum_probs=20.5
Q ss_pred hhHHHHHHHHhcCChHHHHHHHHH
Q 038235 76 RDRYEWLQATRTGDPVQIRDAQLK 99 (514)
Q Consensus 76 raQ~EYLdAles~D~~~ir~a~~k 99 (514)
+.-.|+|.-++.+|..|+.+|+..
T Consensus 13 ~Kl~efl~~vd~~d~vWLeEI~ee 36 (38)
T PF12178_consen 13 QKLQEFLCNVDNKDMVWLEEIQEE 36 (38)
T ss_dssp HHHHHHHHHHHHTHHHHHHHHHHH
T ss_pred HHHHHHHHhccchhhHHHHHHHHh
Confidence 344689999999999999999864
No 6
>PF07834 RanGAP1_C: RanGAP1 C-terminal domain; InterPro: IPR009109 Ran GTPase is a ubiquitous protein required for nuclear transport, spindle assembly, nuclear assembly and mitotic cell cycle regulation. RanGTPase activating protein 1 (RanGAP1) is one of several RanGTPase accessory proteins. During interphase, RanGAP1 is located in the cytoplasm, while during mitosis it becomes associated with the kinetochores []. Cytoplasmic RanGAP1 is required for RanGTPase-directed nuclear transport. The activity of RanGAP1 requires the accessory protein RanBP1. RanBP1 facilitates RanGAP1 hydrolysis of Ran-GTP, both directly and by promoting the dissociation of Ran-GTP from transport receptors, which would otherwise block RanGAP1-mediated hydrolysis. RanGAP1 is thought to bind to the Switch 1 and Switch 2 regions of RanGTPase. The Switch 2 region can be buried in complexes with karyopherin-beta2, and requires the interaction with RanBP1 to permit RanGAP1 function. RanGAP1 can undergo SUMO (small ubiquitin-like modifier) modification, which targets RanGAP1 to RanBP2/Nup358 in the nuclear pore complex, and is required for association with the nuclear pore complex and for nuclear transport []. The enzymes involved in SUMO modification are located on the filaments of the nuclear pore complex. The RanGAP1 N-terminal domain is fairly well conserved between vertebrate and fungal proteins, but yeast does not contain the C-terminal domain. The C-terminal domain is SUMO-modified and required for the localisation of RanGAP1 at the nuclear pore complex. The structure of the C-terminal domain is multihelical, consisting of two curved alpha/alpha layers in a right-handed superhelix.; GO: 0005098 Ran GTPase activator activity, 0007165 signal transduction; PDB: 2IO2_C 2GRQ_B 3UIN_C 2GRO_B 3UIP_C 2IO3_C 2GRN_B 3UIO_C 2GRP_B 2GRR_B ....
Probab=29.05 E-value=24 Score=34.57 Aligned_cols=32 Identities=28% Similarity=0.373 Sum_probs=19.9
Q ss_pred chhhHHHHHHhhhhhccCCCchhhhhHHHHHHHHhcC
Q 038235 52 DEDTYVSAIESIIERDYFPDLSKLRDRYEWLQATRTG 88 (514)
Q Consensus 52 dED~Y~eaLs~II~RDFFPdL~klraQ~EYLdAles~ 88 (514)
+=+--.-+|+||.|+||||-- ...-|.|.-++
T Consensus 131 ~l~G~l~~Leh~vqq~YFp~~-----~~~~L~aFlsK 162 (183)
T PF07834_consen 131 NLPGPLLALEHAVQQDYFPKS-----TRPLLQAFLSK 162 (183)
T ss_dssp HHHHHHHHHHHHCCSTTS-GG-----GHHHHHHHHCS
T ss_pred CCchHHHHHHHHhhhhhccHH-----HHHHHHHHHcC
Confidence 334445699999999999953 23445554444
No 7
>PF12583 TPPII_N: Tripeptidyl peptidase II N terminal; InterPro: IPR022232 This entry represents a region of approximately 190 amino acids in length and is found in association with PF00082 from PFAM. The members are serine peptidases belonging to MEROPS peptidase family S8A, tripeptidyl peptidase II (TPPII), clan SB. They are a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides. ; PDB: 3LXU_X.
Probab=25.13 E-value=42 Score=31.42 Aligned_cols=20 Identities=15% Similarity=0.177 Sum_probs=10.8
Q ss_pred CCCchhhhhHHHHHHHHhcCCh
Q 038235 69 FPDLSKLRDRYEWLQATRTGDP 90 (514)
Q Consensus 69 FPdL~klraQ~EYLdAles~D~ 90 (514)
||+-+ .+-..||+.|++.|.
T Consensus 106 ~P~HL--paHla~i~~lDS~~l 125 (139)
T PF12583_consen 106 HPDHL--PAHLAMIQNLDSPEL 125 (139)
T ss_dssp -TT-T--HHHHHHHHHHHHHSS
T ss_pred CcchH--HHHHHHHHccCcHHH
Confidence 56543 355557777777654
No 8
>PF07729 FCD: FCD domain; InterPro: IPR011711 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family (IPR000524 from INTERPRO), and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR (IPR008920 from INTERPRO), HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA []. This entry represents the C-terminal ligand binding domain of many members of the GntR family. This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in P45427 from SWISSPROT and P31460 from SWISSPROT that are regulators of sugar biosynthesis operons.; PDB: 3SXK_A 3SXY_A 3SXM_B 3SXZ_A 3FMS_A 2DI3_B 2HS5_A 3IHU_B 3C7J_A.
Probab=17.93 E-value=1.9e+02 Score=23.94 Aligned_cols=26 Identities=31% Similarity=0.492 Sum_probs=20.5
Q ss_pred hhHHHHHHHHhcCChHHHHHHHHHHH
Q 038235 76 RDRYEWLQATRTGDPVQIRDAQLKIM 101 (514)
Q Consensus 76 raQ~EYLdAles~D~~~ir~a~~k~~ 101 (514)
+.-.+.++|+++||.+.++++-....
T Consensus 98 ~~h~~i~~ai~~~d~~~a~~~~~~h~ 123 (125)
T PF07729_consen 98 EEHREIIDAIRAGDPEAAREALRQHI 123 (125)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence 55678999999999999998876654
No 9
>PF13060 DUF3921: Protein of unknown function (DUF3921)
Probab=17.03 E-value=85 Score=24.57 Aligned_cols=12 Identities=25% Similarity=0.382 Sum_probs=10.5
Q ss_pred hhHHHHHHHHhc
Q 038235 76 RDRYEWLQATRT 87 (514)
Q Consensus 76 raQ~EYLdAles 87 (514)
++|.|||.||.-
T Consensus 36 kaqeeylsals~ 47 (58)
T PF13060_consen 36 KAQEEYLSALSH 47 (58)
T ss_pred HHHHHHHHHhhH
Confidence 799999999873
No 10
>PRK02733 photosystem I reaction center subunit IX; Provisional
Probab=16.85 E-value=87 Score=23.70 Aligned_cols=16 Identities=38% Similarity=0.650 Sum_probs=9.9
Q ss_pred HHHHHhhhhhccCCCch
Q 038235 57 VSAIESIIERDYFPDLS 73 (514)
Q Consensus 57 ~eaLs~II~RDFFPdL~ 73 (514)
+.+|--.|.| ||||++
T Consensus 22 tag~lIEiNR-ffPD~L 37 (42)
T PRK02733 22 TAGILIEFNR-FFPDLL 37 (42)
T ss_pred HHHHHHHHHH-hCchHh
Confidence 3444444555 999986
Done!