Query psy10146
Match_columns 1902
No_of_seqs 216 out of 445
Neff 1.8
Searched_HMMs 46136
Date Fri Aug 16 19:00:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10146.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10146hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03732 Retrotrans_gag: Retro 97.2 0.00038 8.2E-09 61.4 3.7 88 51-142 3-90 (96)
2 PF03732 Retrotrans_gag: Retro 96.9 0.0007 1.5E-08 59.8 2.7 71 142-228 26-96 (96)
3 PF14893 PNMA: PNMA 95.1 0.026 5.7E-07 64.7 5.2 106 20-131 179-288 (331)
4 PF03564 DUF1759: Protein of u 94.2 0.28 6.1E-06 48.2 9.2 81 20-126 5-86 (145)
5 PF14244 UBN2_3: gag-polypepti 85.4 1.6 3.5E-05 43.9 5.6 96 21-127 16-134 (152)
6 PF14893 PNMA: PNMA 82.8 8.5 0.00018 45.0 10.6 185 25-235 101-314 (331)
7 PF14223 UBN2: gag-polypeptide 58.7 14 0.0003 35.5 4.3 97 147-258 5-111 (119)
8 PF14223 UBN2: gag-polypeptide 48.3 8.7 0.00019 36.9 1.1 100 78-190 2-109 (119)
9 PF02023 SCAN: SCAN domain; I 37.9 36 0.00077 33.5 3.5 78 165-260 5-88 (95)
10 PF00607 Gag_p24: gag gene pro 15.9 1.2E+02 0.0026 33.3 2.8 74 168-258 124-198 (206)
No 1
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=97.16 E-value=0.00038 Score=61.42 Aligned_cols=88 Identities=18% Similarity=0.303 Sum_probs=69.8
Q ss_pred HHHhhChhhHHHhhcCCCCCCCCCccccHHHHHHHHhcccCCccceeeeeeeeecccCCCCCCHHHHHHHHHhhhcCCCC
Q psy10146 51 FLHLIGEECLHIFNSFGLNDKLDNKSLQLEEVISKFTDHFVPKKNLTYVRHKFFTRDQQEGESVENYVAVLNKMSYDCEF 130 (1902)
Q Consensus 51 LLhVIGPEgYEILRSLpfPEkkpPEDKTYDELIEKLEEHFSPKKNVIyERYKFnSRKQQPGESIDQFVTRLRKLAK~CEF 130 (1902)
+.+.++..+..-+.++..... +...+|+++...|..+|.|.......+-.+.+..| ++|||.+|+.+++.++..|.-
T Consensus 3 ~~~~L~g~A~~w~~~~~~~~~--~~~~~W~~~~~~~~~~f~~~~~~~~~~~~l~~l~Q-~~esv~~y~~rf~~l~~~~~~ 79 (96)
T PF03732_consen 3 FPSFLKGPARQWYRNLRPNEI--RDFITWEEFKDAFRKRFFPPDRKEQARQELNSLRQ-GNESVREYVNRFRELARRAPP 79 (96)
T ss_pred chHhccCHHHHHHHHhHhcCC--CCCCCHHHHHHHHHHHHhhhhccccchhhhhhhhc-cCCcHHHHHHHHHHHHHHCCC
Confidence 445667777888888765543 22459999999999999998888888899999999 999999999999999999986
Q ss_pred CchhhHhhhhcc
Q psy10146 131 EKLREDLLDNKS 142 (1902)
Q Consensus 131 GDLLDELLRDRI 142 (1902)
...++++.+++
T Consensus 80 -~~~e~~~v~~f 90 (96)
T PF03732_consen 80 -PMDEEMLVERF 90 (96)
T ss_pred -CcCHHHHHHHH
Confidence 23444444443
No 2
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=96.86 E-value=0.0007 Score=59.77 Aligned_cols=71 Identities=20% Similarity=0.326 Sum_probs=60.7
Q ss_pred chhhHHHHHhhhccccCCccceeeccccccccccCCCCHHHHHHHHHHhhhcCCCchhhhhhhhccchhHHHHHhhhhce
Q psy10146 142 SLQLEEVISKLTDHFVPKKNLTYVRHKFFTRDQQEGESVENYVAVLNKMSYDCEFEKLREDLLDNKSLQLEEVISKLTDH 221 (1902)
Q Consensus 142 ILQYDEIIEKLEEHFSPKKNLIyERYKFySRkQEpGESIDQFVAELRQLAESCEFGDLEDELIrDksLTIEea~EKLRDR 221 (1902)
..+++++...|.++|.|.......+..+.+..| ++||+.+|+++++.++..|.- ...+++ +.++
T Consensus 26 ~~~W~~~~~~~~~~f~~~~~~~~~~~~l~~l~Q-~~esv~~y~~rf~~l~~~~~~-~~~e~~--------------~v~~ 89 (96)
T PF03732_consen 26 FITWEEFKDAFRKRFFPPDRKEQARQELNSLRQ-GNESVREYVNRFRELARRAPP-PMDEEM--------------LVER 89 (96)
T ss_pred CCCHHHHHHHHHHHHhhhhccccchhhhhhhhc-cCCcHHHHHHHHHHHHHHCCC-CcCHHH--------------HHHH
Confidence 347999999999999999888899999999999 999999999999999999986 223332 6788
Q ss_pred eccCCCc
Q psy10146 222 FVPKKNL 228 (1902)
Q Consensus 222 IVcGIrS 228 (1902)
|+.|+++
T Consensus 90 f~~GL~~ 96 (96)
T PF03732_consen 90 FIRGLRP 96 (96)
T ss_pred HHHCCCC
Confidence 8888864
No 3
>PF14893 PNMA: PNMA
Probab=95.12 E-value=0.026 Score=64.70 Aligned_cols=106 Identities=14% Similarity=0.256 Sum_probs=87.5
Q ss_pred cchHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHhhChhhHHHhhcCCCCCCCCCccccHHHHHHHHhcccCCccceeee
Q psy10146 20 ADAWKLWLQRFTIFLRANGHDNAAPEKQVAMFLHLIGEECLHIFNSFGLNDKLDNKSLQLEEVISKFTDHFVPKKNLTYV 99 (1902)
Q Consensus 20 AEnWErWKQRFEnYFeANGITKKPDERKVAILLhVIGPEgYEILRSLpfPEkkpPEDKTYDELIEKLEEHFSPKKNVIyE 99 (1902)
.++|..|.++..--+..-. ..++..|..-+|-.++..+.++.+.+...++ +.+....++.|..+|..+.|...-
T Consensus 179 ee~fe~Wl~~a~~~v~~W~--~~~e~ekrrrlle~L~GpA~~~~r~l~~~nP----~~t~~~~l~aL~~~Fg~~es~~~~ 252 (331)
T PF14893_consen 179 EESFESWLEHANEMVKKWN--DVSEEEKRRRLLESLRGPALDSRRKLQKKNP----KQTAQDCLKALGQVFGSSESRETL 252 (331)
T ss_pred cccHHHHHHHHHHHHHhcc--CCchhhchhhhHHhcccHHHHHHHHHHhcCC----CCCHHHHHHHHHHhcCCcccHHHH
Confidence 5899999999988766633 1368888888888888888999888865443 578999999999999999999999
Q ss_pred eeeeecccCCCCCCHHHHHHHHH----hhhcCCCCC
Q psy10146 100 RHKFFTRDQQEGESVENYVAVLN----KMSYDCEFE 131 (1902)
Q Consensus 100 RYKFnSRKQQPGESIDQFVTRLR----KLAK~CEFG 131 (1902)
+.+|.++.|.+||++..|+.+|. +....|.+.
T Consensus 253 ~~kf~~~~Q~~~E~ls~yv~RlE~lLqkav~k~a~~ 288 (331)
T PF14893_consen 253 EAKFLNTFQEPGEKLSAYVKRLESLLQKAVEKGAIK 288 (331)
T ss_pred HHHHHHhhccCCCCHHHHHHHHHHHHHHHHHhcCCC
Confidence 99999999999999999999774 444566665
No 4
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=94.24 E-value=0.28 Score=48.15 Aligned_cols=81 Identities=9% Similarity=0.251 Sum_probs=66.2
Q ss_pred cchHHHHHHHHHHHHHH-cCCCCCChHHHHHHHHHhhChhhHHHhhcCCCCCCCCCccccHHHHHHHHhcccCCccceee
Q psy10146 20 ADAWKLWLQRFTIFLRA-NGHDNAAPEKQVAMFLHLIGEECLHIFNSFGLNDKLDNKSLQLEEVISKFTDHFVPKKNLTY 98 (1902)
Q Consensus 20 AEnWErWKQRFEnYFeA-NGITKKPDERKVAILLhVIGPEgYEILRSLpfPEkkpPEDKTYDELIEKLEEHFSPKKNVIy 98 (1902)
+..|..|.+.|...+.- ..+ ++..|.++|.+++-.++.+.+..++.++ .+|..+++.|+..|..+..
T Consensus 5 ~~~~~~F~~~F~~~v~~n~~~---~d~~K~~~L~~~L~G~A~~~i~~~~~~~------~~Y~~a~~~L~~~yg~~~~--- 72 (145)
T PF03564_consen 5 PSEWPEFIDQFDSLVHENPDL---SDIEKLNYLRSCLKGEAKELIRGLPLSE------ENYEEAWELLEERYGNPRR--- 72 (145)
T ss_pred HHHHHHHHHHHHHHHhcccCC---CHHHHHHHHHHHhcchHHHHHHcccccc------hhhHHHHHHHHHHhCCchH---
Confidence 46799999999999777 444 7999999999999999999999997644 5899999999999986433
Q ss_pred eeeeeecccCCCCCCHHHHHHHHHhhhc
Q psy10146 99 VRHKFFTRDQQEGESVENYVAVLNKMSY 126 (1902)
Q Consensus 99 ERYKFnSRKQQPGESIDQFVTRLRKLAK 126 (1902)
.+..++.+|+.+..
T Consensus 73 --------------i~~~~~~~l~~l~~ 86 (145)
T PF03564_consen 73 --------------IIQALLEELRNLPP 86 (145)
T ss_pred --------------HHHHHHHHHhcccc
Confidence 34566677776664
No 5
>PF14244 UBN2_3: gag-polypeptide of LTR copia-type
Probab=85.43 E-value=1.6 Score=43.89 Aligned_cols=96 Identities=20% Similarity=0.326 Sum_probs=69.0
Q ss_pred chHHHHHHHHHHHHHHcCCCC-------CCh-------------HHHHHHHHHhhChhhHHHhhcCCCCCCCCCccccHH
Q psy10146 21 DAWKLWLQRFTIFLRANGHDN-------AAP-------------EKQVAMFLHLIGEECLHIFNSFGLNDKLDNKSLQLE 80 (1902)
Q Consensus 21 EnWErWKQRFEnYFeANGITK-------KPD-------------ERKVAILLhVIGPEgYEILRSLpfPEkkpPEDKTYD 80 (1902)
.++..|.++++.++.+.+.-+ .|+ ..=.+.|++.|.+.....+..+ .+-.
T Consensus 16 ~NY~~W~~~~~~~L~~~~l~~~i~g~~~~P~~~~~~~~~W~~~d~~v~swl~~sis~~i~~~i~~~----------~tak 85 (152)
T PF14244_consen 16 SNYLSWSQQMEMALRGKGLWGFIDGTIPKPPETDPAYEKWERKDQLVLSWLLNSISPDILSTIIFC----------ETAK 85 (152)
T ss_pred ccHHHHHHHHHHHHHhCCCcccccCccccccccchhhhhHHHhhhHHHHHHHHhhcHHHHhhhHhh----------hhHH
Confidence 789999999999999977522 121 1223466677777766666544 3567
Q ss_pred HHHHHHhcccCCccc---eeeeeeeeecccCCCCCCHHHHHHHHHhhhcC
Q psy10146 81 EVISKFTDHFVPKKN---LTYVRHKFFTRDQQEGESVENYVAVLNKMSYD 127 (1902)
Q Consensus 81 ELIEKLEEHFSPKKN---VIyERYKFnSRKQQPGESIDQFVTRLRKLAK~ 127 (1902)
++++.|.+.|....| ...=+-.+...+|+ +.|+.+|+.+|+.+...
T Consensus 86 ~~W~~L~~~f~~~~~~~r~~~L~~~l~~~kq~-~~sv~ey~~~lk~l~~~ 134 (152)
T PF14244_consen 86 EIWDALKERFSQKSNASRVFQLRNELHSLKQG-DKSVTEYFNKLKSLWQE 134 (152)
T ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHHHHhhC-CCcHHHHHHHHHHHhHH
Confidence 899999999988774 22234566667765 99999999999988743
No 6
>PF14893 PNMA: PNMA
Probab=82.84 E-value=8.5 Score=44.99 Aligned_cols=185 Identities=18% Similarity=0.194 Sum_probs=113.2
Q ss_pred HHHHHHHHHHHHcCCCCCChHHHHHHHHHhhChhhHHHhhcCCCCC-CCCCccccHHHHHHHHhcccCCccceee-eeee
Q psy10146 25 LWLQRFTIFLRANGHDNAAPEKQVAMFLHLIGEECLHIFNSFGLND-KLDNKSLQLEEVISKFTDHFVPKKNLTY-VRHK 102 (1902)
Q Consensus 25 rWKQRFEnYFeANGITKKPDERKVAILLhVIGPEgYEILRSLpfPE-kkpPEDKTYDELIEKLEEHFSPKKNVIy-ERYK 102 (1902)
.+.+++..|+...+.+ ++-.-..+|.. +.+.+. ...|....-..+-..|.....|-.+.++ .+-.
T Consensus 101 e~l~~l~~fl~~eg~t-------~~~va~~lG~~------~~~~~~~q~~~~~~wa~~l~~~l~a~~qp~~~~~~y~~L~ 167 (331)
T PF14893_consen 101 EFLRRLNEFLQDEGQT-------VEDVARALGSE------SPPPPPNQNQPPENWAEALGQALGAVLQPLLESIAYRDLR 167 (331)
T ss_pred HHHHHHHHHHHhhcch-------HHHHHhhhccC------CCCCccccccCccccchhhhhhhhhccCcchhhhhhhhhh
Confidence 6788888887776642 22223333443 111111 0001112344555677777787664443 3444
Q ss_pred -eecccCC--CCCCHHHHHHHHHhhhcCCC-CC--------------chhhHhhh-----hcchhhHHHHHhhhccccCC
Q psy10146 103 -FFTRDQQ--EGESVENYVAVLNKMSYDCE-FE--------------KLREDLLD-----NKSLQLEEVISKLTDHFVPK 159 (1902)
Q Consensus 103 -FnSRKQQ--PGESIDQFVTRLRKLAK~CE-FG--------------DLLDELLR-----DRILQYDEIIEKLEEHFSPK 159 (1902)
|..+.+. ..|+++.|+..-..+....+ -+ ...+. +| +--.+..+.+..|..+|...
T Consensus 168 iFSG~~~~~~gee~fe~Wl~~a~~~v~~W~~~~e~ekrrrlle~L~GpA~~~-~r~l~~~nP~~t~~~~l~aL~~~Fg~~ 246 (331)
T PF14893_consen 168 IFSGREEPAPGEESFESWLEHANEMVKKWNDVSEEEKRRRLLESLRGPALDS-RRKLQKKNPKQTAQDCLKALGQVFGSS 246 (331)
T ss_pred hhcCCCCCCCCcccHHHHHHHHHHHHHhccCCchhhchhhhHHhcccHHHHH-HHHHHhcCCCCCHHHHHHHHHHhcCCc
Confidence 4444433 26999999988877766655 22 22221 11 11246889999999999999
Q ss_pred ccceeeccccccccccCCCCHHHHHHHHH----HhhhcCCCchhhhhhhhccchhHHHHHhhhhceeccCCCchHHHHhh
Q psy10146 160 KNLTYVRHKFFTRDQQEGESVENYVAVLN----KMSYDCEFEKLREDLLDNKSLQLEEVISKLTDHFVPKKNLTYVRHKF 235 (1902)
Q Consensus 160 KNLIyERYKFySRkQEpGESIDQFVAELR----QLAESCEFGDLEDELIrDksLTIEea~EKLRDRIVcGIrSkaIQRRL 235 (1902)
.+..-.+.+|.++.|++||++..|+.+|- +....|.+..-.-+- -+++..+.-|..+..+|.||
T Consensus 247 es~~~~~~kf~~~~Q~~~E~ls~yv~RlE~lLqkav~k~a~~p~~adq------------~rl~q~l~~a~~~e~lq~kl 314 (331)
T PF14893_consen 247 ESRETLEAKFLNTFQEPGEKLSAYVKRLESLLQKAVEKGAIKPSEADQ------------VRLRQVLSGAVLSESLQDKL 314 (331)
T ss_pred ccHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHhcCCCccccCH------------HHHHHHHccCCCCHHHHHHH
Confidence 99999999999999999999999998655 444678776321110 12445555667777766544
No 7
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=58.70 E-value=14 Score=35.54 Aligned_cols=97 Identities=12% Similarity=0.210 Sum_probs=60.3
Q ss_pred HHHHhhhccccCCcc-----ceeeccccccccccCCCCHHHHHHHHHHhhh---cCCCchhhhhhhhccchhHHHHHhhh
Q psy10146 147 EVISKLTDHFVPKKN-----LTYVRHKFFTRDQQEGESVENYVAVLNKMSY---DCEFEKLREDLLDNKSLQLEEVISKL 218 (1902)
Q Consensus 147 EIIEKLEEHFSPKKN-----LIyERYKFySRkQEpGESIDQFVAELRQLAE---SCEFGDLEDELIrDksLTIEea~EKL 218 (1902)
++++.|...|.+... ...-+..|......+|+||++|+.+++.++. .|+- .+.+.. +
T Consensus 5 e~W~~L~~~y~~~~~~~~~~~~~L~~~l~~~k~~~~~sv~~y~~~~~~i~~~L~~~g~-~i~d~~--------------~ 69 (119)
T PF14223_consen 5 EAWDALKKRYEGQSKVKQARVQQLKSQLENLKMKDGESVDEYISRLKEIVDELRAIGK-PISDED--------------L 69 (119)
T ss_pred HHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHhhhhhhhcCC-cccchh--------------H
Confidence 455566666666554 2333456666676899999999999999983 4433 122321 5
Q ss_pred hceeccCCCchH--HHHhhcCccCCCCCCHHHHHHHHHHhcc
Q psy10146 219 TDHFVPKKNLTY--VRHKFFTRDQQEGESVENYVAVLNKMSY 258 (1902)
Q Consensus 219 RDRIVcGIrSka--IQRRLLeEDd~e~LTLEKAVDIArAmEl 258 (1902)
...|+.|+.+.. +..-+-..++...+|+++.+....+.|.
T Consensus 70 v~~iL~~Lp~~y~~~~~~i~~~~~~~~~t~~el~~~L~~~E~ 111 (119)
T PF14223_consen 70 VSKILRSLPPSYDTFVTAIRNSKDLPKMTLEELISRLLAEEM 111 (119)
T ss_pred HHHHHhcCCchhHHHHHHHHhcCCCCcCCHHHHHHHHHHHHH
Confidence 566777776543 2222333332234689999988888884
No 8
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=48.35 E-value=8.7 Score=36.88 Aligned_cols=100 Identities=12% Similarity=0.195 Sum_probs=58.7
Q ss_pred cHHHHHHHHhcccCCccc---ee--eeeeeeecccCCCCCCHHHHHHHHHhhhcC---CCCCchhhHhhhhcchhhHHHH
Q psy10146 78 QLEEVISKFTDHFVPKKN---LT--YVRHKFFTRDQQEGESVENYVAVLNKMSYD---CEFEKLREDLLDNKSLQLEEVI 149 (1902)
Q Consensus 78 TYDELIEKLEEHFSPKKN---VI--yERYKFnSRKQQPGESIDQFVTRLRKLAK~---CEFGDLLDELLRDRILQYDEII 149 (1902)
|-.++++.|...|.+... .. .-+-.|.+.+.++|+||++|+.+++.++.. |+- ...+..+... ++
T Consensus 2 tA~e~W~~L~~~y~~~~~~~~~~~~~L~~~l~~~k~~~~~sv~~y~~~~~~i~~~L~~~g~-~i~d~~~v~~------iL 74 (119)
T PF14223_consen 2 TAKEAWDALKKRYEGQSKVKQARVQQLKSQLENLKMKDGESVDEYISRLKEIVDELRAIGK-PISDEDLVSK------IL 74 (119)
T ss_pred hHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHhhhhhhhcCC-cccchhHHHH------HH
Confidence 345788899999988766 22 224567777778999999999999977653 332 1233333333 33
Q ss_pred HhhhccccCCccceeeccccccccccCCCCHHHHHHHHHHh
Q psy10146 150 SKLTDHFVPKKNLTYVRHKFFTRDQQEGESVENYVAVLNKM 190 (1902)
Q Consensus 150 EKLEEHFSPKKNLIyERYKFySRkQEpGESIDQFVAELRQL 190 (1902)
.+|-..|.+-...+... ...+.-|+++.+..|..-
T Consensus 75 ~~Lp~~y~~~~~~i~~~------~~~~~~t~~el~~~L~~~ 109 (119)
T PF14223_consen 75 RSLPPSYDTFVTAIRNS------KDLPKMTLEELISRLLAE 109 (119)
T ss_pred hcCCchhHHHHHHHHhc------CCCCcCCHHHHHHHHHHH
Confidence 45544444433332221 111223677777766643
No 9
>PF02023 SCAN: SCAN domain; InterPro: IPR003309 A number of C2H2-zinc finger proteins contain a highly conserved N-terminal motif termed the SCAN domain. The SCAN domain may play an important role in the assembly and function of this newly defined subclass of transcriptional regulators [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3LHR_B 4E6S_A 2FI2_A 1Y7Q_A.
Probab=37.88 E-value=36 Score=33.54 Aligned_cols=78 Identities=23% Similarity=0.251 Sum_probs=55.8
Q ss_pred eccccccccccCCCCHHHHHHHHHHhhhcC------CCchhhhhhhhccchhHHHHHhhhhceeccCCCchHHHHhhcCc
Q psy10146 165 VRHKFFTRDQQEGESVENYVAVLNKMSYDC------EFEKLREDLLDNKSLQLEEVISKLTDHFVPKKNLTYVRHKFFTR 238 (1902)
Q Consensus 165 ERYKFySRkQEpGESIDQFVAELRQLAESC------EFGDLEDELIrDksLTIEea~EKLRDRIVcGIrSkaIQRRLLeE 238 (1902)
-|.+|++..-++|++--+++.+|+.+...- .+..+.+-| +..||++ +....+|..+-+.
T Consensus 5 ~r~~FR~~~~~~~~~p~e~~~rL~~l~~~WL~pe~~tkeqi~ell--------------vlEQFL~-~lP~e~~~wV~e~ 69 (95)
T PF02023_consen 5 YRQRFRSFQYQEGEGPREFLSRLRELCDRWLQPEVHTKEQILELL--------------VLEQFLN-ILPPEVQTWVRER 69 (95)
T ss_dssp HHHHHHT--CCTTTSHHHHHHHHHHHHHHHH-TTTS-HHHHHHHH--------------HHHHHHH-HS-HHHHHHHHTC
T ss_pred HHHHHhCCCCCCCCCHHHHHHHHHHHHHHhCccccCcHHHHHHHH--------------HHHHHHH-HCCHHHHHHHHhc
Confidence 477898888899999999999999998432 222233333 6688887 5567899888887
Q ss_pred cCCCCCCHHHHHHHHHHhcchh
Q psy10146 239 DQQEGESVENYVAVLNKMSYDC 260 (1902)
Q Consensus 239 Dd~e~LTLEKAVDIArAmElAc 260 (1902)
.. -|.++|+.+|-.+..+.
T Consensus 70 ~p---~s~~ea~~Lae~~~~~~ 88 (95)
T PF02023_consen 70 KP---ESAEEAVALAEDYQRAR 88 (95)
T ss_dssp S----SSHHHHHHHHHHHHCCC
T ss_pred CC---CCHHHHHHHHHHHHHhh
Confidence 53 57999999988877655
No 10
>PF00607 Gag_p24: gag gene protein p24 (core nucleocapsid protein); InterPro: IPR000721 The Gag protein from retroviruses, also known as p24, forms the inner protein layer of the nucleocapsid. This protein performs highly complex orchestrated tasks during the assembly, budding, maturation and infection stages of the viral replication cycle. During viral assembly, the proteins form membrane associations and self-associations that ultimately result in budding of an immature virion from the infected cell. Gag precursors also function during viral assembly to selectively bind and package two plus strands of genomic RNA. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.; GO: 0016032 viral reproduction; PDB: 1BMX_A 1SJH_C 1SJE_C 1U57_A 1FGL_B 1G03_A 2XT1_A 2JO0_A 2L6E_A 2HJL_C ....
Probab=15.89 E-value=1.2e+02 Score=33.34 Aligned_cols=74 Identities=16% Similarity=0.214 Sum_probs=46.0
Q ss_pred ccccccccCCCCHHHHHHHHHHhhhcCCCch-hhhhhhhccchhHHHHHhhhhceeccCCCchHHHHhhcCccCCCCCCH
Q psy10146 168 KFFTRDQQEGESVENYVAVLNKMSYDCEFEK-LREDLLDNKSLQLEEVISKLTDHFVPKKNLTYVRHKFFTRDQQEGESV 246 (1902)
Q Consensus 168 KFySRkQEpGESIDQFVAELRQLAESCEFGD-LEDELIrDksLTIEea~EKLRDRIVcGIrSkaIQRRLLeEDd~e~LTL 246 (1902)
.|-...|.|.|++.+||.+|..-+..+.=.. ..+-|+ ++|.++-+..-+| +++.|+. .+ =+|
T Consensus 124 ~~~~I~QGp~Epf~dFv~rl~~a~~~~~~~~~~~~~~~--~~L~~eNAN~~C~-~~~~~l~----------~~----~~l 186 (206)
T PF00607_consen 124 SFTKIKQGPKEPFADFVDRLQKAIRREQGENEVKNILI--RQLAYENANPDCR-RIIRPLG----------KD----APL 186 (206)
T ss_dssp TGGGH-S-TTSHHHHHHHHHHHHHHCSSSTHHHHHHHH--HHHHHHTS-HHHH-HHHHHH-----------TT----STH
T ss_pred cHHHhhhccccchHHHHHHHHHHHhhcccccchhhHHH--HHhhhccchHHHH-HHHHccC----------CC----CCH
Confidence 6778899999999999999999888875532 444442 2455554443322 2222222 22 569
Q ss_pred HHHHHHHHHhcc
Q psy10146 247 ENYVAVLNKMSY 258 (1902)
Q Consensus 247 EKAVDIArAmEl 258 (1902)
++.+..|+.+-.
T Consensus 187 ee~~~~C~~vg~ 198 (206)
T PF00607_consen 187 EEMIRACQGVGG 198 (206)
T ss_dssp HHHHHHTTTTSS
T ss_pred HHHHHHhhccCC
Confidence 999998887663
Done!