Query 010395
Match_columns 511
No_of_seqs 135 out of 156
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 00:02:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010395.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010395hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07899 Frigida: Frigida-like 100.0 5.5E-87 1.2E-91 674.7 29.8 275 116-403 7-287 (290)
2 PF07035 Mic1: Colon cancer-as 94.2 0.1 2.2E-06 50.0 6.1 78 250-329 45-129 (167)
3 KOG0260 RNA polymerase II, lar 88.9 1.5 3.3E-05 52.6 8.7 14 355-368 1336-1349(1605)
4 KOG0260 RNA polymerase II, lar 88.9 1.4 3.1E-05 52.9 8.4 17 246-263 1241-1257(1605)
5 KOG2236 Uncharacterized conser 69.9 41 0.00089 37.3 10.8 19 378-396 320-338 (483)
6 KOG1924 RhoA GTPase effector D 69.8 32 0.00069 40.5 10.3 20 405-424 516-535 (1102)
7 KOG3107 Predicted haloacid deh 58.9 8.7 0.00019 41.6 3.3 9 502-510 107-115 (468)
8 KOG0921 Dosage compensation co 57.7 1.3E+02 0.0028 36.6 12.4 41 359-399 1097-1140(1282)
9 KOG2005 26S proteasome regulat 54.8 4.3E+02 0.0092 31.3 16.3 70 266-335 267-346 (878)
10 PF06705 SF-assemblin: SF-asse 53.8 1.8E+02 0.0039 29.2 11.5 53 120-175 180-234 (247)
11 PF07223 DUF1421: Protein of u 53.0 28 0.00061 37.5 5.9 34 462-499 219-256 (358)
12 PF12925 APP_E2: E2 domain of 51.0 80 0.0017 31.3 8.2 92 4-105 18-122 (193)
13 PF09726 Macoilin: Transmembra 49.3 1.3E+02 0.0028 35.2 10.9 59 19-77 425-496 (697)
14 KOG3875 Peroxisomal biogenesis 39.0 62 0.0014 34.4 5.7 23 458-480 42-66 (362)
15 smart00502 BBC B-Box C-termina 38.3 1.4E+02 0.0031 25.4 7.2 53 10-62 15-68 (127)
16 KOG2236 Uncharacterized conser 38.3 93 0.002 34.7 7.0 10 459-468 438-447 (483)
17 PRK04051 rps4p 30S ribosomal p 36.9 80 0.0017 30.8 5.8 59 247-305 68-130 (177)
18 PF06825 HSBP1: Heat shock fac 34.1 77 0.0017 25.2 4.2 33 34-66 11-43 (54)
19 PF10498 IFT57: Intra-flagella 33.8 2.1E+02 0.0045 30.9 8.8 47 21-67 222-268 (359)
20 PF04156 IncA: IncA protein; 33.4 2.3E+02 0.0049 26.9 8.3 49 13-64 92-143 (191)
21 KOG2893 Zn finger protein [Gen 33.3 1.4E+02 0.003 30.9 6.9 23 397-419 89-112 (341)
22 PF08711 Med26: TFIIS helical 31.6 51 0.0011 25.1 2.9 21 216-236 33-53 (53)
23 PRK06771 hypothetical protein; 31.0 52 0.0011 29.0 3.1 31 284-314 40-77 (93)
24 PF10873 DUF2668: Protein of u 30.9 94 0.002 29.6 4.9 9 486-494 144-152 (155)
25 PF07139 DUF1387: Protein of u 27.1 1.6E+02 0.0034 31.2 6.3 127 13-177 154-290 (302)
26 PF13874 Nup54: Nucleoporin co 27.0 1.5E+02 0.0032 27.4 5.6 38 3-46 17-54 (141)
27 PF12718 Tropomyosin_1: Tropom 26.5 2.8E+02 0.0061 25.9 7.4 46 28-74 58-103 (143)
28 TIGR01837 PHA_granule_1 poly(h 26.1 2.6E+02 0.0056 25.3 6.8 33 365-397 82-114 (118)
29 PF03938 OmpH: Outer membrane 24.3 3.2E+02 0.0069 24.9 7.3 19 87-105 109-127 (158)
30 PF13851 GAS: Growth-arrest sp 24.2 3.9E+02 0.0084 26.3 8.2 55 12-66 72-129 (201)
31 PF10873 DUF2668: Protein of u 23.1 1.4E+02 0.0031 28.5 4.6 41 430-473 106-150 (155)
32 PF04899 MbeD_MobD: MbeD/MobD 22.5 4E+02 0.0087 22.3 6.7 36 9-50 3-38 (70)
33 PF09849 DUF2076: Uncharacteri 22.1 3.9E+02 0.0084 27.5 8.0 17 381-397 57-73 (247)
34 PF11914 DUF3432: Domain of un 21.9 1.4E+02 0.0031 26.3 4.1 20 476-495 57-76 (99)
35 KOG3088 Secretory carrier memb 21.8 49 0.0011 34.7 1.5 26 38-64 52-77 (313)
36 PF05130 FlgN: FlgN protein; 21.3 5.4E+02 0.012 22.2 8.6 14 90-103 54-67 (143)
37 PF12825 DUF3818: Domain of un 20.9 3.3E+02 0.007 29.2 7.4 116 126-262 95-218 (341)
38 PF08946 Osmo_CC: Osmosensory 20.7 1.2E+02 0.0026 23.5 3.0 23 38-64 10-32 (46)
39 PHA01750 hypothetical protein 20.2 2.7E+02 0.0057 23.4 5.1 40 351-398 35-74 (75)
No 1
>PF07899 Frigida: Frigida-like protein; InterPro: IPR012474 This family is composed of plant proteins that are similar to FRIGIDA protein expressed by Arabidopsis thaliana (Mouse-ear cress) (Q9FDW0 from SWISSPROT). This protein is probably nuclear and is required for the regulation of flowering time in the late-flowering phenotype. It is known to increase RNA levels of flowering locus C. Allelic variation at the FRIGIDA locus is a major determinant of natural variation in flowering time [].
Probab=100.00 E-value=5.5e-87 Score=674.72 Aligned_cols=275 Identities=48% Similarity=0.749 Sum_probs=260.3
Q ss_pred CccchHHHHHHHhhhcchHHHHHHHHhhhchHHHHHhhHHHHhhcCCChhhHHHHHhhcccCCCCCCC--CCCchhhHHH
Q 010395 116 DGDGLLMILMSYCLKMEARGFWKFVVTKKKEIEELRNALPAALSECVDPAKFVMEAISEVFPVDKRSD--KSGNDLGWAC 193 (511)
Q Consensus 116 ~~~~~~~~L~~lCe~MD~~gL~~fi~~~~ke~~~lr~Elp~ALr~ApDPAkLVLdai~~fy~~~~~~~--~~~~~~~~aC 193 (511)
....++++|+.||++||++||++||++|+|++.+||+|||+||++|||||+||||||+|||+++.+.+ ....+.+|+|
T Consensus 7 ~~~~~~~~L~~lC~~MD~~gL~~fv~~~~k~~~~lr~Ev~~AL~~A~DPAkLVLdai~~f~~~~~~~~~~~~~~~~r~~c 86 (290)
T PF07899_consen 7 VEVKPRPELKSLCEKMDGKGLRKFVSENRKELASLREEVPAALRCAPDPAKLVLDAIEGFYPPGSKNKKDSKLVDVRRAC 86 (290)
T ss_pred CCcchHHHHHHHHHHCCHHHHHHHHHHhhhhHHHHHHHHHHHHHcCCChHHHHHHHHHcccCCccccccCcchhhHHHHH
Confidence 35568999999999999999999999999999999999999999999999999999999999876442 3355789999
Q ss_pred HHHHHHhccccCCccccccCCCCChhHHHHHHHHHHHHHHHhhhccCCCCCCchhHHHHHHHHHHhcCCcccCHHHHHHH
Q 010395 194 VLVLESLIPVMVDPVIGKMRMLVTPSVKEKAKEIAERWKASLEERGGIENVKTPDVHTFLQLLVTFGIVKKEDVDLYRKL 273 (511)
Q Consensus 194 ilLLE~L~~~l~~p~~g~~~p~vs~~vkeeAk~lA~~WK~kl~~~g~~~~~~~lea~gFLqlLa~fGI~seFd~del~~L 273 (511)
|+|||+|++ .+|.++++||++|++||.+||++|+ ++++.+++|||||||||++|||+++||.|||++|
T Consensus 87 ilLLE~L~~---------~~~~is~~vke~A~~lA~~WK~~l~---~~~~~~~lea~gFL~lla~fgi~s~Fd~del~~L 154 (290)
T PF07899_consen 87 ILLLEQLMR---------ISPEISPEVKEEAKKLAEEWKSKLD---GVNNENSLEALGFLQLLAAFGIVSEFDEDELLKL 154 (290)
T ss_pred HHHHHHHhh---------cCCCCCHHHHHHHHHHHHHHHHHHH---hcccCCCHHHHHHHHHHHHcCCccccCHHHHHHH
Confidence 999999986 3578999999999999999999996 4467889999999999999999999999999999
Q ss_pred hccccchhhhHHHHHHhCCCCchh----hhhhcCcchHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhcCCCCch
Q 010395 274 VVGSAWRKQMPKLAVSLGLGDKMP----ELISRGQQLDAVHFTYEVGLVDKFPPVPLLKAFLKDAKKAAVSILEDPNNAG 349 (511)
Q Consensus 274 v~~va~rkq~~eL~~sLGL~dKmp----~LI~kGk~IeAV~fi~aF~L~dkFpPvpLLK~yl~~akk~~~~~~~~g~~s~ 349 (511)
|..+++|+|+++||++|||+|||| +||++||||+||+|||+|||+||||||||||+||+++|++++.++++++++
T Consensus 155 v~~va~~~~a~~L~~sLgl~~k~~d~V~~LI~~g~~ieAv~fi~~f~L~dkfpPv~lLk~yl~~~k~~~~~~~~~~~~~- 233 (290)
T PF07899_consen 155 VVSVARRKQAPELCRSLGLSDKMPDIVEKLIKKGKQIEAVRFIYAFGLVDKFPPVPLLKSYLEDSKKAAKRIRKKGNSS- 233 (290)
T ss_pred HHHhcchHhhHHHHHHcCchhhhHHHHHHHHHCCCccchHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHhcCCCh-
Confidence 999999999999999999999999 999999999999999999999999999999999999999999999998888
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHhhcCCCCCChhHHHHHHHHHHHhhhhccCCCC
Q 010395 350 RAAHLAARKEQSALRAVIKCIEDYKLQGEFPPENLKKRLEQLEKAKTEKKKPAA 403 (511)
Q Consensus 350 ~a~~eA~~kEl~aLksViKcIEdhkLese~p~~~L~krI~qLEK~k~ekkr~~~ 403 (511)
.+++++++||+++||+|||||||||||++||+++|++||.||||+|++|||+++
T Consensus 234 ~a~~ea~~kel~aL~~vikcIee~kLes~~~~~~l~kri~~Lek~~~~~kr~~~ 287 (290)
T PF07899_consen 234 EAQNEANEKELAALKSVIKCIEEHKLESEFPLEPLQKRIEQLEKQKADRKRAAE 287 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccccccChHHHHHHHHHHHHHHHHHhhccc
Confidence 999999999999999999999999999999999999999999999999999875
No 2
>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1.
Probab=94.21 E-value=0.1 Score=49.98 Aligned_cols=78 Identities=21% Similarity=0.269 Sum_probs=60.2
Q ss_pred HHHHHHHHHhcCCcccCHHHHHHHhccccc-----hhhhHHHHHHhCCCCchh--hhhhcCcchHHHHHHHHhcCCCCCC
Q 010395 250 HTFLQLLVTFGIVKKEDVDLYRKLVVGSAW-----RKQMPKLAVSLGLGDKMP--ELISRGQQLDAVHFTYEVGLVDKFP 322 (511)
Q Consensus 250 ~gFLqlLa~fGI~seFd~del~~Lv~~va~-----rkq~~eL~~sLGL~dKmp--~LI~kGk~IeAV~fi~aF~L~dkFp 322 (511)
...|+.+..|++.. |...+...+++... +.-+.+.++.||..+..- -|+.+|+.++|++||...+-++..|
T Consensus 45 ~~~L~qllq~~Vi~--DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~~~~~~iievLL~~g~vl~ALr~ar~~~~~~~~~ 122 (167)
T PF07035_consen 45 FSQLHQLLQYHVIP--DSKPLACQLLSLGNQYPPAYQLGLDMLKRLGTAYEEIIEVLLSKGQVLEALRYARQYHKVDSVP 122 (167)
T ss_pred HHHHHHHHhhcccC--CcHHHHHHHHHhHccChHHHHHHHHHHHHhhhhHHHHHHHHHhCCCHHHHHHHHHHcCCcccCC
Confidence 47788888999998 76666655554432 445677789999665544 6999999999999999999999998
Q ss_pred ChHHHHH
Q 010395 323 PVPLLKA 329 (511)
Q Consensus 323 PvpLLK~ 329 (511)
|.-+|.+
T Consensus 123 ~~~fLeA 129 (167)
T PF07035_consen 123 ARKFLEA 129 (167)
T ss_pred HHHHHHH
Confidence 8776543
No 3
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=88.90 E-value=1.5 Score=52.62 Aligned_cols=14 Identities=14% Similarity=0.166 Sum_probs=6.3
Q ss_pred HHHHHHHHHHHHHH
Q 010395 355 AARKEQSALRAVIK 368 (511)
Q Consensus 355 A~~kEl~aLksViK 368 (511)
.|=+-++.|..|+-
T Consensus 1336 VnyrhlaLl~dvmT 1349 (1605)
T KOG0260|consen 1336 VNYRHLALLCDVMT 1349 (1605)
T ss_pred hhHHHHHHHHHHHh
Confidence 44444444444443
No 4
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=88.90 E-value=1.4 Score=52.90 Aligned_cols=17 Identities=12% Similarity=0.128 Sum_probs=7.9
Q ss_pred chhHHHHHHHHHHhcCCc
Q 010395 246 TPDVHTFLQLLVTFGIVK 263 (511)
Q Consensus 246 ~lea~gFLqlLa~fGI~s 263 (511)
+.|+.++.- +.-+||..
T Consensus 1241 ~Ie~~ml~~-~~l~G~~~ 1257 (1605)
T KOG0260|consen 1241 CIEANMLGD-MTLRGIPD 1257 (1605)
T ss_pred HHHHhhhhh-cccCCccc
Confidence 445554433 34556543
No 5
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=69.92 E-value=41 Score=37.28 Aligned_cols=19 Identities=16% Similarity=0.433 Sum_probs=9.0
Q ss_pred CCChhHHHHHHHHHHHhhh
Q 010395 378 EFPPENLKKRLEQLEKAKT 396 (511)
Q Consensus 378 e~p~~~L~krI~qLEK~k~ 396 (511)
+|+-+.=+.--.++.||+.
T Consensus 320 dfSDDEkEaeak~~kKQrk 338 (483)
T KOG2236|consen 320 DFSDDEKEAEAKQMKKQRK 338 (483)
T ss_pred ccchHHHHHHHHHHHHHhh
Confidence 4554444444455545443
No 6
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=69.84 E-value=32 Score=40.53 Aligned_cols=20 Identities=20% Similarity=0.315 Sum_probs=12.1
Q ss_pred CCccCcccCCCCCCCCcccc
Q 010395 405 PATKRTRASNGGPMPPAKAG 424 (511)
Q Consensus 405 ~~~KR~R~s~g~~~p~a~~~ 424 (511)
.+++-+-..+|-++||+...
T Consensus 516 s~~~~~~~~~~iP~PP~~pp 535 (1102)
T KOG1924|consen 516 SPSQLLPIDGGIPPPPPLPP 535 (1102)
T ss_pred CcccCCCCCCCCCCCCCCCC
Confidence 34555555667677776554
No 7
>KOG3107 consensus Predicted haloacid dehalogenase-like hydrolase (eyes absent) [General function prediction only]
Probab=58.93 E-value=8.7 Score=41.60 Aligned_cols=9 Identities=44% Similarity=0.907 Sum_probs=5.2
Q ss_pred Ccccccccc
Q 010395 502 APAYQQAYY 510 (511)
Q Consensus 502 ~~~~~~~y~ 510 (511)
|-+||+.||
T Consensus 107 q~qY~~yY~ 115 (468)
T KOG3107|consen 107 QAQYQNYYY 115 (468)
T ss_pred hHhhccccc
Confidence 346666665
No 8
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=57.75 E-value=1.3e+02 Score=36.56 Aligned_cols=41 Identities=15% Similarity=0.153 Sum_probs=27.8
Q ss_pred HHHHHHHHHHH--HHhhcCCCC-CChhHHHHHHHHHHHhhhhcc
Q 010395 359 EQSALRAVIKC--IEDYKLQGE-FPPENLKKRLEQLEKAKTEKK 399 (511)
Q Consensus 359 El~aLksViKc--IEdhkLese-~p~~~L~krI~qLEK~k~ekk 399 (511)
=|.+||+.++- +|-.|--+. -.+|+...|+.++=++-....
T Consensus 1097 cItgLr~AmEaLvvev~knPaiIsqLdpvnarllnmiRdIs~pS 1140 (1282)
T KOG0921|consen 1097 CITGLRPAMEALVVEVCKNPAIISQLDPVNARLLNMIRDISRPS 1140 (1282)
T ss_pred HHhhhHHHHHHHHHHHhcChhHhhccCchhHHHHHHHHHhcccc
Confidence 47778887765 455554443 446888889988888776543
No 9
>KOG2005 consensus 26S proteasome regulatory complex, subunit RPN1/PSMD2 [Posttranslational modification, protein turnover, chaperones]
Probab=54.83 E-value=4.3e+02 Score=31.30 Aligned_cols=70 Identities=17% Similarity=0.343 Sum_probs=50.5
Q ss_pred CHHHHHHHhcccc---chhhhHHHHHHhCCCCch---h---hhhhcCcchHHH-HHHHHhcCCCCCCChHHHHHHHHHHH
Q 010395 266 DVDLYRKLVVGSA---WRKQMPKLAVSLGLGDKM---P---ELISRGQQLDAV-HFTYEVGLVDKFPPVPLLKAFLKDAK 335 (511)
Q Consensus 266 d~del~~Lv~~va---~rkq~~eL~~sLGL~dKm---p---~LI~kGk~IeAV-~fi~aF~L~dkFpPvpLLK~yl~~ak 335 (511)
|.+++.+.|.+.. .+||+.-+...-|+.-.+ + ..++||+--|-. .++.+.++.+-=-|-.|+|+|++++|
T Consensus 267 ~~~~v~~vf~s~~D~~~kKQ~~ymLaR~~i~~e~~~~e~l~di~sN~~Lse~f~~LarELeimepk~pedIyK~hl~~~r 346 (878)
T KOG2005|consen 267 DMKEVKEVFTSCTDPLLKKQMAYMLARHGIYFELSEDEELQDILSNGKLSEHFLYLARELEIMEPKVPEDIYKSHLEDSR 346 (878)
T ss_pred cHHHHHHHHHhccCHHHHHHHHHHHHhcCCceecCcCHHHHHHHccccHHHHHHHHHHHhcccCCCChHHHHHHHHhccc
Confidence 4555555554443 357777766555644333 2 778888877654 46889999999999999999999998
No 10
>PF06705 SF-assemblin: SF-assemblin/beta giardin
Probab=53.79 E-value=1.8e+02 Score=29.18 Aligned_cols=53 Identities=25% Similarity=0.257 Sum_probs=28.7
Q ss_pred hHHHHHHHhhh--cchHHHHHHHHhhhchHHHHHhhHHHHhhcCCChhhHHHHHhhcc
Q 010395 120 LLMILMSYCLK--MEARGFWKFVVTKKKEIEELRNALPAALSECVDPAKFVMEAISEV 175 (511)
Q Consensus 120 ~~~~L~~lCe~--MD~~gL~~fi~~~~ke~~~lr~Elp~ALr~ApDPAkLVLdai~~f 175 (511)
++..|..+|.. -+-.+|+.|+.+ ++..|+..|-..-..=-+---.+++||..+
T Consensus 180 l~~~le~~~~~~~~~~e~f~~~v~~---Ei~~lk~~l~~e~~~R~~~Dd~Iv~aln~y 234 (247)
T PF06705_consen 180 LRSELEEVKRRREKGDEQFQNFVLE---EIAALKNALALESQEREQSDDDIVQALNHY 234 (247)
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHH---HHHHHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence 45566666642 234455665554 566777766444444344445556666544
No 11
>PF07223 DUF1421: Protein of unknown function (DUF1421); InterPro: IPR010820 This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.
Probab=53.02 E-value=28 Score=37.46 Aligned_cols=34 Identities=41% Similarity=0.879 Sum_probs=17.6
Q ss_pred cCCCCCC-CCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCC
Q 010395 462 VYGSRSP-PYAYSPEAAPPLA---GSYPGAPMNYPAYGGYGN 499 (511)
Q Consensus 462 ~y~~~~~-~y~y~~~~~~~~~---~~y~~~~~~~~~~~~y~~ 499 (511)
.||...+ +|.|.+....+.+ ..|..++ +|+|||+
T Consensus 219 ~~~~~~~~~y~y~~~~~~p~~~~~~~~~~~p----~~~Gy~~ 256 (358)
T PF07223_consen 219 FYGEPDPSPYMYGPPASRPPSGMPQHQQPPP----SQGGYGY 256 (358)
T ss_pred cCCCCCCCCcccCCCCCCCCccccccCCCCc----ccccccC
Confidence 3444443 7888887544432 3454444 3444544
No 12
>PF12925 APP_E2: E2 domain of amyloid precursor protein; InterPro: IPR024329 Amyloid-beta precursor protein (APP, or A4) is associated with Alzheimer's disease (AD), because one of its breakdown products, amyloid-beta (A-beta), aggregates to form amyloid or senile plaques [, ]. Mutations in APP or in proteins that process APP have been linked with early-onset, familial AD. Individuals with Down's syndrome carry an extra copy of chromosome 21, which contains the APP gene, and almost invariably develop amyloid plaques and Alzheimer's symptoms. APP is important for the neurogenesis and neuronal regeneration, either through the intact protein, or through its many breakdown products []. APP consists of a large N-terminal extracellular region containing heparin-binding and copper-binding sites, a short hydrophobic transmembrane domain, and a short C-terminal intracellular domain. The N-terminal region is similar in structure to cysteine-rich growth factors and appears to function as a cell surface receptor, contributing to neurite growth, neuronal adhesion, axonogenesis and cell mobility []. APP acts as a kinesin I membrane receptor to mediate the axonal transport of beta-secretase and presenilin 1. The N-terminal domain can regulate neurite outgrowth through its binding to heparin and collagen I and IV, which are components of the extracellular matrix. APP is also coupled to apoptosis-inducing pathways, and is involved in copper homeostasis/oxidative stress through copper ion reduction, where copper-metallated APP induces neuronal death []. The C-terminal intracellular domain appears to be involved in transcription regulation through protein-protein interactions. APP can promote transcription activation through binding to APBB1/Tip60, and may bind to the adaptor protein FE65 to transactivate a wide variety of different promoters. APP can be processed by different sets of enzymes: In the non-amyloidogenic (non-plaque-forming) pathway, APP is cleaved by alpha-secretase to yield a soluble N-terminal sAPP-alpha (neuroprotective) and a membrane-bound CTF-alpha. CTF-alpha is broken-down by presenilin-containing gamma-secretase to yield soluble p3 and membrane-bound AICD (nuclear signalling). In the amyloidogenic pathway (plaque-forming), APP is broken down by beta-secretase to yield soluble sAPP-beta and membrane-bound CTF-beta. CTF-beta is broken down by gamma-secretase to yield soluble amyloid-beta and membrane-bound AICD. Amyloid-beta is required for neuronal function, but can aggregate to form amyloid plaques that seem to disrupt brain cells by clogging points of cell-cell contact. The E2 domain is the largest of the conserved domains in the amyloidogenic glycoproteins. The structure of E2 consists of two coiled-coil sub-structures connected through a continuous helix, and bears an unexpected resemblance to the spectrin family of protein structures. E2 can reversibly dimerise in solution, and the dimerisation occurs along the longest dimension of the molecule in an antiparallel orientation, which enables the N-terminal substructure of one monomer to pack against the C-terminal substructure of a second monomer. The high degree of conservation of residues at the putative dimer interface suggests that the E2 dimer observed in the crystal could be physiologically relevant. Heparin sulphate proteoglycans, the putative ligands for the precursor present in extracellular matrix, bind to E2 at a conserved and positively charged site near the dimer interface [].; PDB: 3K6B_A 3K66_A 1TKN_A 3NYL_A 3NYJ_A 3UMH_A 3UMK_A 3UMI_A 3QMK_B 3PMR_B ....
Probab=51.02 E-value=80 Score=31.29 Aligned_cols=92 Identities=13% Similarity=0.274 Sum_probs=56.7
Q ss_pred CCCCchhhhhchhHHHHHHh-hhhhhhhhccchhHHHhhHHHH-----------HHHHHHHHHHHHHHHhhhhhhhh-hH
Q 010395 4 IPDPGELSELNPLSFDEFQR-QTSLMTSCTLLWKELSDHFTSL-----------EQNLQKKSAALRHKIQTLDTQTK-AS 70 (511)
Q Consensus 4 ~~~~~~~~e~l~kaF~eLqs-~~s~l~s~tl~W~eL~~HF~sL-----------e~sL~~r~e~L~~k~~~~e~~~~-~~ 70 (511)
.|||..--+..++|=..|+. |+-=++..--.|+|+++++..| .+.|..||+..-....+ ... +.
T Consensus 18 ~~~~~~Eh~~f~~Ak~rLe~~hr~r~~~VmkeW~eaE~~~~~l~~~DPk~Ae~~k~~m~~rFQ~~v~aLE~---e~~~er 94 (193)
T PF12925_consen 18 HPDPENEHQRFKEAKERLEEKHRERMTKVMKEWSEAEERYKELPKADPKKAEQFKKEMTQRFQKTVQALEQ---EAAAER 94 (193)
T ss_dssp SSTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHH
T ss_pred cCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhhHHHHHHHHHHHHHHHHHHH---HHHHHH
Confidence 46777777888888888864 4444556678999999999765 56777777766544322 211 11
Q ss_pred HHHhhhhcccccccHHHHHHhhhhhHHHHHhhhhc
Q 010395 71 LDVLKKREVTIDGSVEIAMEKLEDRTEATLNSISR 105 (511)
Q Consensus 71 ~~~l~~re~~i~~~~~~~l~~~~e~~~aa~~s~~~ 105 (511)
.++. ..-.+-...-|.++|.+|+...-.
T Consensus 95 ~qL~-------~~H~qRV~a~Lnerkr~al~~y~~ 122 (193)
T PF12925_consen 95 QQLV-------ETHQQRVQAMLNERKRAALENYTA 122 (193)
T ss_dssp HHHH-------HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHH-------HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1111 112222334556888888877544
No 13
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=49.32 E-value=1.3e+02 Score=35.21 Aligned_cols=59 Identities=29% Similarity=0.402 Sum_probs=35.9
Q ss_pred HHHHhhhhhhhhhccchhHHHhhHHHHHHH----------HHHHHHHHHHHHhhhhhhh---hhHHHHhhhh
Q 010395 19 DEFQRQTSLMTSCTLLWKELSDHFTSLEQN----------LQKKSAALRHKIQTLDTQT---KASLDVLKKR 77 (511)
Q Consensus 19 ~eLqs~~s~l~s~tl~W~eL~~HF~sLe~s----------L~~r~e~L~~k~~~~e~~~---~~~~~~l~~r 77 (511)
.|+++.++-|.+....=.||-.|.++|..+ |++.-|+|+.|...+...- ++++..|++|
T Consensus 425 ~dvkkLraeLq~~Rq~E~ELRsqis~l~~~Er~lk~eL~qlr~ene~Lq~Kl~~L~~aRq~DKq~l~~LEkr 496 (697)
T PF09726_consen 425 ADVKKLRAELQSSRQSEQELRSQISSLTNNERSLKSELSQLRQENEQLQNKLQNLVQARQQDKQSLQQLEKR 496 (697)
T ss_pred HHHHHHHHHHHhhhhhHHHHHHHHhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355555555555566667888887766665 6666666666665553322 3555666665
No 14
>KOG3875 consensus Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport]
Probab=39.03 E-value=62 Score=34.40 Aligned_cols=23 Identities=17% Similarity=0.423 Sum_probs=11.5
Q ss_pred CCCCcCCCCC--CCCCCCCCCCCCC
Q 010395 458 SPPAVYGSRS--PPYAYSPEAAPPL 480 (511)
Q Consensus 458 ~~~~~y~~~~--~~y~y~~~~~~~~ 480 (511)
+.+++|+++. ++|+..+--++++
T Consensus 42 T~~G~~~~~~~g~s~~~g~~~mN~f 66 (362)
T KOG3875|consen 42 TGPGIYGNSNYGISYVTGHYSMNTF 66 (362)
T ss_pred CCCCccccccCCCccccCCcccccc
Confidence 4444443332 2666666555553
No 15
>smart00502 BBC B-Box C-terminal domain. Coiled coil region C-terminal to (some) B-Box domains
Probab=38.29 E-value=1.4e+02 Score=25.43 Aligned_cols=53 Identities=9% Similarity=0.116 Sum_probs=36.0
Q ss_pred hhhhchhHHHHHHhhhhhh-hhhccchhHHHhhHHHHHHHHHHHHHHHHHHHhh
Q 010395 10 LSELNPLSFDEFQRQTSLM-TSCTLLWKELSDHFTSLEQNLQKKSAALRHKIQT 62 (511)
Q Consensus 10 ~~e~l~kaF~eLqs~~s~l-~s~tl~W~eL~~HF~sLe~sL~~r~e~L~~k~~~ 62 (511)
+.+.+..+...|+.....+ .++.-.+.++.++|..|.+.|..+=+.|-++...
T Consensus 15 ~~~~~~~~~~~l~~~~~~l~~~~~~~~~~I~~~f~~l~~~L~~~e~~ll~~l~~ 68 (127)
T smart00502 15 KAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEE 68 (127)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445556666666555554 4677778888888888888888777777555543
No 16
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.26 E-value=93 Score=34.65 Aligned_cols=10 Identities=50% Similarity=1.172 Sum_probs=4.3
Q ss_pred CCCcCCCCCC
Q 010395 459 PPAVYGSRSP 468 (511)
Q Consensus 459 ~~~~y~~~~~ 468 (511)
+++-||...|
T Consensus 438 p~~~~g~~~P 447 (483)
T KOG2236|consen 438 PPANFGQANP 447 (483)
T ss_pred CcccccccCc
Confidence 3344444444
No 17
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=36.93 E-value=80 Score=30.77 Aligned_cols=59 Identities=20% Similarity=0.347 Sum_probs=47.8
Q ss_pred hhHHHHHHHHHHhcCCccc-CHHHHHHHhccccchhhhHHHHHHhCCCCchh---hhhhcCcc
Q 010395 247 PDVHTFLQLLVTFGIVKKE-DVDLYRKLVVGSAWRKQMPKLAVSLGLGDKMP---ELISRGQQ 305 (511)
Q Consensus 247 lea~gFLqlLa~fGI~seF-d~del~~Lv~~va~rkq~~eL~~sLGL~dKmp---~LI~kGk~ 305 (511)
.+.-.||.-|.-+||.++- +.|++.+|-+..-.++....+...+||+..+. .||..|+.
T Consensus 68 ~~~~~Ll~kL~~~Gil~~~~~L~~vl~L~v~~~lerRLd~il~r~gla~S~~~Ar~lI~hGhV 130 (177)
T PRK04051 68 KEEEQLLGKLKRYGILKENATLDDVLSLTVEDILERRLQTIVYRKGLARTPKQARQFIVHGHI 130 (177)
T ss_pred HHHHHHHHHHHHcCCCCCCCCHHHHHhccHHHHHHhHHHHHHHHccCcCCHHHHHHHHHcCCE
Confidence 4567999999999999873 46777777666666778888999999999988 88888764
No 18
>PF06825 HSBP1: Heat shock factor binding protein 1; InterPro: IPR009643 Heat shock factor binding protein 1 (HSBP1) appears to be a negative regulator of the heat shock response [].; PDB: 3CI9_A.
Probab=34.07 E-value=77 Score=25.24 Aligned_cols=33 Identities=15% Similarity=0.462 Sum_probs=28.3
Q ss_pred chhHHHhhHHHHHHHHHHHHHHHHHHHhhhhhh
Q 010395 34 LWKELSDHFTSLEQNLQKKSAALRHKIQTLDTQ 66 (511)
Q Consensus 34 ~W~eL~~HF~sLe~sL~~r~e~L~~k~~~~e~~ 66 (511)
.-.+++++|..+-..|-.|.++...++-.+|..
T Consensus 11 lL~qmq~kFq~mS~~I~~riDeM~~RIDdLE~s 43 (54)
T PF06825_consen 11 LLQQMQDKFQTMSDQILGRIDEMSSRIDDLEKS 43 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence 347889999999999999999999888888754
No 19
>PF10498 IFT57: Intra-flagellar transport protein 57 ; InterPro: IPR019530 Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated []. This protein is known as Huntington-interacting protein-1 in humans.
Probab=33.82 E-value=2.1e+02 Score=30.86 Aligned_cols=47 Identities=13% Similarity=0.199 Sum_probs=32.2
Q ss_pred HHhhhhhhhhhccchhHHHhhHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 010395 21 FQRQTSLMTSCTLLWKELSDHFTSLEQNLQKKSAALRHKIQTLDTQT 67 (511)
Q Consensus 21 Lqs~~s~l~s~tl~W~eL~~HF~sLe~sL~~r~e~L~~k~~~~e~~~ 67 (511)
|+.-+.+..++.-.+.+...|+..|++.+.+-.+.+.++++.+.++.
T Consensus 222 leqm~~~~~~I~~~~~~~~~~L~kl~~~i~~~lekI~sREk~iN~ql 268 (359)
T PF10498_consen 222 LEQMKQHKKSIESALPETKSQLDKLQQDISKTLEKIESREKYINNQL 268 (359)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44444444556667778888888888888888888877777665544
No 20
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=33.40 E-value=2.3e+02 Score=26.91 Aligned_cols=49 Identities=14% Similarity=0.262 Sum_probs=23.3
Q ss_pred hchhHHHHHHhhhhhhhhhccchhHHHhhHHHHH---HHHHHHHHHHHHHHhhhh
Q 010395 13 LNPLSFDEFQRQTSLMTSCTLLWKELSDHFTSLE---QNLQKKSAALRHKIQTLD 64 (511)
Q Consensus 13 ~l~kaF~eLqs~~s~l~s~tl~W~eL~~HF~sLe---~sL~~r~e~L~~k~~~~e 64 (511)
++++-+++++.+... ..-.+.++.+-+..++ ++...+.+.+++..+.+.
T Consensus 92 ~l~~el~~l~~~~~~---~~~~l~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~ 143 (191)
T PF04156_consen 92 QLQEELDQLQERIQE---LESELEKLKEDLQELRELLKSVEERLDSLDESIKELE 143 (191)
T ss_pred HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555555555443 4444555555555544 344444444444444443
No 21
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=33.32 E-value=1.4e+02 Score=30.88 Aligned_cols=23 Identities=43% Similarity=0.716 Sum_probs=17.3
Q ss_pred hccCCCC-CCCccCcccCCCCCCC
Q 010395 397 EKKKPAA-VPATKRTRASNGGPMP 419 (511)
Q Consensus 397 ekkr~~~-~~~~KR~R~s~g~~~p 419 (511)
++++++. +++.||-|.-+|.+|+
T Consensus 89 ~~r~~~de~~~ekr~~~d~~~~~~ 112 (341)
T KOG2893|consen 89 AYRGAADEEPDEKRSRMDNGPPMP 112 (341)
T ss_pred hhhhhhhcCchhhhhcccCCCCCC
Confidence 3455544 7888999999997787
No 22
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.
Probab=31.61 E-value=51 Score=25.13 Aligned_cols=21 Identities=29% Similarity=0.729 Sum_probs=17.5
Q ss_pred CChhHHHHHHHHHHHHHHHhh
Q 010395 216 VTPSVKEKAKEIAERWKASLE 236 (511)
Q Consensus 216 vs~~vkeeAk~lA~~WK~kl~ 236 (511)
-++++++.|+.|-..||..++
T Consensus 33 ~~~~i~~~A~~Li~~Wk~~v~ 53 (53)
T PF08711_consen 33 ENPEIRKLAKELIKKWKRIVD 53 (53)
T ss_dssp S-HHHHHHHHHHHHHHHHHH-
T ss_pred CCHHHHHHHHHHHHHHhHhcC
Confidence 468999999999999999863
No 23
>PRK06771 hypothetical protein; Provisional
Probab=31.05 E-value=52 Score=29.02 Aligned_cols=31 Identities=29% Similarity=0.500 Sum_probs=25.4
Q ss_pred HHHHHHhCCCCchh-------hhhhcCcchHHHHHHHH
Q 010395 284 PKLAVSLGLGDKMP-------ELISRGQQLDAVHFTYE 314 (511)
Q Consensus 284 ~eL~~sLGL~dKmp-------~LI~kGk~IeAV~fi~a 314 (511)
-.++.-+|+.+-.+ .|+..||.|+||+..++
T Consensus 40 ~~I~~~~Gi~~~~~~~~~e~~~Li~~Gkki~AIK~~Re 77 (93)
T PRK06771 40 QLITKEMGIVDREPPVNKELRQLMEEGQTVTAVKRVRE 77 (93)
T ss_pred HHHHHHcCCCCCcccccHHHHHHHHcCCchHHHHHHHH
Confidence 34777888887743 99999999999999875
No 24
>PF10873 DUF2668: Protein of unknown function (DUF2668); InterPro: IPR022640 Members in this family of proteins are annotated as cysteine and tyrosine-rich protein 1, however currently no function is known [].
Probab=30.91 E-value=94 Score=29.62 Aligned_cols=9 Identities=33% Similarity=0.722 Sum_probs=5.0
Q ss_pred CCCCCCCCC
Q 010395 486 GAPMNYPAY 494 (511)
Q Consensus 486 ~~~~~~~~~ 494 (511)
+||+.||++
T Consensus 144 spPppYpg~ 152 (155)
T PF10873_consen 144 SPPPPYPGN 152 (155)
T ss_pred CCccCCCCC
Confidence 355566654
No 25
>PF07139 DUF1387: Protein of unknown function (DUF1387); InterPro: IPR009816 This family represents a conserved region approximately 300 residues long within a number of hypothetical proteins of unknown function that seem to be restricted to mammals.
Probab=27.06 E-value=1.6e+02 Score=31.23 Aligned_cols=127 Identities=19% Similarity=0.290 Sum_probs=75.3
Q ss_pred hchhHHHHHHh-------hhhhh-hhhccchhHHHhhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHhhhhccccccc
Q 010395 13 LNPLSFDEFQR-------QTSLM-TSCTLLWKELSDHFTSLEQNLQKKSAALRHKIQTLDTQTKASLDVLKKREVTIDGS 84 (511)
Q Consensus 13 ~l~kaF~eLqs-------~~s~l-~s~tl~W~eL~~HF~sLe~sL~~r~e~L~~k~~~~e~~~~~~~~~l~~re~~i~~~ 84 (511)
.|.|+.-|||+ ++.+| .-|...-+.+..-|..|+.-|..|--.| ..++|....+++++|..|+....
T Consensus 154 nIEKSvKDLqRctvSL~RYr~~lkee~d~S~k~ik~~F~~l~~cL~dREvaL---l~EmdkVK~EAmeiL~aRqkkAe-- 228 (302)
T PF07139_consen 154 NIEKSVKDLQRCTVSLTRYRVVLKEEMDSSIKKIKQTFAELQSCLMDREVAL---LAEMDKVKAEAMEILDARQKKAE-- 228 (302)
T ss_pred cHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH--
Confidence 45555556555 44444 4667778888899999999998887777 45667777788999988865432
Q ss_pred HHHHHHhhhhhHHHHHhhhhccCCCCCCCCCCccchHHHHHHHhhhcchHHHHHHHHhhhchHHHHHhhHHHHhhcCCCh
Q 010395 85 VEIAMEKLEDRTEATLNSISRGQELGDGEVDDGDGLLMILMSYCLKMEARGFWKFVVTKKKEIEELRNALPAALSECVDP 164 (511)
Q Consensus 85 ~~~~l~~~~e~~~aa~~s~~~~~~~~~~~v~~~~~~~~~L~~lCe~MD~~gL~~fi~~~~ke~~~lr~Elp~ALr~ApDP 164 (511)
.|.++- |-|.. +++ .+|..|= .-+.-||.++. .-+||--|.|..=|+
T Consensus 229 ---eLkrlt---d~A~~-MsE----------------~Ql~ELR-----adIK~fvs~rk-----~de~lg~~~rf~~d~ 275 (302)
T PF07139_consen 229 ---ELKRLT---DRASQ-MSE----------------EQLAELR-----ADIKHFVSERK-----YDEELGRAARFTCDP 275 (302)
T ss_pred ---HHHHHH---HHHhh-cCH----------------HHHHHHH-----HHHHHHhhhhh-----hHHHHhHhhhcccCH
Confidence 122221 11111 111 1222221 12345677764 347888888888887
Q ss_pred hhH--HHHHhhcccC
Q 010395 165 AKF--VMEAISEVFP 177 (511)
Q Consensus 165 AkL--VLdai~~fy~ 177 (511)
-.| +++..+.+++
T Consensus 276 ~~l~~~i~~~g~v~~ 290 (302)
T PF07139_consen 276 EQLKKSIMSFGEVSH 290 (302)
T ss_pred HHHHHHHHhcCcccc
Confidence 655 4444445554
No 26
>PF13874 Nup54: Nucleoporin complex subunit 54; PDB: 3T97_B.
Probab=26.99 E-value=1.5e+02 Score=27.43 Aligned_cols=38 Identities=21% Similarity=0.455 Sum_probs=4.4
Q ss_pred CCCCCchhhhhchhHHHHHHhhhhhhhhhccchhHHHhhHHHHH
Q 010395 3 SIPDPGELSELNPLSFDEFQRQTSLMTSCTLLWKELSDHFTSLE 46 (511)
Q Consensus 3 ~~~~~~~~~e~l~kaF~eLqs~~s~l~s~tl~W~eL~~HF~sLe 46 (511)
.-|||+.+.--.=..|+||... .+.|=.++..|-..|+
T Consensus 17 ~nPdP~~~~Pv~i~GF~dL~~R------~~~Q~~~~~~~~~~l~ 54 (141)
T PF13874_consen 17 DNPDPSRLIPVPIIGFEDLKKR------VEAQEEEIAQHRERLK 54 (141)
T ss_dssp -----------------------------------HHHHHHHHH
T ss_pred HCcCCcCeeeehhhhHHHHHHH------HHHHHHHHHHHHHHHH
Confidence 3599988888888999998654 2344445555544444
No 27
>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].
Probab=26.54 E-value=2.8e+02 Score=25.87 Aligned_cols=46 Identities=13% Similarity=0.232 Sum_probs=23.6
Q ss_pred hhhhccchhHHHhhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHh
Q 010395 28 MTSCTLLWKELSDHFTSLEQNLQKKSAALRHKIQTLDTQTKASLDVL 74 (511)
Q Consensus 28 l~s~tl~W~eL~~HF~sLe~sL~~r~e~L~~k~~~~e~~~~~~~~~l 74 (511)
|....-.-.+-+.|++..| +|.+|...|+......+.+-.++.+-|
T Consensus 58 l~~~k~~lee~~~~~~~~E-~l~rriq~LEeele~ae~~L~e~~ekl 103 (143)
T PF12718_consen 58 LKEAKEKLEESEKRKSNAE-QLNRRIQLLEEELEEAEKKLKETTEKL 103 (143)
T ss_pred HHHHHHHHHhHHHHHHhHH-HHHhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444455555555555 555555555555555554444444444
No 28
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=26.05 E-value=2.6e+02 Score=25.26 Aligned_cols=33 Identities=21% Similarity=0.258 Sum_probs=25.6
Q ss_pred HHHHHHHhhcCCCCCChhHHHHHHHHHHHhhhh
Q 010395 365 AVIKCIEDYKLQGEFPPENLKKRLEQLEKAKTE 397 (511)
Q Consensus 365 sViKcIEdhkLese~p~~~L~krI~qLEK~k~e 397 (511)
.|-+.+...++-+.=-++.|.+||.+||++-.+
T Consensus 82 ~v~~~L~~lg~~tk~ev~~L~~RI~~Le~~l~~ 114 (118)
T TIGR01837 82 RVEQALNRLNIPSREEIEALSAKIEQLAVQVEE 114 (118)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 466777888888765568999999999987544
No 29
>PF03938 OmpH: Outer membrane protein (OmpH-like); InterPro: IPR005632 This entry includes outer membrane proteins such as OmpH (Skp) among others. OmpH (outer membrane protein H) is a major structural protein of the outer membrane. In Pasteurella multocida it acts as a channel-forming transmembrane porin []. Porins act as molecular sieves to allow the diffusion of small hydrophilic solutes through the outer membrane and also acts as a receptor for bacteriophages and bacteriocins. Porins are highly immunogenic and are conserved in bacterial families, making them attractive vaccine candidates []. The 17kDa protein (Skp, OmpH) of Escherichia coli is a homotrimeric periplasmic chaperone for newly synthesised outer-membrane proteins, the X-ray structure of which has been reported at resolutions of 2.35 A and 2.30 A [, ]. Three hairpin-shaped alpha-helical extensions reach out by approximately 60 A from a trimerisation domain, which is composed of three intersubunit beta-sheets that wind around a central axis. The alpha-helical extensions approach each other at their distal turns, resulting in a fold that resembles a 'three-pronged grasping forcep'. The overall shape of Skp is reminiscent of the cytosolic chaperone prefoldin (IPR009053 from INTERPRO), although it is based on a radically different topology. The peculiar architecture, with apparent plasticity of the prongs and distinct electrostatic and hydrophobic surface properties, supports the recently proposed biochemical mechanism of this chaperone: formation of a Skp(3)-Omp complex protects the outer membrane protein from aggregation during passage through the bacterial periplasm. The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP. Skp can interact directly with membrane lipids and lipopolysaccharide. These interactions are needed for efficient Skp-assisted folding of membrane proteins [].; GO: 0051082 unfolded protein binding; PDB: 1SG2_C 1U2M_C.
Probab=24.28 E-value=3.2e+02 Score=24.93 Aligned_cols=19 Identities=0% Similarity=0.251 Sum_probs=8.9
Q ss_pred HHHHhhhhhHHHHHhhhhc
Q 010395 87 IAMEKLEDRTEATLNSISR 105 (511)
Q Consensus 87 ~~l~~~~e~~~aa~~s~~~ 105 (511)
..+.++.++-..++..+++
T Consensus 109 ~~~~~i~~~i~~~v~~~a~ 127 (158)
T PF03938_consen 109 ELLQPIQKKINKAVEEYAK 127 (158)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3444444444455555444
No 30
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=24.18 E-value=3.9e+02 Score=26.31 Aligned_cols=55 Identities=15% Similarity=0.237 Sum_probs=40.1
Q ss_pred hhchhHHHHHHhhhhhhhhhccchhHHHhhHHHHH---HHHHHHHHHHHHHHhhhhhh
Q 010395 12 ELNPLSFDEFQRQTSLMTSCTLLWKELSDHFTSLE---QNLQKKSAALRHKIQTLDTQ 66 (511)
Q Consensus 12 e~l~kaF~eLqs~~s~l~s~tl~W~eL~~HF~sLe---~sL~~r~e~L~~k~~~~e~~ 66 (511)
+.|++-..+.++....|.+....-++++.++..|+ ..|..||+.++....++..+
T Consensus 72 ~eL~k~L~~y~kdK~~L~~~k~rl~~~ek~l~~Lk~e~evL~qr~~kle~ErdeL~~k 129 (201)
T PF13851_consen 72 EELRKQLKNYEKDKQSLQNLKARLKELEKELKDLKWEHEVLEQRFEKLEQERDELYRK 129 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677777778888888888888888888888886 46777777777666555433
No 31
>PF10873 DUF2668: Protein of unknown function (DUF2668); InterPro: IPR022640 Members in this family of proteins are annotated as cysteine and tyrosine-rich protein 1, however currently no function is known [].
Probab=23.05 E-value=1.4e+02 Score=28.46 Aligned_cols=41 Identities=41% Similarity=0.841 Sum_probs=20.8
Q ss_pred ccCCCCC-CCccccCCCCCC-CCCCCC-CC-CCCCCcCCCCCCCCCCC
Q 010395 430 YVSSFPA-PPTFVRSPSHTQ-YPAGVT-AY-ASPPAVYGSRSPPYAYS 473 (511)
Q Consensus 430 ~~~s~~~-~~~~~~~~~~~~-~~~~~~-~y-p~~~~~y~~~~~~y~y~ 473 (511)
-++|+|+ ||++.- +|++ |+...| || |. +..|.++++|-.|+
T Consensus 106 ~v~SyP~apPpysy--~~e~~~~~d~PPpYsp~-~~~~~~~spPppYp 150 (155)
T PF10873_consen 106 AVSSYPAAPPPYSY--DHEMEYPPDLPPPYSPT-PQQSAQRSPPPPYP 150 (155)
T ss_pred cccccCCCCCCccc--cccccccCCCCcCCCCc-ccccccCCCccCCC
Confidence 3557773 444332 3332 555554 77 44 34466677644444
No 32
>PF04899 MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids [].
Probab=22.51 E-value=4e+02 Score=22.26 Aligned_cols=36 Identities=17% Similarity=0.264 Sum_probs=23.6
Q ss_pred hhhhhchhHHHHHHhhhhhhhhhccchhHHHhhHHHHHHHHH
Q 010395 9 ELSELNPLSFDEFQRQTSLMTSCTLLWKELSDHFTSLEQNLQ 50 (511)
Q Consensus 9 ~~~e~l~kaF~eLqs~~s~l~s~tl~W~eL~~HF~sLe~sL~ 50 (511)
|+--+|.-||+.||.- ++-+=++.+++|..|++.+.
T Consensus 3 eLE~qLl~ale~Lq~~------y~~q~~~Wq~sy~~Lq~~~~ 38 (70)
T PF04899_consen 3 ELEKQLLSALEELQQS------YEKQQQEWQSSYADLQHMFE 38 (70)
T ss_pred HHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHH
Confidence 4555666777777653 66677777777777766543
No 33
>PF09849 DUF2076: Uncharacterized protein conserved in bacteria (DUF2076); InterPro: IPR018648 This family of hypothetical prokaryotic proteins has no known function but includes putative perimplasmic ligand-binding sensor proteins.
Probab=22.13 E-value=3.9e+02 Score=27.46 Aligned_cols=17 Identities=18% Similarity=0.335 Sum_probs=13.9
Q ss_pred hhHHHHHHHHHHHhhhh
Q 010395 381 PENLKKRLEQLEKAKTE 397 (511)
Q Consensus 381 ~~~L~krI~qLEK~k~e 397 (511)
++.++.||.+||.+-..
T Consensus 57 L~~a~~ri~eLe~ql~q 73 (247)
T PF09849_consen 57 LKQAQARIQELEAQLQQ 73 (247)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 56899999999988644
No 34
>PF11914 DUF3432: Domain of unknown function (DUF3432); InterPro: IPR021839 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 100 amino acids in length. This domain is found associated with PF00096 from PFAM. This domain has two conserved sequence motifs: YPSPV and PSP.
Probab=21.95 E-value=1.4e+02 Score=26.31 Aligned_cols=20 Identities=20% Similarity=0.464 Sum_probs=13.6
Q ss_pred CCCCCCCCCCCCCCCCCCCC
Q 010395 476 AAPPLAGSYPGAPMNYPAYG 495 (511)
Q Consensus 476 ~~~~~~~~y~~~~~~~~~~~ 495 (511)
+-++++-.|++.+-+||.|.
T Consensus 57 PSPsvAtTy~S~~~aF~tqv 76 (99)
T PF11914_consen 57 PSPSVATTYPSVTPAFQTQV 76 (99)
T ss_pred CCcceeeeccCCCccccccc
Confidence 33447777888777777665
No 35
>KOG3088 consensus Secretory carrier membrane protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.82 E-value=49 Score=34.72 Aligned_cols=26 Identities=31% Similarity=0.396 Sum_probs=15.3
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHhhhh
Q 010395 38 LSDHFTSLEQNLQKKSAALRHKIQTLD 64 (511)
Q Consensus 38 L~~HF~sLe~sL~~r~e~L~~k~~~~e 64 (511)
+++| +..-+.++++-.+|+.|+++|+
T Consensus 52 ~~~~-~~~a~~~~~kq~eL~~rqeEL~ 77 (313)
T KOG3088|consen 52 LDSP-STQAKDLAKKQAELLKKQEELR 77 (313)
T ss_pred CCCC-cchhhHHHHHHHHHHHHHHHHH
Confidence 3444 5556666666666666665553
No 36
>PF05130 FlgN: FlgN protein; InterPro: IPR007809 Flagella synthesis protein FlgN is an export chaperone involved in flagellar synthesis []. This entry represents a FlgN-like domain, consisting of a 4 long helices bundle, where the last helix is shorter than the three others.; GO: 0009296 flagellum assembly, 0019861 flagellum; PDB: 2FUP_A 3OPC_A.
Probab=21.30 E-value=5.4e+02 Score=22.23 Aligned_cols=14 Identities=21% Similarity=0.425 Sum_probs=5.8
Q ss_pred HhhhhhHHHHHhhh
Q 010395 90 EKLEDRTEATLNSI 103 (511)
Q Consensus 90 ~~~~e~~~aa~~s~ 103 (511)
..+++++...+..+
T Consensus 54 ~~le~~r~~~~~~~ 67 (143)
T PF05130_consen 54 RELEKQRQQLLAKL 67 (143)
T ss_dssp HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHh
Confidence 33444444444433
No 37
>PF12825 DUF3818: Domain of unknown function in PX-proteins (DUF3818); InterPro: IPR024554 The function of this domain is not known, but it is almost always found C-terminal to a PX-domain (IPR001683 from INTERPRO).
Probab=20.85 E-value=3.3e+02 Score=29.22 Aligned_cols=116 Identities=16% Similarity=0.174 Sum_probs=67.0
Q ss_pred HHhhhcchHHHHHHHHhhhchHHHHHhhHHHHhhcCCChhhHHHHHhhcccCCCCCCCCCCchhh--------HHHHHHH
Q 010395 126 SYCLKMEARGFWKFVVTKKKEIEELRNALPAALSECVDPAKFVMEAISEVFPVDKRSDKSGNDLG--------WACVLVL 197 (511)
Q Consensus 126 ~lCe~MD~~gL~~fi~~~~ke~~~lr~Elp~ALr~ApDPAkLVLdai~~fy~~~~~~~~~~~~~~--------~aCilLL 197 (511)
+|..+|-+-.|-.=+.+-.|+...++..+.. ..-++++|..|.-.+... .+ ..| -.++.+|
T Consensus 95 sLlQrifs~~L~~d~~~~~k~i~~le~~i~~--------~~~~~~~ik~~v~~~~~~-~~--~ir~~s~~~~~~iv~~IL 163 (341)
T PF12825_consen 95 SLLQRIFSMVLNDDIKEFEKEIDKLEKKIGD--------SPEMCEKIKAFVYAPREE-KD--EIREESEEENEDIVVAIL 163 (341)
T ss_pred cHHHHHHHHHHhhhHHHHHHHHHHHHHhhcC--------HHHHHHHHHHHHcCCHHH-HH--HHHHHHHHcCCCchHHHH
Confidence 3444444444444344444555555555532 889999999997533211 11 111 1255555
Q ss_pred HHhccccCCccccccCCCCChhHHHHHHHHHHHHHHHhhhccCCCCCCchhHHHHHHHHHHhcCC
Q 010395 198 ESLIPVMVDPVIGKMRMLVTPSVKEKAKEIAERWKASLEERGGIENVKTPDVHTFLQLLVTFGIV 262 (511)
Q Consensus 198 E~L~~~l~~p~~g~~~p~vs~~vkeeAk~lA~~WK~kl~~~g~~~~~~~lea~gFLqlLa~fGI~ 262 (511)
+.-- ..|.+++...++-...-..|+..........+...-+|+-|.++---+.+-
T Consensus 164 ~~~~----------~~p~L~~~~~~~v~~sy~~~~~~~~~~~~~~~~~~~~a~lf~~lk~yl~l~ 218 (341)
T PF12825_consen 164 RSSD----------IEPKLSPEQLQRVLESYKAWKNAVESVPDDDGEENEDAWLFSDLKEYLKLY 218 (341)
T ss_pred hCCC----------CCCCCCHHHHHHHHHHHHHHHHhhhccccCCCccchhhHHHHHHHHHHHHH
Confidence 5331 236788888889889999999988654222334456788887665544443
No 38
>PF08946 Osmo_CC: Osmosensory transporter coiled coil; InterPro: IPR015041 The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function []. ; PDB: 1R48_B.
Probab=20.68 E-value=1.2e+02 Score=23.46 Aligned_cols=23 Identities=26% Similarity=0.668 Sum_probs=10.2
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHhhhh
Q 010395 38 LSDHFTSLEQNLQKKSAALRHKIQTLD 64 (511)
Q Consensus 38 L~~HF~sLe~sL~~r~e~L~~k~~~~e 64 (511)
|.+|+..+|+.+ +.++.+..+++
T Consensus 10 Lqe~~d~IEqki----edid~qIaeLe 32 (46)
T PF08946_consen 10 LQEHYDNIEQKI----EDIDEQIAELE 32 (46)
T ss_dssp -----THHHHHH----HHHHHHHHHHH
T ss_pred HHHHHHhHHHhH----HHHHHHHHHHH
Confidence 678888888765 34444444444
No 39
>PHA01750 hypothetical protein
Probab=20.17 E-value=2.7e+02 Score=23.36 Aligned_cols=40 Identities=23% Similarity=0.386 Sum_probs=25.6
Q ss_pred HhhHHHHHHHHHHHHHHHHHHhhcCCCCCChhHHHHHHHHHHHhhhhc
Q 010395 351 AAHLAARKEQSALRAVIKCIEDYKLQGEFPPENLKKRLEQLEKAKTEK 398 (511)
Q Consensus 351 a~~eA~~kEl~aLksViKcIEdhkLese~p~~~L~krI~qLEK~k~ek 398 (511)
|..|.-.+||.-|+.-|.-+. .-.|.|+++|.++ |.|-+|
T Consensus 35 AvkeIV~~ELdNL~~ei~~~k-------ikqDnl~~qv~ei-k~k~dk 74 (75)
T PHA01750 35 AVKEIVNSELDNLKTEIEELK-------IKQDELSRQVEEI-KRKLDK 74 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-------HhHHHHHHHHHHH-HHhhcc
Confidence 456778889888887655443 2345677777777 334333
Done!