Query psy16066
Match_columns 182
No_of_seqs 162 out of 221
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 19:57:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16066.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16066hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2758|consensus 100.0 4.3E-63 9.2E-68 442.1 13.4 139 40-178 221-360 (432)
2 KOG2758|consensus 99.9 5.6E-25 1.2E-29 197.6 6.8 90 1-114 236-333 (432)
3 PF01399 PCI: PCI domain; Int 97.1 0.0017 3.7E-08 46.4 6.4 70 108-178 2-71 (105)
4 smart00088 PINT motif in prote 91.5 0.3 6.4E-06 34.6 3.8 34 145-178 2-35 (88)
5 smart00753 PAM PCI/PINT associ 91.5 0.3 6.4E-06 34.6 3.8 34 145-178 2-35 (88)
6 PF10075 PCI_Csn8: COP9 signal 72.1 10 0.00022 29.5 5.2 68 107-178 38-108 (143)
7 KOG0687|consensus 62.6 61 0.0013 30.5 8.9 106 67-178 216-328 (393)
8 PF12783 Sec7_N: Guanine nucle 54.2 90 0.002 24.6 7.7 21 6-26 64-85 (168)
9 KOG1464|consensus 45.9 73 0.0016 29.7 6.6 78 100-178 293-375 (440)
10 PF00502 Phycobilisome: Phycob 44.3 1.1E+02 0.0023 24.7 6.7 23 63-85 74-96 (157)
11 PF08664 YcbB: YcbB domain; I 43.7 63 0.0014 26.1 5.2 48 85-135 70-118 (134)
12 PF10454 DUF2458: Protein of u 37.9 46 0.001 27.1 3.7 43 14-56 6-54 (150)
13 cd05132 RasGAP_GAPA GAPA is an 35.6 1.4E+02 0.0031 26.7 6.8 30 73-102 179-219 (331)
14 cd05131 RasGAP_IQGAP2 IQGAP2 i 33.8 1.2E+02 0.0025 27.6 6.0 43 73-115 180-245 (339)
15 PF04858 TH1: TH1 protein; In 31.6 2.2E+02 0.0048 28.1 7.8 45 3-47 430-475 (584)
16 cd05127 RasGAP_IQGAP_related T 31.3 2.1E+02 0.0046 25.3 7.1 29 73-101 178-217 (325)
17 TIGR00823 EIIA-LAC phosphotran 30.6 43 0.00093 25.4 2.2 21 117-137 28-48 (99)
18 cd00215 PTS_IIA_lac PTS_IIA, P 30.2 44 0.00095 25.3 2.2 20 118-137 27-46 (97)
19 PF06878 Pkip-1: Pkip-1 protei 29.3 77 0.0017 26.5 3.7 49 105-159 60-113 (163)
20 PF02255 PTS_IIA: PTS system, 28.5 48 0.001 24.9 2.2 20 118-137 26-45 (96)
21 KOG2247|consensus 28.1 67 0.0015 31.8 3.6 44 37-87 427-470 (615)
22 cd05128 RasGAP_GAP1_like The G 27.4 4.1E+02 0.009 23.9 8.3 31 73-103 187-228 (315)
23 PF01997 Translin: Translin fa 27.3 2E+02 0.0042 23.8 5.8 58 122-179 37-103 (200)
24 COG3378 Phage associated DNA p 26.8 99 0.0021 30.1 4.5 55 66-121 372-427 (517)
25 PRK09591 celC cellobiose phosp 26.7 57 0.0012 25.0 2.3 20 118-137 32-51 (104)
26 PF03399 SAC3_GANP: SAC3/GANP/ 24.9 1.7E+02 0.0037 23.3 4.9 70 105-178 130-203 (204)
27 PF10779 XhlA: Haemolysin XhlA 24.7 88 0.0019 21.9 2.8 23 8-30 42-64 (71)
28 smart00323 RasGAP GTPase-activ 24.5 2.2E+02 0.0047 25.4 5.9 63 73-136 204-281 (344)
29 PF12070 DUF3550: Protein of u 23.8 1.1E+02 0.0024 29.9 4.2 58 74-141 123-180 (513)
30 COG5173 SEC6 Exocyst complex s 22.9 3.7E+02 0.0081 27.2 7.5 36 142-177 180-215 (742)
31 cd05395 RasGAP_RASA4 Ras GTPas 22.5 5.1E+02 0.011 23.8 8.0 30 73-102 205-245 (337)
32 PF05149 Flagellar_rod: Parafl 22.4 3.6E+02 0.0079 24.4 6.9 65 13-77 61-149 (289)
33 PRK10454 PTS system N,N'-diace 21.7 73 0.0016 25.0 2.1 20 118-137 43-62 (115)
34 PHA02818 hypothetical protein; 21.7 73 0.0016 24.4 2.0 25 47-77 17-41 (92)
35 PF08631 SPO22: Meiosis protei 21.5 3.2E+02 0.0069 23.4 6.2 62 73-135 86-150 (278)
36 PF00514 Arm: Armadillo/beta-c 21.5 1.6E+02 0.0034 17.7 3.2 33 44-79 9-41 (41)
37 PF00619 CARD: Caspase recruit 21.4 2.2E+02 0.0048 19.5 4.4 38 33-77 45-82 (85)
38 cd05392 RasGAP_Neurofibromin_l 21.1 2.7E+02 0.0058 24.6 5.8 69 8-101 135-217 (323)
No 1
>KOG2758|consensus
Probab=100.00 E-value=4.3e-63 Score=442.06 Aligned_cols=139 Identities=70% Similarity=1.118 Sum_probs=136.8
Q ss_pred HHHHHhhhchhHHHHHHhCChhhhHHHHhhchhHHHHHHHHHHhh-hchhHHHHHHHHHHhhccccCCCcHHHHHHHHhh
Q psy16066 40 LVKVIQQVSRDLIIDMFLNRPHYLNAIQTMCPHILRYLATAVIIN-RSKRNALKDLVKVIQQESYTYKDPITEFLEHLYV 118 (182)
Q Consensus 40 lVrvIqqEgrd~i~d~Fl~~~~Yln~IQt~cPhlLRYla~AvI~n-r~rr~~lkdlv~vI~qe~y~Y~DPiTeFl~~L~v 118 (182)
+|.++|++|||.|+|+|+++|.|||||||+|||||||||+||++| |+||+.|||+|+|||||+|+|+||+|||++||||
T Consensus 221 fv~fnhpkgrd~iid~fly~p~YLNaIQt~cPhllRYLatAvvtnk~~rr~~lkdlvkVIqqE~ysYkDPiteFl~clyv 300 (432)
T KOG2758|consen 221 FVFFNHPKGRDTIIDMFLYQPPYLNAIQTSCPHLLRYLATAVVTNKRRRRNRLKDLVKVIQQESYSYKDPITEFLECLYV 300 (432)
T ss_pred HhhccCCChhhHHHHHHccCHHHHHHHHhhCHHHHHHHHHHhhcchHhhHHHHHHHHHHHHHhccccCCcHHHHHHHHhh
Confidence 678999999999999999999999999999999999999999999 7889999999999999999999999999999999
Q ss_pred ccchHHHHHHHHHHHhhhhcccchhhhHHHHHHHHHHHHHHHhhhhcccccHHHHHhHhh
Q psy16066 119 SFDFESAREKLTECTEVLDNDFFLVACLDEFVENARLMIFETFCRIHQCISIQKESNVID 178 (182)
Q Consensus 119 ~fDFe~Aq~~L~~~e~v~~~DfFL~~~~~~f~e~AR~lIfEtYCrIH~~I~I~~la~~L~ 178 (182)
+||||+||++|+|||+|+.|||||+++.|+|+|+||++|||||||||+||+|+|||+||+
T Consensus 301 n~DFdgAq~kl~eCeeVl~nDfFLva~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLn 360 (432)
T KOG2758|consen 301 NYDFDGAQKKLRECEEVLVNDFFLVALLDEFLENARLLIFETFCRIHQCITIDMLADKLN 360 (432)
T ss_pred ccchHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999999999999999997
No 2
>KOG2758|consensus
Probab=99.91 E-value=5.6e-25 Score=197.59 Aligned_cols=90 Identities=52% Similarity=0.839 Sum_probs=79.0
Q ss_pred CCCCChhhHHHHhhhchHHHHHHHHHHHHc-ccchhhhHHHHHHHhhh---chhHHHHHHhCChhhhHHHHhhchhHHHH
Q psy16066 1 MFLNRPHYLNAIQTMCPHILRYLATAVIIN-RSKRNALKDLVKVIQQV---SRDLIIDMFLNRPHYLNAIQTMCPHILRY 76 (182)
Q Consensus 1 ~fl~~~~ylnaiQt~~p~lLRYl~~avi~~-~~r~~~lkdlVrvIqqE---grd~i~d~Fl~~~~Yln~IQt~cPhlLRY 76 (182)
|||++|.|||||||+|||||||||+|||+| +|||+.||||||||||| .+|||+| |+
T Consensus 236 ~fly~p~YLNaIQt~cPhllRYLatAvvtnk~~rr~~lkdlvkVIqqE~ysYkDPite-Fl------------------- 295 (432)
T KOG2758|consen 236 MFLYQPPYLNAIQTSCPHLLRYLATAVVTNKRRRRNRLKDLVKVIQQESYSYKDPITE-FL------------------- 295 (432)
T ss_pred HHccCHHHHHHHHhhCHHHHHHHHHHhhcchHhhHHHHHHHHHHHHHhccccCCcHHH-HH-------------------
Confidence 689999999999999999999999999999 57789999999999999 4889999 88
Q ss_pred HHHHHHhh---hchhHHHHHHHHHHhhccccCCCcH-HHHHH
Q psy16066 77 LATAVIIN---RSKRNALKDLVKVIQQESYTYKDPI-TEFLE 114 (182)
Q Consensus 77 la~AvI~n---r~rr~~lkdlv~vI~qe~y~Y~DPi-TeFl~ 114 (182)
+|+.+| .+.|..|++|..|+.++.|. -|+ .+|+|
T Consensus 296 --~clyvn~DFdgAq~kl~eCeeVl~nDfFL--va~l~~F~E 333 (432)
T KOG2758|consen 296 --ECLYVNYDFDGAQKKLRECEEVLVNDFFL--VALLDEFLE 333 (432)
T ss_pred --HHHhhccchHHHHHHHHHHHHHHhcchhH--HHHHHHHHH
Confidence 799998 58899999999999876554 233 55654
No 3
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=97.14 E-value=0.0017 Score=46.38 Aligned_cols=70 Identities=24% Similarity=0.319 Sum_probs=59.8
Q ss_pred cHHHHHHHHhhccchHHHHHHHHHHHhhhhcccchhhhHHHHHHHHHHHHHHHhhhhcccccHHHHHhHhh
Q psy16066 108 PITEFLEHLYVSFDFESAREKLTECTEVLDNDFFLVACLDEFVENARLMIFETFCRIHQCISIQKESNVID 178 (182)
Q Consensus 108 PiTeFl~~L~v~fDFe~Aq~~L~~~e~v~~~DfFL~~~~~~f~e~AR~lIfEtYCrIH~~I~I~~la~~L~ 178 (182)
|+.++++++ ..-|+.+..+.+.+.++-+..|-++..+.+.+.+..+...+-.+++.+++|+++.+|+.++
T Consensus 2 ~~~~l~~~~-~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~ 71 (105)
T PF01399_consen 2 PYSELLRAF-RSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQ 71 (105)
T ss_dssp HHHHHHHHH-HCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHT
T ss_pred HHHHHHHHH-HhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhc
Confidence 567777655 6778999999999996677778888889999999999999999999999999999999885
No 4
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=91.47 E-value=0.3 Score=34.58 Aligned_cols=34 Identities=12% Similarity=0.201 Sum_probs=31.2
Q ss_pred hHHHHHHHHHHHHHHHhhhhcccccHHHHHhHhh
Q psy16066 145 CLDEFVENARLMIFETFCRIHQCISIQKESNVID 178 (182)
Q Consensus 145 ~~~~f~e~AR~lIfEtYCrIH~~I~I~~la~~L~ 178 (182)
+.+.+.++.|...+..||+.|++|++++||+.++
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~ 35 (88)
T smart00088 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLG 35 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhC
Confidence 4678999999999999999999999999998875
No 5
>smart00753 PAM PCI/PINT associated module.
Probab=91.47 E-value=0.3 Score=34.58 Aligned_cols=34 Identities=12% Similarity=0.201 Sum_probs=31.2
Q ss_pred hHHHHHHHHHHHHHHHhhhhcccccHHHHHhHhh
Q psy16066 145 CLDEFVENARLMIFETFCRIHQCISIQKESNVID 178 (182)
Q Consensus 145 ~~~~f~e~AR~lIfEtYCrIH~~I~I~~la~~L~ 178 (182)
+.+.+.++.|...+..||+.|++|++++||+.++
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~ 35 (88)
T smart00753 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLG 35 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhC
Confidence 4678999999999999999999999999998875
No 6
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=72.06 E-value=10 Score=29.46 Aligned_cols=68 Identities=13% Similarity=0.099 Sum_probs=43.0
Q ss_pred CcHHHHHHH---HhhccchHHHHHHHHHHHhhhhcccchhhhHHHHHHHHHHHHHHHhhhhcccccHHHHHhHhh
Q psy16066 107 DPITEFLEH---LYVSFDFESAREKLTECTEVLDNDFFLVACLDEFVENARLMIFETFCRIHQCISIQKESNVID 178 (182)
Q Consensus 107 DPiTeFl~~---L~v~fDFe~Aq~~L~~~e~v~~~DfFL~~~~~~f~e~AR~lIfEtYCrIH~~I~I~~la~~L~ 178 (182)
||-...+-. ..-.=||.+.-+.++..+- +| .+.+.-..|.++-|..|+..--+-|++|+++.+|+.||
T Consensus 38 ~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~---~~-~~~~~v~~~~~~iR~~i~~~i~~aY~sIs~~~la~~Lg 108 (143)
T PF10075_consen 38 DPEIKAIWSLGQALWEGDYSKFWQALRSNPW---SP-DYKPFVPGFEDTIRERIAHLISKAYSSISLSDLAEMLG 108 (143)
T ss_dssp -TTHHHHHHHHHHHHTT-HHHHHHHS-TT--------HHHHTSTTHHHHHHHHHHHHHHHH-SEE-HHHHHHHTT
T ss_pred hHHHHHHHHHHHHHHCCCHHHHHHHHHhccc---hH-HHHHHHHHHHHHHHHHHHHHHHHHHhHcCHHHHHHHhC
Confidence 455443333 2345588877765554411 12 33455677899999999999999999999999999997
No 7
>KOG0687|consensus
Probab=62.63 E-value=61 Score=30.48 Aligned_cols=106 Identities=13% Similarity=0.312 Sum_probs=73.3
Q ss_pred HhhchhHHHHHHHHHHhh-hch--hHHH---HHHHHHHhhccccCCCcHHHHHHHHhhccchHHHHHHHHHH-Hhhhhcc
Q psy16066 67 QTMCPHILRYLATAVIIN-RSK--RNAL---KDLVKVIQQESYTYKDPITEFLEHLYVSFDFESAREKLTEC-TEVLDND 139 (182)
Q Consensus 67 Qt~cPhlLRYla~AvI~n-r~r--r~~l---kdlv~vI~qe~y~Y~DPiTeFl~~L~v~fDFe~Aq~~L~~~-e~v~~~D 139 (182)
-++=+.+.||-+...++. .|+ +... .++..++.+ --|+.+|+.+||- =|.++==..|... ++.+.-|
T Consensus 216 l~~Y~~~v~Ytv~~g~i~leR~dlktKVi~~~Evl~vl~~-----l~~~~q~l~SLY~-C~Y~~Ff~~L~~~~~~~lk~D 289 (393)
T KOG0687|consen 216 LMSYETFVRYTVITGLIALERVDLKTKVIKCPEVLEVLHK-----LPSVSQLLNSLYE-CDYSDFFNDLAAVEAKQLKDD 289 (393)
T ss_pred cccHHHHHHHHHHHhhheeccchHHhhhcCcHHHHHHhhc-----CchHHHHHHHHHh-ccHHHHHHHHHHHHHHhhccc
Confidence 345678899987666554 222 2222 244444433 2456889988873 3444544556444 6789999
Q ss_pred cchhhhHHHHHHHHHHHHHHHhhhhcccccHHHHHhHhh
Q psy16066 140 FFLVACLDEFVENARLMIFETFCRIHQCISIQKESNVID 178 (182)
Q Consensus 140 fFL~~~~~~f~e~AR~lIfEtYCrIH~~I~I~~la~~L~ 178 (182)
.||+++-+-|+-..|+-.-+...-=++.++++++|+--|
T Consensus 290 ~~l~~h~~yyvREMR~rvY~QlLESYrsl~l~~MA~aFg 328 (393)
T KOG0687|consen 290 RYLGPHYRYYVREMRRRVYAQLLESYRSLTLESMAKAFG 328 (393)
T ss_pred hhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 999999999999999987776666678999999997654
No 8
>PF12783 Sec7_N: Guanine nucleotide exchange factor in Golgi transport N-terminal
Probab=54.18 E-value=90 Score=24.58 Aligned_cols=21 Identities=29% Similarity=0.847 Sum_probs=15.8
Q ss_pred hhhHHHH-hhhchHHHHHHHHH
Q psy16066 6 PHYLNAI-QTMCPHILRYLATA 26 (182)
Q Consensus 6 ~~ylnai-Qt~~p~lLRYl~~a 26 (182)
|..++.+ +.-||+++|.++..
T Consensus 64 ~~l~~~lk~~l~~~Ll~~~~~~ 85 (168)
T PF12783_consen 64 PSLINLLKDDLCPALLKNLSSS 85 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHhhh
Confidence 3788887 66788888888653
No 9
>KOG1464|consensus
Probab=45.94 E-value=73 Score=29.73 Aligned_cols=78 Identities=22% Similarity=0.301 Sum_probs=65.1
Q ss_pred hccccCC-CcH----HHHHHHHhhccchHHHHHHHHHHHhhhhcccchhhhHHHHHHHHHHHHHHHhhhhcccccHHHHH
Q psy16066 100 QESYTYK-DPI----TEFLEHLYVSFDFESAREKLTECTEVLDNDFFLVACLDEFVENARLMIFETFCRIHQCISIQKES 174 (182)
Q Consensus 100 qe~y~Y~-DPi----TeFl~~L~v~fDFe~Aq~~L~~~e~v~~~DfFL~~~~~~f~e~AR~lIfEtYCrIH~~I~I~~la 174 (182)
||.--|+ ||- |..+ +-|-+=|-.+-.+.|+.-.+-+-.|-|+..+.++.+.|-|--+.=.-.|=+..|.|+-+|
T Consensus 293 QEAKPyKNdPEIlAMTnlv-~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis 371 (440)
T KOG1464|consen 293 QEAKPYKNDPEILAMTNLV-AAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFIS 371 (440)
T ss_pred cccCCCCCCHHHHHHHHHH-HHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhH
Confidence 5555564 774 6666 456777877778889988999999999999999999999988888888889999999999
Q ss_pred hHhh
Q psy16066 175 NVID 178 (182)
Q Consensus 175 ~~L~ 178 (182)
++|+
T Consensus 372 ~~Ln 375 (440)
T KOG1464|consen 372 KELN 375 (440)
T ss_pred hhcC
Confidence 9986
No 10
>PF00502 Phycobilisome: Phycobilisome protein; InterPro: IPR012128 Cyanobacteria and red algae harvest light through water-soluble complexes, called phycobilisomes, which are attached to the outer face of the thylakoid membrane []. These complexes are capable of transferring the absorbed energy to the photosynthetic reaction centre with greater than 95% efficiency. Phycobilisomes contain various photosynthetic light harvesting proteins known as biliproteins, and linker proteins which help assemble the structure. The two main structural elements of the complex are a core located near the photosynthetic reaction centre, and rods attached to this core. Allophycocyanin is the major component of the core, while the rods contain phycocyanins, phycoerythrins and linker proteins. The rod biliproteins harvest photons, with the excitation energy being passed through the rods into the allophycocyanin in the core. Other core biliproteins subsequently pass this energy to chlorophyll within the thylakoid membrane. This entry represents the alpha and beta subunits found in biliproteins from cyanobacteria and red algae. Structural studies indicate that the basic structural unit of most biliproteins is a heterodimer composed of these alpha and beta subunits [, , , ]. The full protein is a ring-like trimer assembly of these heterodimers. Each subunit of the heterodimer has eight helices and binds chromophores through thioester bonds formed at particular cysteine residues. These chromophores, also known as bilins, are open-chain tetrapyrroles whose number and type vary with the particular biliprotein eg R-phyocerythrin binds five phycoerythrobilins per heterodimer, while allophycocyanin binds two phycocyanobilins per heterodimer.; GO: 0015979 photosynthesis, 0030089 phycobilisome; PDB: 2VML_I 2VJR_A 1KTP_B 3L0F_B 1JBO_B 3KVS_B 1PHN_B 3BRP_B 2C7K_B 2C7L_B ....
Probab=44.25 E-value=1.1e+02 Score=24.66 Aligned_cols=23 Identities=26% Similarity=0.254 Sum_probs=18.6
Q ss_pred hHHHHhhchhHHHHHHHHHHhhh
Q psy16066 63 LNAIQTMCPHILRYLATAVIINR 85 (182)
Q Consensus 63 ln~IQt~cPhlLRYla~AvI~nr 85 (182)
..+-.--|-|.|||.+-|++.+.
T Consensus 74 ~~~C~RD~~~~LR~i~ya~l~gd 96 (157)
T PF00502_consen 74 REACWRDIWHYLRYITYAMLAGD 96 (157)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHHHHHHHHHHHHhcc
Confidence 35556677899999999999984
No 11
>PF08664 YcbB: YcbB domain; InterPro: IPR013972 YcbB is a DNA-binding protein [].
Probab=43.66 E-value=63 Score=26.06 Aligned_cols=48 Identities=29% Similarity=0.511 Sum_probs=37.9
Q ss_pred hchhHHHHHHHHHHhhccccCCCcH-HHHHHHHhhccchHHHHHHHHHHHhh
Q psy16066 85 RSKRNALKDLVKVIQQESYTYKDPI-TEFLEHLYVSFDFESAREKLTECTEV 135 (182)
Q Consensus 85 r~rr~~lkdlv~vI~qe~y~Y~DPi-TeFl~~L~v~fDFe~Aq~~L~~~e~v 135 (182)
|-||-..+-+.++-.-..-.|.+|. .+|=..| |||++-.+++.+.+.-
T Consensus 70 RIRRai~~al~nlAsLGl~Dy~N~~Fe~YA~~l---FdF~~Vr~eM~~i~~~ 118 (134)
T PF08664_consen 70 RIRRAIKQALTNLASLGLEDYSNPIFEEYASRL---FDFEEVRKEMKEIRGK 118 (134)
T ss_pred HHHHHHHHHHHHHHHhCCcccCChHHHHHHHHc---CCHHHHHHHHHHHHCC
Confidence 3466777777788777888899998 7777766 8999999999887653
No 12
>PF10454 DUF2458: Protein of unknown function (DUF2458); InterPro: IPR018858 This entry represents a family of uncharacterised proteins.
Probab=37.88 E-value=46 Score=27.07 Aligned_cols=43 Identities=26% Similarity=0.347 Sum_probs=27.9
Q ss_pred hhchHHHHHHHHHHHHcccchhhhHHHHHHHhh------hchhHHHHHH
Q psy16066 14 TMCPHILRYLATAVIINRSKRNALKDLVKVIQQ------VSRDLIIDMF 56 (182)
Q Consensus 14 t~~p~lLRYl~~avi~~~~r~~~lkdlVrvIqq------Egrd~i~d~F 56 (182)
|+=|+.|||+...|.-|--....||.|++-=+. +||+.|+.-+
T Consensus 6 t~w~~ALryv~~~v~~n~~~~~~Ir~Li~~Q~~~Er~w~~~Re~l~~k~ 54 (150)
T PF10454_consen 6 TTWPAALRYVMKTVAQNPEFLQRIRRLIKEQHDHERQWWEGREALIAKQ 54 (150)
T ss_pred hcHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 677999999998888775555556666543332 2566666543
No 13
>cd05132 RasGAP_GAPA GAPA is an IQGAP-related protein and is predicted to bind to small GTPases, which are yet to be identified. IQGAP proteins are integral components of cytoskeletal regulation. Results from truncated GAPAs indicated that almost the entire region of GAPA homologous to IQGAP is required for cytokinesis in Dictyostelium. More members of the IQGAP family are emerging, and evidence suggests that there are both similarities and differences in their function.
Probab=35.57 E-value=1.4e+02 Score=26.73 Aligned_cols=30 Identities=23% Similarity=0.496 Sum_probs=20.0
Q ss_pred HHHHHHHHHHhhh-----------chhHHHHHHHHHHhhcc
Q psy16066 73 ILRYLATAVIINR-----------SKRNALKDLVKVIQQES 102 (182)
Q Consensus 73 lLRYla~AvI~nr-----------~rr~~lkdlv~vI~qe~ 102 (182)
.+||++-|++.-. +.++.|..+.|++|+=+
T Consensus 179 flRfi~PAIvsP~~fgl~~~~~~~~~rrnL~lIaKvLQ~la 219 (331)
T cd05132 179 FLRFINPAIVTPQAYMLVDGEPSDTARKNLTLIAKMLQNLA 219 (331)
T ss_pred HHHHhhHHhcCchhcCCcCCCCCHHHHHHHHHHHHHHHHHh
Confidence 4788877765321 34667888888887644
No 14
>cd05131 RasGAP_IQGAP2 IQGAP2 is a member of the IQGAP family that contains a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeat, a single WW domain, four IQ motifs which mediate interactions with calmodulin, and a Ras-GTPase-activating protein (GAP)-related domain that binds Rho family GTPases. IQGAP2 and IQGAP3 play important roles in the regulation of the cytoskeleton for axon outgrowth in hippocampal neurons and are thought to stay in a common regulatory pathway. The results of RNA interference studies indicated that IQGAP3 partially compensates functions of IQGAP2, but has lesser ability than IQGAP2 to promote axon outgrowth in hippocampal neuron. Morevover, IQGAP2 is required for the cadherin-mediated cell-to-cell adhesion in Xenopus laevis embryos.
Probab=33.78 E-value=1.2e+02 Score=27.64 Aligned_cols=43 Identities=21% Similarity=0.512 Sum_probs=26.0
Q ss_pred HHHHHHHHHHh-------h--------hchhHHHHHHHHHHhhcc----cc----CCCcHHHHHHH
Q psy16066 73 ILRYLATAVII-------N--------RSKRNALKDLVKVIQQES----YT----YKDPITEFLEH 115 (182)
Q Consensus 73 lLRYla~AvI~-------n--------r~rr~~lkdlv~vI~qe~----y~----Y~DPiTeFl~~ 115 (182)
.+||++-|++. + .+.|+.|..+.||+|+-. |. |=.|+-+|+..
T Consensus 180 flRfi~PAIvsPe~f~ii~~~~~~~~~~~~rrnL~~iaKvLq~lan~~~F~~~e~~m~pLN~fi~~ 245 (339)
T cd05131 180 YYRYMNPAIVAPDGFDIIDMTAGGQIHSDQRRNLGSVAKVLQHAASNKLFEGENDHLSSMNSYLSQ 245 (339)
T ss_pred HHHHccchhcCchhcCccccccCCCCCHHHHhhHHHHHHHHHHHHCCCCCCCcChHHHhHHHHHHH
Confidence 36888777661 1 122678888899988654 21 34555555544
No 15
>PF04858 TH1: TH1 protein; InterPro: IPR006942 TH1 is a highly conserved but uncharacterised metazoan protein. No homologue has been identified in Caenorhabditis elegans []. TH1 binds specifically to A-Raf kinase [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=31.61 E-value=2.2e+02 Score=28.13 Aligned_cols=45 Identities=22% Similarity=0.390 Sum_probs=28.0
Q ss_pred CCChhhHHHHhhhchHHHHHHHHHHHHccc-chhhhHHHHHHHhhh
Q psy16066 3 LNRPHYLNAIQTMCPHILRYLATAVIINRS-KRNALKDLVKVIQQV 47 (182)
Q Consensus 3 l~~~~ylnaiQt~~p~lLRYl~~avi~~~~-r~~~lkdlVrvIqqE 47 (182)
|.+|.|.+.+...+|..|--|--.+.-+.. |-.++.=|++....+
T Consensus 430 l~~~~~~~~~~~~~p~~L~LLdeIa~~Hp~lr~~vl~lL~~~le~~ 475 (584)
T PF04858_consen 430 LTDPSYFSSITELTPVHLALLDEIATRHPLLRPSVLDLLVRLLESE 475 (584)
T ss_pred hcCcchhhhccccCchHHHHhhHHHhcCHhhHHHHHHHHHHHHHcc
Confidence 568889999998899988877444433322 334444444444433
No 16
>cd05127 RasGAP_IQGAP_related This family represents IQ motif containing GTPase activating protein (IQGAP) which associated with the Ras GTP-binding protein. A primary function of IQGAP proteins is to modulate cytoskeletal architecture. There are three known IQGAP family members: IQGAP1, IQGAP2 and IQGAP3. Human IQGAP1 and IQGAP2 share 62% indentity. IQGAPs are multi-domain molecules having a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeats, a single WW domain, four IQ motifs that mediate interactions with calmodulin, and a RasGAP related domain that binds active Rho family GTPases. IQGAP is an essential regulator of cytoskeletal function. IQGAP1 negatively regulates Ras family GTPases by stimulating their intrinsic GTPase activity, the protein actually lacks GAP activity. Both IQGAP1 and IQGAP2 specifically bind to Cdc42 and Rac1, but not to RhoA. Despite of their similarities to part of the sequence of RasGAP, neither IQGAP1 nor IQGAP2 interacts with Ras. IQGA
Probab=31.34 E-value=2.1e+02 Score=25.26 Aligned_cols=29 Identities=28% Similarity=0.541 Sum_probs=20.0
Q ss_pred HHHHHHHHHHhhh-----------chhHHHHHHHHHHhhc
Q psy16066 73 ILRYLATAVIINR-----------SKRNALKDLVKVIQQE 101 (182)
Q Consensus 73 lLRYla~AvI~nr-----------~rr~~lkdlv~vI~qe 101 (182)
.+||++-|++.-. ..++.|-.+.+|+|+=
T Consensus 178 flRfi~PAIvsP~~~gl~~~~~~~~~rrnL~~iaKvLq~l 217 (325)
T cd05127 178 YYRFINPAIVSPENFGIVDGSPTPDQRRNLGEVAKVLQQA 217 (325)
T ss_pred HHHHHHHHhCCchhcCCcCCCCCHHHHhhHHHHHHHHHHH
Confidence 4788877765421 2467888888888764
No 17
>TIGR00823 EIIA-LAC phosphotransferase system enzyme II, lactose-specific, factor III. operon. While the Lac permeases consist of two polypeptide chains (IIA and IICB), the Chb permease of E. coli consists of three (IIA, IIB and IIC). In B. subtilis, a PTS permease similar to the Chb permease of E. coli is believed to transport lichenan (a b-1,3;1,4 glucan) degradation products, oligosaccharides of 2-4 glucose units. This model is specific for the IIA subunit of the Lac PTS family.
Probab=30.55 E-value=43 Score=25.42 Aligned_cols=21 Identities=24% Similarity=0.253 Sum_probs=17.3
Q ss_pred hhccchHHHHHHHHHHHhhhh
Q psy16066 117 YVSFDFESAREKLTECTEVLD 137 (182)
Q Consensus 117 ~v~fDFe~Aq~~L~~~e~v~~ 137 (182)
.-+.||++|+++|+++++.+.
T Consensus 28 a~~gdfe~A~~~l~eA~~~l~ 48 (99)
T TIGR00823 28 AKAGDFAKARALVEQAGMCLN 48 (99)
T ss_pred HHcCCHHHHHHHHHHHHHHHH
Confidence 357899999999999987554
No 18
>cd00215 PTS_IIA_lac PTS_IIA, PTS system, lactose/cellobiose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. This family of proteins normally function as a homotrimer, stabilized by a centrally located metal ion. Separation into subunits is thought to occur after phosphorylation.
Probab=30.17 E-value=44 Score=25.27 Aligned_cols=20 Identities=35% Similarity=0.433 Sum_probs=16.8
Q ss_pred hccchHHHHHHHHHHHhhhh
Q psy16066 118 VSFDFESAREKLTECTEVLD 137 (182)
Q Consensus 118 v~fDFe~Aq~~L~~~e~v~~ 137 (182)
-+-||++|+++|+++++.+.
T Consensus 27 ~~g~fe~A~~~l~ea~~~l~ 46 (97)
T cd00215 27 KEGDFAEAEELLEEANDSLN 46 (97)
T ss_pred HcCCHHHHHHHHHHHHHHHH
Confidence 56799999999999987543
No 19
>PF06878 Pkip-1: Pkip-1 protein; InterPro: IPR009672 This family consists of several Pkip-1 proteins, which seem to be specific to Nucleopolyhedroviruses. The function of this family is unknown although it has been found that Pkip-1 is not essential for virus replication in cell culture or by in vivo intrahaemocoelic injection [].
Probab=29.34 E-value=77 Score=26.47 Aligned_cols=49 Identities=22% Similarity=0.411 Sum_probs=31.6
Q ss_pred CCCcH-HHHHHHHhhccchHHHHHHHHHHHhhhh---cc-cchhhhHHHHHHHHHHHHHH
Q psy16066 105 YKDPI-TEFLEHLYVSFDFESAREKLTECTEVLD---ND-FFLVACLDEFVENARLMIFE 159 (182)
Q Consensus 105 Y~DPi-TeFl~~L~v~fDFe~Aq~~L~~~e~v~~---~D-fFL~~~~~~f~e~AR~lIfE 159 (182)
.+|+- ++|+..| -++||+.+ +.|+++. +| ||+......=.-.+-.-+|+
T Consensus 60 ~~~~~k~dFindl-~eLd~~~~-----~ie~l~~~~~~~~~l~~ky~~~~~~~~~~~~~~ 113 (163)
T PF06878_consen 60 ATDEEKLDFINDL-SELDFDNE-----EIESLCARKDNDEYLLKKYNADRLPEAIQKVFD 113 (163)
T ss_pred cchHHHHHHHhhh-hhcCCCHH-----HHHHHHhcccHHHHHHHhcchhhhHHHHHHHHH
Confidence 44665 9999999 99999985 5677776 33 78765433223333444444
No 20
>PF02255 PTS_IIA: PTS system, Lactose/Cellobiose specific IIA subunit; InterPro: IPR003188 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIA PTS system enzymes. This family of proteins normally function as a homotrimer, stabilised by a centrally located metal ion []. Separation into subunits is thought to occur after phosphorylation.; GO: 0005351 sugar:hydrogen symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane; PDB: 3L8R_D 2E2A_B 1E2A_C 3K1S_C 2LRK_C 2LRL_A 2WY2_A 1WCR_A 2WWV_C.
Probab=28.52 E-value=48 Score=24.87 Aligned_cols=20 Identities=45% Similarity=0.380 Sum_probs=15.8
Q ss_pred hccchHHHHHHHHHHHhhhh
Q psy16066 118 VSFDFESAREKLTECTEVLD 137 (182)
Q Consensus 118 v~fDFe~Aq~~L~~~e~v~~ 137 (182)
-+.||++|.++|+++++.+.
T Consensus 26 ~~~~fe~A~~~l~~a~~~l~ 45 (96)
T PF02255_consen 26 REGDFEEAEELLKEADEELL 45 (96)
T ss_dssp HTT-HHHHHHHHHHHHHHHH
T ss_pred HhCCHHHHHHHHHHHHHHHH
Confidence 56799999999999987654
No 21
>KOG2247|consensus
Probab=28.14 E-value=67 Score=31.76 Aligned_cols=44 Identities=25% Similarity=0.332 Sum_probs=35.8
Q ss_pred hHHHHHHHhhhchhHHHHHHhCChhhhHHHHhhchhHHHHHHHHHHhhhch
Q psy16066 37 LKDLVKVIQQVSRDLIIDMFLNRPHYLNAIQTMCPHILRYLATAVIINRSK 87 (182)
Q Consensus 37 lkdlVrvIqqEgrd~i~d~Fl~~~~Yln~IQt~cPhlLRYla~AvI~nr~r 87 (182)
=+|+....||+.|+.+.+ =.|+.+++.+|=| ||++|+...+|.+
T Consensus 427 nRdlfY~mhQ~areK~~r-----veylmtv~~I~LH--syyaa~~f~~r~~ 470 (615)
T KOG2247|consen 427 NRDLFYDMHQSAREKINR-----VEYLMTVTNIQLH--SYYAAVNFGSRLR 470 (615)
T ss_pred hHHHHHHHHHHHHHHhhc-----cchhhhhhHHHHH--HHHHHHHHHhHHH
Confidence 478888889999998655 3589999999977 7998888888754
No 22
>cd05128 RasGAP_GAP1_like The GAP1 family of Ras GTPase-activating proteins includes GAP1(m) (or RASA2), GAP1_IP4BP (or RASA3), Ca2+ -promoted Ras inactivator (CAPRI, or RASAL4), and Ras GTPase activating-like proteins (RASAL) or RASAL1. The members are characterized by a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin homology domain that is associated with a Bruton's tyrosine kinase motif. While this domain structure is conserved, a small change in the function of each individual domain and the interaction between domains has a marked effect on the regulation of each protein.
Probab=27.42 E-value=4.1e+02 Score=23.94 Aligned_cols=31 Identities=26% Similarity=0.371 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhhh-----------chhHHHHHHHHHHhhccc
Q psy16066 73 ILRYLATAVIINR-----------SKRNALKDLVKVIQQESY 103 (182)
Q Consensus 73 lLRYla~AvI~nr-----------~rr~~lkdlv~vI~qe~y 103 (182)
.|||++-|++.-+ +.++.|--+.+++|+=..
T Consensus 187 FLRfi~PAIvsP~~f~l~~~~p~~~~rR~L~lIaKvLQnlaN 228 (315)
T cd05128 187 FLRFFAPAILSPKLFHLRPHHADARTSRTLLLLSKAVQTLGN 228 (315)
T ss_pred HHHHHhHHhcChHhcCCCCCCCCHHHHHHHHHHHHHHHHHhC
Confidence 5899987776432 235678888888877654
No 23
>PF01997 Translin: Translin family; InterPro: IPR002848 Translins are DNA-binding proteins that specifically recognise consensus sequences at the breakpoint junctions in chromosomal translocations, mostly involving immunoglobulin (Ig)/T-cell receptor gene segments. They seem to recognise single-stranded DNA ends generated by staggered breaks occuring at recombination hot spots []. Translin folds into an alpha-alpha superhelix, consisting of two curved layers of alpha/alpha topology [, ].; GO: 0043565 sequence-specific DNA binding; PDB: 3QB5_K 3PJA_L 1J1J_D 3RIU_C 3AXJ_B 4DG7_C 2QVA_C 2QRX_A 1KEY_C.
Probab=27.26 E-value=2e+02 Score=23.85 Aligned_cols=58 Identities=19% Similarity=0.291 Sum_probs=39.2
Q ss_pred hHHHHHHHHHHHhhhh-------cccc--hhhhHHHHHHHHHHHHHHHhhhhcccccHHHHHhHhhh
Q psy16066 122 FESAREKLTECTEVLD-------NDFF--LVACLDEFVENARLMIFETFCRIHQCISIQKESNVIDK 179 (182)
Q Consensus 122 Fe~Aq~~L~~~e~v~~-------~DfF--L~~~~~~f~e~AR~lIfEtYCrIH~~I~I~~la~~L~~ 179 (182)
+++|++.+.++.+.+. .||+ -......+.|-+....|-.|..--.-++.+++++.|+-
T Consensus 37 l~~a~~~l~~l~~~~~~l~~~~~~~~~~y~~~~s~~lQE~vEa~~f~~~l~~~~L~t~~ev~~~l~~ 103 (200)
T PF01997_consen 37 LEEAEEKLKELKKLLKQLAELPGHPFYRYHGAYSPGLQEYVEAISFYHYLETGRLLTPEEVGEILGF 103 (200)
T ss_dssp HHHHHHHHHHHHCHSHHHHHCTTCGHHHHGGGTHHHHHHHHHHHHHHHHHHHSSS--HHHHHHHCTC
T ss_pred HHHHHHHHHHHHHHHhhhcccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhh
Confidence 3566666666666665 3443 23446666666777889999999999999999987764
No 24
>COG3378 Phage associated DNA primase [General function prediction only]
Probab=26.78 E-value=99 Score=30.05 Aligned_cols=55 Identities=20% Similarity=0.257 Sum_probs=39.2
Q ss_pred HHhhchhHHHHHHHHHH-hhhchhHHHHHHHHHHhhccccCCCcHHHHHHHHhhccc
Q psy16066 66 IQTMCPHILRYLATAVI-INRSKRNALKDLVKVIQQESYTYKDPITEFLEHLYVSFD 121 (182)
Q Consensus 66 IQt~cPhlLRYla~AvI-~nr~rr~~lkdlv~vI~qe~y~Y~DPiTeFl~~L~v~fD 121 (182)
+...-|-+|+|+.+... +++-+. ..-..+.-...|...+.||++.|+...++.+.
T Consensus 372 l~~E~~~IL~~~v~g~~~~~~~g~-~~pq~~~~~~ee~k~~~D~v~~F~~d~~~~~~ 427 (517)
T COG3378 372 LAAERPGILNWLVAGFLDLQREGL-DQPQAVLDALEEYKRENDPVFQFCDDECVLGE 427 (517)
T ss_pred HHHhhHHHHHHHHHHHHHHHhcCC-CchhhHHHHHHHHHHhccHHHHHHHHHhhccc
Confidence 34557899999977666 444333 45555666666667888999999998887764
No 25
>PRK09591 celC cellobiose phosphotransferase system IIA component; Reviewed
Probab=26.72 E-value=57 Score=25.01 Aligned_cols=20 Identities=30% Similarity=0.318 Sum_probs=16.7
Q ss_pred hccchHHHHHHHHHHHhhhh
Q psy16066 118 VSFDFESAREKLTECTEVLD 137 (182)
Q Consensus 118 v~fDFe~Aq~~L~~~e~v~~ 137 (182)
-+-||++|.++|+++++.+.
T Consensus 32 k~gdf~~A~~~l~eA~~~l~ 51 (104)
T PRK09591 32 REGNFDLAEQKLNQSNEELL 51 (104)
T ss_pred HcCCHHHHHHHHHHHHHHHH
Confidence 56799999999999987543
No 26
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=24.94 E-value=1.7e+02 Score=23.28 Aligned_cols=70 Identities=10% Similarity=0.246 Sum_probs=44.5
Q ss_pred CCCcHHHHHHHH---hhccchHHHHHHHHHHHhhhhcccchhhhHHHHHHHHHHHHHHHhhhhccc-ccHHHHHhHhh
Q psy16066 105 YKDPITEFLEHL---YVSFDFESAREKLTECTEVLDNDFFLVACLDEFVENARLMIFETFCRIHQC-ISIQKESNVID 178 (182)
Q Consensus 105 Y~DPiTeFl~~L---~v~fDFe~Aq~~L~~~e~v~~~DfFL~~~~~~f~e~AR~lIfEtYCrIH~~-I~I~~la~~L~ 178 (182)
-++|...|.-.+ +-+-+|-.--+.+ ++ -+.++......+-|++..|.-...+.++-+.+ |+++.|++-|+
T Consensus 130 ~~~~~i~~al~l~~a~~~gny~~ff~l~---~~-~~~~~l~~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~ 203 (204)
T PF03399_consen 130 LSSPYIQFALELCRALMEGNYVRFFRLY---RS-KSAPYLFACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLG 203 (204)
T ss_dssp HTSHHHHHHHHHHHHH--TTHHHHHHHH---T--TTS-HHHHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT
T ss_pred hcCHHHHHHHHHHHHHHcCCHHHHHHHH---hc-cCCChHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcC
Confidence 446776665433 3344444433333 11 13344444446669999999999999999999 99999999875
No 27
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [].
Probab=24.70 E-value=88 Score=21.92 Aligned_cols=23 Identities=26% Similarity=0.310 Sum_probs=19.9
Q ss_pred hHHHHhhhchHHHHHHHHHHHHc
Q psy16066 8 YLNAIQTMCPHILRYLATAVIIN 30 (182)
Q Consensus 8 ylnaiQt~~p~lLRYl~~avi~~ 30 (182)
-|+.|..+--|++|..+.|+|+.
T Consensus 42 ~l~~I~~n~kW~~r~iiGaiI~~ 64 (71)
T PF10779_consen 42 QLEKIKSNTKWIWRTIIGAIITA 64 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 47789999999999999998863
No 28
>smart00323 RasGAP GTPase-activator protein for Ras-like GTPases. All alpha-helical domain that accelerates the GTPase activity of Ras, thereby "switching" it into an "off" position. Improved domain limits from structure.
Probab=24.55 E-value=2.2e+02 Score=25.36 Aligned_cols=63 Identities=24% Similarity=0.340 Sum_probs=36.9
Q ss_pred HHHHHHHHHHhh-----------hchhHHHHHHHHHHhhccc----cCCCcHHHHHHHHhhccchHHHHHHHHHHHhhh
Q psy16066 73 ILRYLATAVIIN-----------RSKRNALKDLVKVIQQESY----TYKDPITEFLEHLYVSFDFESAREKLTECTEVL 136 (182)
Q Consensus 73 lLRYla~AvI~n-----------r~rr~~lkdlv~vI~qe~y----~Y~DPiTeFl~~L~v~fDFe~Aq~~L~~~e~v~ 136 (182)
.|||++-|++-- .+.++.|..+.+++|+=.. .-+.|.-+.+ +=|++=.++.-++-|.++.++-
T Consensus 204 FLRfi~PAIvsP~~~~l~~~~~~~~~rr~L~liaKvLQ~lan~~~f~~ke~~m~~l-n~fi~~~~~~~~~fl~~i~~~~ 281 (344)
T smart00323 204 FLRFFCPAIVSPKLFNLVDEHPDPTTRRTLTLIAKVLQNLANLSEFGSKEPWMEPL-NDFLLSHKDRVKDFLDELSSVP 281 (344)
T ss_pred HHHHhhhHhCChHhhCCCCCCCChhhhhhHHHHHHHHHHHhCCCCCCCcchHHHHH-HHHHHHHHHHHHHHHHHHcCCC
Confidence 489986666542 1346788888888876543 2234443333 2334445666666676666654
No 29
>PF12070 DUF3550: Protein of unknown function (DUF3550/UPF0682); InterPro: IPR022709 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 249 to 606 amino acids in length.
Probab=23.80 E-value=1.1e+02 Score=29.86 Aligned_cols=58 Identities=24% Similarity=0.339 Sum_probs=40.0
Q ss_pred HHHHHHHHHhhhchhHHHHHHHHHHhhccccCCCcHHHHHHHHhhccchHHHHHHHHHHHhhhhcccc
Q psy16066 74 LRYLATAVIINRSKRNALKDLVKVIQQESYTYKDPITEFLEHLYVSFDFESAREKLTECTEVLDNDFF 141 (182)
Q Consensus 74 LRYla~AvI~nr~rr~~lkdlv~vI~qe~y~Y~DPiTeFl~~L~v~fDFe~Aq~~L~~~e~v~~~DfF 141 (182)
=|+++||+++||+ ++.+++++-+....-+|+ .-|-.=|+.+-+-.+.|+..-++.|=.
T Consensus 123 ARFivVcLlLnr~--~~V~~Lv~el~~~v~dy~--------~~~~~~d~~EW~lVlqEI~~Fl~Ad~~ 180 (513)
T PF12070_consen 123 ARFIVVCLLLNRM--EMVKDLVRELSKLVDDYT--------STYQESDQKEWSLVLQEIKRFLKADSA 180 (513)
T ss_pred HHHHHHHHHhhhH--HHHHHHHHHHHHHHHHHH--------hcCCCcCcccHHHHHHHHHHHHhCccc
Confidence 3667788888764 677777766644333332 234445888999999999998888864
No 30
>COG5173 SEC6 Exocyst complex subunit SEC6 [Intracellular trafficking and secretion]
Probab=22.92 E-value=3.7e+02 Score=27.22 Aligned_cols=36 Identities=14% Similarity=0.287 Sum_probs=28.6
Q ss_pred hhhhHHHHHHHHHHHHHHHhhhhcccccHHHHHhHh
Q psy16066 142 LVACLDEFVENARLMIFETFCRIHQCISIQKESNVI 177 (182)
Q Consensus 142 L~~~~~~f~e~AR~lIfEtYCrIH~~I~I~~la~~L 177 (182)
+-+...+|+|++|-==.|+--||++.++...-++.+
T Consensus 180 vl~~~~~iie~vksghi~~~~~ifkIve~EE~~De~ 215 (742)
T COG5173 180 VLEISEEIIENVKSGHIEAMDKIFKIVEKEEARDEL 215 (742)
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhhhHHH
Confidence 345678899999999899999999988877655443
No 31
>cd05395 RasGAP_RASA4 Ras GTPase activating-like 4 protein (RASAL4), also known as Ca2+ -promoted Ras inactivator (CAPRI), is a member of the GAP1 family. Members of the GAP1 family are characterized by a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin-homology domain that is associated with a Bruton's tyrosine kinase motif. RASAL4, like RASAL, is a cytosolic protein that undergoes a rapid translocation to the plasma membrane in response to a receptor-mediated elevation in the concentration of intracellular free Ca2+ ([Ca2+]i). However, unlike RASAL, RASAL4 does not sense oscillations in [Ca2+]i.
Probab=22.47 E-value=5.1e+02 Score=23.76 Aligned_cols=30 Identities=23% Similarity=0.380 Sum_probs=20.3
Q ss_pred HHHHHHHHHHhhh-----------chhHHHHHHHHHHhhcc
Q psy16066 73 ILRYLATAVIINR-----------SKRNALKDLVKVIQQES 102 (182)
Q Consensus 73 lLRYla~AvI~nr-----------~rr~~lkdlv~vI~qe~ 102 (182)
.|||++-|++.-+ +.++.|--+.|+||+=.
T Consensus 205 FLRFicPAIvSP~~f~L~~~~p~~~~rR~LtLIAKvLQnLA 245 (337)
T cd05395 205 CLRFFSPAIMSPKLFHLREKHADARTSRTLLLLAKAVQTVG 245 (337)
T ss_pred HHHHhccccCCchhcCccCCCCCHHHHhHHHHHHHHHHHHh
Confidence 4899977766432 23567888888887544
No 32
>PF05149 Flagellar_rod: Paraflagellar rod protein; InterPro: IPR007824 This family consists of several eukaryotic paraflagellar rod component proteins. The eukaryotic flagellum represents one of the most complex macromolecular structures found in any organism and contains more than 250 proteins []. In addition to its locomotive role, the flagellum is probably involved in nutrient uptake since receptors for host low-density lipoproteins are localised on the flagellar membrane as well as on the flagellar pocket membrane [].; GO: 0005516 calmodulin binding, 0009434 microtubule-based flagellum
Probab=22.43 E-value=3.6e+02 Score=24.42 Aligned_cols=65 Identities=15% Similarity=0.233 Sum_probs=40.1
Q ss_pred hhhchHHHHHHHHHHH-HcccchhhhHHHHHHHhhh-chhHHHHHHhC----------------------ChhhhHHHHh
Q psy16066 13 QTMCPHILRYLATAVI-INRSKRNALKDLVKVIQQV-SRDLIIDMFLN----------------------RPHYLNAIQT 68 (182)
Q Consensus 13 Qt~~p~lLRYl~~avi-~~~~r~~~lkdlVrvIqqE-grd~i~d~Fl~----------------------~~~Yln~IQt 68 (182)
|..|+.-+--|..-+. +...|+...++=++...++ +|..--+-|+. .+.|-+.|+.
T Consensus 61 q~~lw~~i~el~~~L~~l~~er~~~v~~ri~~~eqE~~R~~~~~~Fl~~~~qh~q~L~~~~~n~~~~~~~~~~~~~~V~~ 140 (289)
T PF05149_consen 61 QQELWREIQELERELQDLAEERREEVERRIEMREQEAKRRTAAEEFLQAASQHKQRLRRCEENCDRALSCAESLEEYVQE 140 (289)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5556655555544333 2345667777777777765 44444444441 3457888999
Q ss_pred hchhHHHHH
Q psy16066 69 MCPHILRYL 77 (182)
Q Consensus 69 ~cPhlLRYl 77 (182)
+||+|+.++
T Consensus 141 ~~~~l~~~~ 149 (289)
T PF05149_consen 141 GCPKLPKKH 149 (289)
T ss_pred HHHHHHHHH
Confidence 999999664
No 33
>PRK10454 PTS system N,N'-diacetylchitobiose-specific transporter subunit IIA; Provisional
Probab=21.75 E-value=73 Score=24.96 Aligned_cols=20 Identities=20% Similarity=0.310 Sum_probs=16.4
Q ss_pred hccchHHHHHHHHHHHhhhh
Q psy16066 118 VSFDFESAREKLTECTEVLD 137 (182)
Q Consensus 118 v~fDFe~Aq~~L~~~e~v~~ 137 (182)
-+-||++|+++|+++++.+.
T Consensus 43 k~gdfe~A~~~l~eA~e~l~ 62 (115)
T PRK10454 43 KQGDFAAAKAMMDQSRMALN 62 (115)
T ss_pred HhCCHHHHHHHHHHHHHHHH
Confidence 46799999999999987543
No 34
>PHA02818 hypothetical protein; Provisional
Probab=21.72 E-value=73 Score=24.41 Aligned_cols=25 Identities=16% Similarity=0.269 Sum_probs=19.8
Q ss_pred hchhHHHHHHhCChhhhHHHHhhchhHHHHH
Q psy16066 47 VSRDLIIDMFLNRPHYLNAIQTMCPHILRYL 77 (182)
Q Consensus 47 Egrd~i~d~Fl~~~~Yln~IQt~cPhlLRYl 77 (182)
.+-+.++| +. ++-|.-.|||++|=.
T Consensus 17 ~~NEKflD-cI-----I~eie~~~~~i~RP~ 41 (92)
T PHA02818 17 KYNEKFIE-CI-----IQEIEKQQYFILKPI 41 (92)
T ss_pred hhhhHHHH-HH-----HHHHHccCchhHhHH
Confidence 36788888 66 678899999987753
No 35
>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []. It is also involved in sporulation [].
Probab=21.50 E-value=3.2e+02 Score=23.41 Aligned_cols=62 Identities=27% Similarity=0.296 Sum_probs=36.0
Q ss_pred HHHHHHHHHHhhhchhHHHHHHHHHHhhccccCCCcHHHH---HHHHhhccchHHHHHHHHHHHhh
Q psy16066 73 ILRYLATAVIINRSKRNALKDLVKVIQQESYTYKDPITEF---LEHLYVSFDFESAREKLTECTEV 135 (182)
Q Consensus 73 lLRYla~AvI~nr~rr~~lkdlv~vI~qe~y~Y~DPiTeF---l~~L~v~fDFe~Aq~~L~~~e~v 135 (182)
+||+|+.|.+-..... -...+.++++.-.-+|.+|..=| ++-+-..+|-+++.+.|.+.-.-
T Consensus 86 iL~~La~~~l~~~~~~-~~~ka~~~l~~l~~e~~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~ 150 (278)
T PF08631_consen 86 ILRLLANAYLEWDTYE-SVEKALNALRLLESEYGNKPEVFLLKLEILLKSFDEEEYEEILMRMIRS 150 (278)
T ss_pred HHHHHHHHHHcCCChH-HHHHHHHHHHHHHHhCCCCcHHHHHHHHHHhccCChhHHHHHHHHHHHh
Confidence 6888877776543332 22224444433334455655333 45555578899988888776554
No 36
>PF00514 Arm: Armadillo/beta-catenin-like repeat; InterPro: IPR000225 The armadillo (Arm) repeat is an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila melanogaster segment polarity gene armadillo involved in signal transduction through wingless. Animal Arm-repeat proteins function in various processes, including intracellular signalling and cytoskeletal regulation, and include such proteins as beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumour suppressor protein, and the nuclear transport factor importin-alpha, amongst others []. A subset of these proteins is conserved across eukaryotic kingdoms. In higher plants, some Arm-repeat proteins function in intracellular signalling like their mammalian counterparts, while others have novel functions []. The 3-dimensional fold of an armadillo repeat is known from the crystal structure of beta-catenin, where the 12 repeats form a superhelix of alpha helices with three helices per unit []. The cylindrical structure features a positively charged grove, which presumably interacts with the acidic surfaces of the known interaction partners of beta-catenin.; GO: 0005515 protein binding; PDB: 2Z6G_A 1IQ1_C 3RZX_A 2C1M_A 3BTR_C 3OQS_A 3TPO_A 1IAL_A 1Q1S_C 1PJM_B ....
Probab=21.46 E-value=1.6e+02 Score=17.74 Aligned_cols=33 Identities=15% Similarity=0.246 Sum_probs=23.9
Q ss_pred HhhhchhHHHHHHhCChhhhHHHHhhchhHHHHHHH
Q psy16066 44 IQQVSRDLIIDMFLNRPHYLNAIQTMCPHILRYLAT 79 (182)
Q Consensus 44 IqqEgrd~i~d~Fl~~~~Yln~IQt~cPhlLRYla~ 79 (182)
++..+-.+++++.- ++. ..+|..|=|-|+++++
T Consensus 9 ~~~g~i~~Lv~ll~-~~~--~~v~~~a~~al~nl~~ 41 (41)
T PF00514_consen 9 VEAGGIPPLVQLLK-SPD--PEVQEEAAWALGNLAA 41 (41)
T ss_dssp HHTTHHHHHHHHTT-SSS--HHHHHHHHHHHHHHHT
T ss_pred HHcccHHHHHHHHc-CCC--HHHHHHHHHHHHHHhC
Confidence 45567788888544 444 5788899999998863
No 37
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=21.35 E-value=2.2e+02 Score=19.48 Aligned_cols=38 Identities=16% Similarity=0.354 Sum_probs=27.3
Q ss_pred chhhhHHHHHHHhhhchhHHHHHHhCChhhhHHHHhhchhHHHHH
Q psy16066 33 KRNALKDLVKVIQQVSRDLIIDMFLNRPHYLNAIQTMCPHILRYL 77 (182)
Q Consensus 33 r~~~lkdlVrvIqqEgrd~i~d~Fl~~~~Yln~IQt~cPhlLRYl 77 (182)
+++..+.|+.++...|..+.-. | +++++..+||+-..|
T Consensus 45 ~~~k~~~LLd~l~~kg~~a~~~-F------~~~L~~~~~~La~~L 82 (85)
T PF00619_consen 45 RQDKARKLLDILKRKGPEAFDI-F------CQALRENQPHLADDL 82 (85)
T ss_dssp HHHHHHHHHHHHHHCCHHHHHH-H------HHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHCHHHHHH-H------HHHHHhhCHHHHHHH
Confidence 4566778888888777665433 4 478888999998765
No 38
>cd05392 RasGAP_Neurofibromin_like Neurofibromin-like proteins include the Saccharomyces cerevisiae RasGAP proteins Ira1 and Ira2, the closest homolog of neurofibromin, which is responsible for the human autosomal dominant disease neurofibromatosis type I (NF1). The RasGAP Ira1/2 proteins are negative regulators of the Ras-cAMP signaling pathway and conserved from yeast to human. In yeast Ras proteins are activated by GEFs, and inhibited by two GAPs, Ira1 and Ira2. Ras proteins activate the cAMP/protein kinase A (PKA) pathway, which controls metabolism, stress resistance, growth, and meiosis. Recent studies showed that the kelch proteins Gpb1 and Gpb2 inhibit Ras activity via association with Ira1 and Ira2. Gpb1/2 bind to a conserved C-terminal domain of Ira1/2, and loss of Gpb1/2 results in a destabilization of Ira1 and Ira2, leading to elevated levels of Ras2-GTP and uninhibited cAMP-PKA signaling. Since the Gpb1/2 binding domain on Ira1/2 is conserved in the human neurofibromin prote
Probab=21.14 E-value=2.7e+02 Score=24.65 Aligned_cols=69 Identities=25% Similarity=0.346 Sum_probs=39.3
Q ss_pred hHHHHh---hhchHHHHHHHHHHHHcccchhhhHHHHHHHhhhchhHHHHHHhCChhhhHHHHhhchhHHHHHHHHHHhh
Q psy16066 8 YLNAIQ---TMCPHILRYLATAVIINRSKRNALKDLVKVIQQVSRDLIIDMFLNRPHYLNAIQTMCPHILRYLATAVIIN 84 (182)
Q Consensus 8 ylnaiQ---t~~p~lLRYl~~avi~~~~r~~~lkdlVrvIqqEgrd~i~d~Fl~~~~Yln~IQt~cPhlLRYla~AvI~n 84 (182)
++++|. ..||+-+||++..+ ++.|+--.++.....+--|+ .|||++-|++.=
T Consensus 135 ~l~~I~~s~~~~P~~lr~i~~~l----------~~~v~~kfp~~~~~~Vg~fi---------------FLRfi~PAIvsP 189 (323)
T cd05392 135 FIDAIISSLDRFPPELREICHHI----------YEVVSEKFPDSALSAVGSFI---------------FLRFFCPAIVSP 189 (323)
T ss_pred HHHHHHHhHHhCCHHHHHHHHHH----------HHHHHHHCCCchHHHHHHHH---------------HHHHhhhhhCCc
Confidence 455543 45788888885432 12222223333334444455 489987766532
Q ss_pred h-----------chhHHHHHHHHHHhhc
Q psy16066 85 R-----------SKRNALKDLVKVIQQE 101 (182)
Q Consensus 85 r-----------~rr~~lkdlv~vI~qe 101 (182)
. +.|+.|-.+.|++|+=
T Consensus 190 ~~~~l~~~~~~~~~rr~L~~iaKvLQ~l 217 (323)
T cd05392 190 ESEGIVDTKPSPKARRSLILLAKVLQNI 217 (323)
T ss_pred hhcCCCCCCCChhhchhHHHHHHHHHHH
Confidence 1 3467888888888873
Done!