Query 030999
Match_columns 167
No_of_seqs 104 out of 347
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 07:43:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030999.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030999hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3106 ER lumen protein retai 100.0 8.9E-73 1.9E-77 456.7 11.2 164 1-166 1-164 (212)
2 COG5196 ERD2 ER lumen protein 100.0 2.8E-63 6E-68 396.5 13.7 164 1-166 1-165 (214)
3 PF00810 ER_lumen_recept: ER l 100.0 3.7E-56 8E-61 348.9 12.3 138 28-167 1-142 (147)
4 TIGR00951 2A43 Lysosomal Cysti 95.0 1.8 3.8E-05 36.0 15.4 35 11-45 14-48 (220)
5 PF04193 PQ-loop: PQ loop repe 94.2 0.15 3.2E-06 33.4 5.1 50 118-167 2-51 (61)
6 PF04193 PQ-loop: PQ loop repe 92.1 0.27 5.8E-06 32.1 3.9 42 6-47 7-48 (61)
7 smart00679 CTNS Repeated motif 86.6 0.39 8.5E-06 27.5 1.2 22 19-40 6-27 (32)
8 KOG3211 Predicted endoplasmic 82.6 23 0.00049 30.0 10.3 136 20-163 50-190 (230)
9 PHA02246 hypothetical protein 53.6 76 0.0017 25.9 7.1 118 20-158 24-149 (192)
10 COG4095 Uncharacterized conser 48.6 59 0.0013 23.8 5.2 44 124-167 11-54 (89)
11 PF02790 COX2_TM: Cytochrome C 42.0 63 0.0014 21.8 4.4 21 94-114 61-81 (84)
12 PTZ00154 40S ribosomal protein 39.8 23 0.00049 27.7 2.1 27 5-38 49-75 (134)
13 COG4095 Uncharacterized conser 35.5 78 0.0017 23.1 4.1 35 8-42 12-46 (89)
14 PF00833 Ribosomal_S17e: Ribos 32.4 38 0.00082 26.1 2.2 27 5-38 49-75 (121)
15 PF03083 MtN3_slv: Sugar efflu 30.7 59 0.0013 22.3 2.9 34 4-37 3-39 (87)
No 1
>KOG3106 consensus ER lumen protein retaining receptor [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=8.9e-73 Score=456.73 Aligned_cols=164 Identities=56% Similarity=0.950 Sum_probs=162.0
Q ss_pred CchhhhhhhHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHhhhccccchhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 030999 1 MNIFRLAGDMTHLASVLVLLLKIHTIKSCAGISLKTQELYALVFATRYLDIFTNYISFYNTIMKLIFLGSSFSIVWYIKR 80 (167)
Q Consensus 1 mn~fr~~gd~~hl~s~~iLl~ki~~~kS~~GiSlkTQ~ly~~vf~~Ryldl~~~~~s~Yn~~mki~~i~~s~~iiyl~~~ 80 (167)
||.||++||++|++|+++|++||+|+|||+|||+|||++|++||++||+|+++++.|.||++||+++++++.+++|+|++
T Consensus 1 mn~fr~~gd~~H~~~i~vLi~Ki~ktrsCaGiSlKSQ~L~Alvf~~Ryldlf~~~~s~ynt~mki~fl~~t~~ivymi~~ 80 (212)
T KOG3106|consen 1 MNNFRFAGDLSHLAAIIVLILKIWKTKSCAGISLKSQELFALVFATRYLDLFTFYESLYNTIMKIAFLASTLWIVYMIRF 80 (212)
T ss_pred CcchhhHHHHHHHHHHHHHHHHHHhcCccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccccccccccccchhHHHHHHHHHHHHhhcCCcchhhHHHHHHHHHHHHhhhhHHHHHhhcCCcchhHHHHHHHHHHH
Q 030999 81 HKIVHRSYDKDQDTFRHWFIVLPCLVLALLINERFTFKEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLGAA 160 (167)
Q Consensus 81 ~~~~~~TY~~~~D~f~~~~li~p~~vLa~~~~~~~~~~ei~WtfSi~LEsvAiLPQL~mlqk~~~ve~~tshYv~~Lg~y 160 (167)
| +|+|||+|+|||+++|+++||+++|+++||++++.|++|+||+|||||||||||+|+||+||+|++|+|||+|||+|
T Consensus 81 k--~~~tYd~~~DtFri~~llvp~~vlsl~i~~~~t~~eilWtFsiyLEsVaILPQL~~lq~tg~~E~~TahYvfaLG~y 158 (212)
T KOG3106|consen 81 K--LRATYDKEKDTFRIEYLLVPSAVLSLLINHSFTILEILWTFSIYLESVAILPQLFMLQKTGEAETITAHYLFALGLY 158 (212)
T ss_pred H--HHHHHhcccCceeEEEEehhheeeeeeecCCccHHHHHHHHHHHHHHHHHhHHHHHHHhcCCccchHHHHHHHHHHH
Confidence 4 89999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhc
Q 030999 161 HTVRCT 166 (167)
Q Consensus 161 R~~~~~ 166 (167)
|+++|+
T Consensus 159 R~ly~~ 164 (212)
T KOG3106|consen 159 RALYIA 164 (212)
T ss_pred HHHHHH
Confidence 999996
No 2
>COG5196 ERD2 ER lumen protein retaining receptor [Intracellular trafficking and secretion]
Probab=100.00 E-value=2.8e-63 Score=396.53 Aligned_cols=164 Identities=45% Similarity=0.772 Sum_probs=159.9
Q ss_pred CchhhhhhhHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHhhhccccc-hhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 030999 1 MNIFRLAGDMTHLASVLVLLLKIHTIKSCAGISLKTQELYALVFATRYLDIF-TNYISFYNTIMKLIFLGSSFSIVWYIK 79 (167)
Q Consensus 1 mn~fr~~gd~~hl~s~~iLl~ki~~~kS~~GiSlkTQ~ly~~vf~~Ryldl~-~~~~s~Yn~~mki~~i~~s~~iiyl~~ 79 (167)
||.||++||++|++|+.+|+.||+++|+|+|+|+|||.+|++||++||+|++ +.+.|+||.+||++||+++.+|+++|+
T Consensus 1 m~~Fr~lGD~~Hlasi~vLih~ik~tr~csGlSlKtq~Ly~lVfitRYldLf~f~~~slYn~lMki~FI~s~~yI~~lm~ 80 (214)
T COG5196 1 MDTFRFLGDFLHLASIAVLIHKIKRTRSCSGLSLKTQFLYSLVFITRYLDLFDFYARSLYNSLMKILFIGSQVYILFLMR 80 (214)
T ss_pred CcHHHHHhHHHHHHHHHHHHHHhhhcceecceehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999999999999999999999999999999999999999 567899999999999999999999999
Q ss_pred hccccccccccccccchhHHHHHHHHHHHHhhcCCcchhhHHHHHHHHHHHHhhhhHHHHHhhcCCcchhHHHHHHHHHH
Q 030999 80 RHKIVHRSYDKDQDTFRHWFIVLPCLVLALLINERFTFKEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLGA 159 (167)
Q Consensus 80 ~~~~~~~TY~~~~D~f~~~~li~p~~vLa~~~~~~~~~~ei~WtfSi~LEsvAiLPQL~mlqk~~~ve~~tshYv~~Lg~ 159 (167)
.+ +++|||+..|+|+..++++||+++++++|++.++.+++||||+|||||||||||+|+||.||-|++|+||++++|+
T Consensus 81 ~~--~r~tYdk~lDtF~i~~ll~gsav~slff~~~~tisnvlwtfS~wLESVAILPQL~mLq~~GeteslT~hYvfamgL 158 (214)
T COG5196 81 FK--YRSTYDKKLDTFNILTLLVGSAVFSLFFTRGGTISNVLWTFSLWLESVAILPQLVMLQEAGETESLTSHYVFAMGL 158 (214)
T ss_pred hc--ccchHHHhhhhhhhhhhhhhhhhheeeecCCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeHHHHHHHHHH
Confidence 85 7899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Hhhhhhc
Q 030999 160 AHTVRCT 166 (167)
Q Consensus 160 yR~~~~~ 166 (167)
||+++.-
T Consensus 159 YRalYip 165 (214)
T COG5196 159 YRALYIP 165 (214)
T ss_pred HHHhhhh
Confidence 9999864
No 3
>PF00810 ER_lumen_recept: ER lumen protein retaining receptor; InterPro: IPR000133 Proteins resident in the lumen of the endoplasmic reticulum (ER) contain a C-terminal tetrapeptide, commonly known as Lys-Asp-Glu-Leu (KDEL) in mammals and His-Asp-Glu-Leu (HDEL) in yeast (Saccharomyces cerevisiae) that acts as a signal for their retrieval from subsequent compartments of the secretory pathway. The receptor for this signal is a ~26 kDa Golgi membrane protein, initially identified as the ERD2 gene product in S. cerevisiae. The receptor molecule, known variously as the ER lumen protein retaining receptor or the 'KDEL receptor', is believed to cycle between the cis side of the Golgi apparatus and the ER. It has also been characterised in a number of other species, including plants, Plasmodium, Drosophila and mammals. In mammals, 2 highly related forms of the receptor are known. The KDEL receptor is a highly hydrophobic protein of 220 residues; its sequence exhibits 7 hydrophobic regions, all of which have been suggested to traverse the membrane []. More recently, however, it has been suggested that only 6 of these regions are transmembrane (TM), resulting in both N- and C-termini on the cytoplasmic side of the membrane.; GO: 0046923 ER retention sequence binding, 0006621 protein retention in ER lumen, 0016021 integral to membrane
Probab=100.00 E-value=3.7e-56 Score=348.91 Aligned_cols=138 Identities=53% Similarity=0.930 Sum_probs=132.1
Q ss_pred cccccccchhHHHHHHHhhhcccc--chhhHHHHHHHHHHHHHHHHHHHHHHHHhccccccccccccccchhHHHHHHHH
Q 030999 28 SCAGISLKTQELYALVFATRYLDI--FTNYISFYNTIMKLIFLGSSFSIVWYIKRHKIVHRSYDKDQDTFRHWFIVLPCL 105 (167)
Q Consensus 28 S~~GiSlkTQ~ly~~vf~~Ryldl--~~~~~s~Yn~~mki~~i~~s~~iiyl~~~~~~~~~TY~~~~D~f~~~~li~p~~ 105 (167)
||+|+|+|||+||++|+++||+|+ +.++.+.||++||+++++++++++|+|+. +||+|||+++|+|+..++++||+
T Consensus 1 S~~GlSlktq~ly~~vf~~Ryldl~~f~~~~s~y~~~~k~~~i~~s~~iiyli~~--~~~~Ty~~~~D~f~~~~li~p~~ 78 (147)
T PF00810_consen 1 SCSGLSLKTQILYAIVFLTRYLDLFWFESYLSLYNTIMKVFFIVSSLYIIYLIFF--KYKSTYDKEIDTFRLEYLIVPCF 78 (147)
T ss_pred CcchhhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhhhe--eehhhhhccccchhhhHHHHHHH
Confidence 899999999999999999999999 77788999999999999999999999965 59999999999999999999999
Q ss_pred HHHHhhcC--CcchhhHHHHHHHHHHHHhhhhHHHHHhhcCCcchhHHHHHHHHHHHhhhhhcC
Q 030999 106 VLALLINE--RFTFKEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLGAAHTVRCTY 167 (167)
Q Consensus 106 vLa~~~~~--~~~~~ei~WtfSi~LEsvAiLPQL~mlqk~~~ve~~tshYv~~Lg~yR~~~~~~ 167 (167)
+||+++|| ++++.|++||||+|||||||+|||+|+||+||||++|+|||++||+||++++++
T Consensus 79 vLa~i~~p~~~~~~~ei~wtfSi~LEsvAIlPQL~m~~k~~~ve~ltshYv~~Lg~yR~ly~~~ 142 (147)
T PF00810_consen 79 VLALIFHPLNSFFFLEILWTFSIYLESVAILPQLFMLQKTGEVENLTSHYVFALGLYRALYLLN 142 (147)
T ss_pred HHHHHHhccccchHHHHHHHHHHHHHHHHHhHHHHHHHHhcCeeehHHHHHHHHHHHHHHHHHH
Confidence 99999994 578999999999999999999999999999999999999999999999999863
No 4
>TIGR00951 2A43 Lysosomal Cystine Transporter.
Probab=95.00 E-value=1.8 Score=36.01 Aligned_cols=35 Identities=23% Similarity=0.194 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHhhcccccccccchhHHHHHHHh
Q 030999 11 THLASVLVLLLKIHTIKSCAGISLKTQELYALVFA 45 (167)
Q Consensus 11 ~hl~s~~iLl~ki~~~kS~~GiSlkTQ~ly~~vf~ 45 (167)
....+++=-+.|+.|+||++|+|+..-.+-.+.+.
T Consensus 14 ~~~~~~~PQi~~n~k~ks~~GlS~~~~~l~~~g~~ 48 (220)
T TIGR00951 14 AWSISFYPQIIKNWRRKSAEGLSFDFVMLNLVGFT 48 (220)
T ss_pred HHHHHHhhHHHHHHhccccCCcCHHHHHHHHHHHH
Confidence 34556666679999999999999998775444443
No 5
>PF04193 PQ-loop: PQ loop repeat
Probab=94.23 E-value=0.15 Score=33.40 Aligned_cols=50 Identities=16% Similarity=0.285 Sum_probs=42.0
Q ss_pred hhHHHHHHHHHHHHhhhhHHHHHhhcCCcchhHHHHHHHHHHHhhhhhcC
Q 030999 118 KEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLGAAHTVRCTY 167 (167)
Q Consensus 118 ~ei~WtfSi~LEsvAiLPQL~mlqk~~~ve~~tshYv~~Lg~yR~~~~~~ 167 (167)
.+++...+.-+++++-+||+....|++++|.+.--++.......+++.+|
T Consensus 2 ~~~~g~i~~~~~~~~~lPQi~~~~k~ks~~glS~~~~~l~~~g~~~~~~~ 51 (61)
T PF04193_consen 2 SNILGIISIVLWIISFLPQIIKNYKRKSTGGLSLWFLLLWLIGSILWVLY 51 (61)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHccccccccHHHHHHHHHHHHHHHHH
Confidence 46788889999999999999999999999999888887777766666543
No 6
>PF04193 PQ-loop: PQ loop repeat
Probab=92.12 E-value=0.27 Score=32.10 Aligned_cols=42 Identities=21% Similarity=0.124 Sum_probs=30.3
Q ss_pred hhhhHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHhhh
Q 030999 6 LAGDMTHLASVLVLLLKIHTIKSCAGISLKTQELYALVFATR 47 (167)
Q Consensus 6 ~~gd~~hl~s~~iLl~ki~~~kS~~GiSlkTQ~ly~~vf~~R 47 (167)
.+|=..-+.+.+=-+.|.+|+||+.|+|..+..+..+..+.+
T Consensus 7 ~i~~~~~~~~~lPQi~~~~k~ks~~glS~~~~~l~~~g~~~~ 48 (61)
T PF04193_consen 7 IISIVLWIISFLPQIIKNYKRKSTGGLSLWFLLLWLIGSILW 48 (61)
T ss_pred HHHHHHHHHHHHhHHHHHHHccccccccHHHHHHHHHHHHHH
Confidence 334444455565667999999999999999887766655544
No 7
>smart00679 CTNS Repeated motif present between transmembrane helices in cystinosin, yeast ERS1p, mannose-P-dolichol utilization defect 1, and other hypothetical proteins. Function unknown, but likely to be associated with the glycosylation machinery.
Probab=86.60 E-value=0.39 Score=27.47 Aligned_cols=22 Identities=27% Similarity=0.280 Sum_probs=18.0
Q ss_pred HHHHHhhcccccccccchhHHH
Q 030999 19 LLLKIHTIKSCAGISLKTQELY 40 (167)
Q Consensus 19 Ll~ki~~~kS~~GiSlkTQ~ly 40 (167)
-+.|++|+||+.|+|.-...+-
T Consensus 6 Qi~~~~~~ks~~glS~~~~~l~ 27 (32)
T smart00679 6 QIIKNYRRKSTEGLSILFVLLW 27 (32)
T ss_pred HHHHHHHcCCcCcCCHHHHHHH
Confidence 4689999999999998865543
No 8
>KOG3211 consensus Predicted endoplasmic reticulum membrane protein Lec35/MPDU1 involved in monosaccharide-P-dolichol utilization [General function prediction only]
Probab=82.63 E-value=23 Score=29.99 Aligned_cols=136 Identities=15% Similarity=0.093 Sum_probs=68.6
Q ss_pred HHHHhhcccccccccchhHHHHHHHh--hhccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhccccccccccccccchh
Q 030999 20 LLKIHTIKSCAGISLKTQELYALVFA--TRYLDIFTNYISFYNTIMKLIFLGSSFSIVWYIKRHKIVHRSYDKDQDTFRH 97 (167)
Q Consensus 20 l~ki~~~kS~~GiSlkTQ~ly~~vf~--~Ryldl~~~~~s~Yn~~mki~~i~~s~~iiyl~~~~~~~~~TY~~~~D~f~~ 97 (167)
+.||...||+.|+|..+|+|=.+.++ .+|.-- ..| -...-++..++..+..++-.+-++ |+- -.-+.|.|-.
T Consensus 50 I~kI~aakSa~GLSv~s~~LElvgytvtl~Y~~~-~g~--pFss~gE~~fLl~Q~vili~~if~--f~~-~~~~~v~~l~ 123 (230)
T KOG3211|consen 50 IMKIRAAKSARGLSVVSLLLELVGYTVTLSYSYT-SGY--PFSSYGEYPFLLLQAVILILCIFH--FSG-QTVTVVQFLG 123 (230)
T ss_pred HHHHHhhcccccccHHHHHHHHHHHHheeeehhh-cCC--CchhHHHHHHHHHHHHHHHHHHHH--hcc-ceeehhhHHH
Confidence 48999999999999999998877776 333110 001 111334666666666655555443 331 1112344443
Q ss_pred HHHHHHHHHHHHhhcCCcchhhHHHHHHHHHHHHhhhhHHHHHhhc---CCcchhHHHHHHHHHHHhhh
Q 030999 98 WFIVLPCLVLALLINERFTFKEVMWTFSLYLEAVAILPQLVLLQRT---RNIDNLTGQYVFLLGAAHTV 163 (167)
Q Consensus 98 ~~li~p~~vLa~~~~~~~~~~ei~WtfSi~LEsvAiLPQL~mlqk~---~~ve~~tshYv~~Lg~yR~~ 163 (167)
.+.+++....+.. .|- .+.+..=+-.+-.-.++=+||+.-..|+ |...-+|--=-+.=.+.|.+
T Consensus 124 ~~~~v~~~~~sk~-~p~-~~~~L~~~~~l~i~v~sr~~Qi~~n~~~~~tgqls~it~fLsf~g~lARif 190 (230)
T KOG3211|consen 124 YIALVVSVLASKA-LPL-WIITLAQNLCLPIVVVSRLLQIQCNYHNRSTGQLSLITVFLSFGGCLARIF 190 (230)
T ss_pred HHHHHHHHHHHhh-hhH-HHHHHHHhcCchhhhHHHHHHHHHHhcccccchhHHHHHHHHhhhHHHHHH
Confidence 3434433332211 111 1112221222222336668898887764 55555554433433444443
No 9
>PHA02246 hypothetical protein
Probab=53.64 E-value=76 Score=25.85 Aligned_cols=118 Identities=24% Similarity=0.409 Sum_probs=60.8
Q ss_pred HHHHhhcccccccccchhHHHHHHHhhhccccchhhHHHHHHHHH------HHHH--HHHHHHHHHHHhccccccccccc
Q 030999 20 LLKIHTIKSCAGISLKTQELYALVFATRYLDIFTNYISFYNTIMK------LIFL--GSSFSIVWYIKRHKIVHRSYDKD 91 (167)
Q Consensus 20 l~ki~~~kS~~GiSlkTQ~ly~~vf~~Ryldl~~~~~s~Yn~~mk------i~~i--~~s~~iiyl~~~~~~~~~TY~~~ 91 (167)
+..+.++||..|+|-- .-|++++.. -.|.||...- ++.. -....++-+.. ..| |+
T Consensus 24 L~slvk~~nv~GvS~~--FWYLi~~tv--------giSfyNlL~T~~~~fqi~svg~nl~lgivcLlv------~~~-rk 86 (192)
T PHA02246 24 LVALVKAESVKGVSNY--FWYLIVATV--------GISFYNLLLTDASVFQIVSVGLNLTLGIVCLLV------ASY-RK 86 (192)
T ss_pred HHHHhhhcccccHHHH--HHHHHHHHH--------HHHHHHHHhcCCceEEEeeeehhhhhhhhheee------ehh-hc
Confidence 3678899999999843 446665543 2356663211 1000 00111111111 122 23
Q ss_pred cccchhHHHHHHHHHHHHhhcCCcchhhHHHHHHHHHHHHhhhhHHHHHhhcCCcchhHHHHHHHHH
Q 030999 92 QDTFRHWFIVLPCLVLALLINERFTFKEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLG 158 (167)
Q Consensus 92 ~D~f~~~~li~p~~vLa~~~~~~~~~~ei~WtfSi~LEsvAiLPQL~mlqk~~~ve~~tshYv~~Lg 158 (167)
+|-|...++++-++.+-.+ .......|..=+-|+ -.|-.||...+.|++..|....-.-..+|
T Consensus 87 kd~f~~~fiiifSLllfll-~~~~evtQtVat~tI---iLaYi~QIIqfyKTK~SEg~n~~l~lii~ 149 (192)
T PHA02246 87 KDYFSIPFIIVFSLLLFLL-SDFTALTQTVATITI---ILAYVTQITTFYKTKSAEGTNRFLFLIIG 149 (192)
T ss_pred cccccchHHHHHHHHHHHH-hhhHHHHHHHHHHHH---HHHHHHHHHHHhhhcccCCCChhHHHHHH
Confidence 5666666666555433322 111223333333333 45789999999999988876654433333
No 10
>COG4095 Uncharacterized conserved protein [Function unknown]
Probab=48.62 E-value=59 Score=23.79 Aligned_cols=44 Identities=25% Similarity=0.366 Sum_probs=32.7
Q ss_pred HHHHHHHHhhhhHHHHHhhcCCcchhHHHHHHHHHHHhhhhhcC
Q 030999 124 FSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLGAAHTVRCTY 167 (167)
Q Consensus 124 fSi~LEsvAiLPQL~mlqk~~~ve~~tshYv~~Lg~yR~~~~~~ 167 (167)
.+--+-.+|.+||+.-.-|+++-.+++--....+..++++-+.|
T Consensus 11 ia~ilttf~flPQ~iki~ktK~t~~Isl~~fii~~ia~~lwliy 54 (89)
T COG4095 11 IAGILTTFAFLPQLIKIIKTKNTASISLPMFIILNIALFLWLIY 54 (89)
T ss_pred HHHHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHH
Confidence 34445678999999999999888887777777677666665443
No 11
>PF02790 COX2_TM: Cytochrome C oxidase subunit II, transmembrane domain This family corresponds to chains b and o.; InterPro: IPR011759 Cytochrome c oxidase (1.9.3.1 from EC) [, ] is an oligomeric enzymatic complex which is a component of the respiratory chain and is involved in the transfer of electrons from cytochrome c to oxygen. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. The enzyme complex consists of 3-4 subunits (prokaryotes) to up to 13 polypeptides (mammals). Subunit 2 (CO II) transfers the electrons from cytochrome c to the catalytic subunit 1. It contains two adjacent transmembrane regions in its N terminus and the major part of the protein is exposed to the periplasmic or to the mitochondrial intermembrane space, respectively. CO II provides the substrate-binding site and contains a copper centre called Cu(A) (see IPR001505 from INTERPRO), probably the primary acceptor in cytochrome c oxidase. An exception is the corresponding subunit of the cbb3-type oxidase which lacks the copper A redox-centre. Several bacterial CO II have a C-terminal extension that contains a covalently bound haem c. The N-terminal domain of cytochrome C oxidase contains two transmembrane alpha-helices. ; GO: 0004129 cytochrome-c oxidase activity, 0005507 copper ion binding, 0009055 electron carrier activity, 0022900 electron transport chain, 0016021 integral to membrane; PDB: 3VRJ_C 2EIN_B 3AG3_B 2DYR_O 3AG1_B 2EIK_O 3ASN_B 1OCR_B 2EIJ_B 1OCC_O ....
Probab=41.97 E-value=63 Score=21.81 Aligned_cols=21 Identities=14% Similarity=0.407 Sum_probs=14.2
Q ss_pred cchhHHHHHHHHHHHHhhcCC
Q 030999 94 TFRHWFIVLPCLVLALLINER 114 (167)
Q Consensus 94 ~f~~~~li~p~~vLa~~~~~~ 114 (167)
+.-..+-++|++++..+.-|+
T Consensus 61 ~lE~~WTiiP~iiLl~l~~pS 81 (84)
T PF02790_consen 61 KLEIIWTIIPAIILLFLAFPS 81 (84)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhhhhHHHHHHHHHHHhhh
Confidence 344457789998887765554
No 12
>PTZ00154 40S ribosomal protein S17; Provisional
Probab=39.75 E-value=23 Score=27.74 Aligned_cols=27 Identities=48% Similarity=0.582 Sum_probs=19.8
Q ss_pred hhhhhHHHHHHHHHHHHHHhhcccccccccchhH
Q 030999 5 RLAGDMTHLASVLVLLLKIHTIKSCAGISLKTQE 38 (167)
Q Consensus 5 r~~gd~~hl~s~~iLl~ki~~~kS~~GiSlkTQ~ 38 (167)
|++|...|+ .|-.+...+.|||+|.|+
T Consensus 49 rIAGYIThl-------mkri~~gpvrgis~klqe 75 (134)
T PTZ00154 49 KIAGFVTHL-------MKRIQKGPVRGISLKLQE 75 (134)
T ss_pred HHHHHHHHH-------HhhhccCCccccceehhH
Confidence 566666664 444566789999999996
No 13
>COG4095 Uncharacterized conserved protein [Function unknown]
Probab=35.49 E-value=78 Score=23.14 Aligned_cols=35 Identities=26% Similarity=0.253 Sum_probs=26.3
Q ss_pred hhHHHHHHHHHHHHHHhhcccccccccchhHHHHH
Q 030999 8 GDMTHLASVLVLLLKIHTIKSCAGISLKTQELYAL 42 (167)
Q Consensus 8 gd~~hl~s~~iLl~ki~~~kS~~GiSlkTQ~ly~~ 42 (167)
|...-.++++--+.|+.|+||.+++|+-.-....+
T Consensus 12 a~ilttf~flPQ~iki~ktK~t~~Isl~~fii~~i 46 (89)
T COG4095 12 AGILTTFAFLPQLIKIIKTKNTASISLPMFIILNI 46 (89)
T ss_pred HHHHHHHHHHHHHHHHHhccccccccHHHHHHHHH
Confidence 44455677888889999999999999876544433
No 14
>PF00833 Ribosomal_S17e: Ribosomal S17; InterPro: IPR001210 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaebacterial ribosomal proteins can be grouped in this family of ribosomal proteins, S17e. They include, vertebrate, Drosophila and Neurospora crassa (crp-3) S17's as well as yeast S17a (RP51A) and S17b (RP51B) and archaebacterial S17e [, , ].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1RQ6_A 2XZM_V 2XZN_V 3IZ6_Q 3IZB_Q 3O30_K 3O2Z_K 3U5G_R 3U5C_R.
Probab=32.41 E-value=38 Score=26.08 Aligned_cols=27 Identities=44% Similarity=0.585 Sum_probs=19.2
Q ss_pred hhhhhHHHHHHHHHHHHHHhhcccccccccchhH
Q 030999 5 RLAGDMTHLASVLVLLLKIHTIKSCAGISLKTQE 38 (167)
Q Consensus 5 r~~gd~~hl~s~~iLl~ki~~~kS~~GiSlkTQ~ 38 (167)
|++|...|+ .|-.+.....|+|+|.|+
T Consensus 49 kIAGYvThl-------mKriq~g~vrgis~klqE 75 (121)
T PF00833_consen 49 KIAGYVTHL-------MKRIQRGPVRGISIKLQE 75 (121)
T ss_dssp HHHHHHHHH-------HHHHTSSSSTTCSSCCCC
T ss_pred HHHHHHHHH-------HHHHHhccccccchhhhH
Confidence 456666663 455566778899999986
No 15
>PF03083 MtN3_slv: Sugar efflux transporter for intercellular exchange; InterPro: IPR004316 This family includes proteins such as Drosophila saliva [], MtN3 involved in root nodule development [] and proteins involved in activation and expression of recombination activation genes (RAGs) []. Although the molecular function of these proteins is unknown, they are almost certainly transmembrane proteins. This signature maps to transmembrane helices which are found in two copies in most members of the family.; GO: 0016021 integral to membrane
Probab=30.71 E-value=59 Score=22.31 Aligned_cols=34 Identities=12% Similarity=0.201 Sum_probs=24.1
Q ss_pred hhhhhhHHHHHHH---HHHHHHHhhcccccccccchh
Q 030999 4 FRLAGDMTHLASV---LVLLLKIHTIKSCAGISLKTQ 37 (167)
Q Consensus 4 fr~~gd~~hl~s~---~iLl~ki~~~kS~~GiSlkTQ 37 (167)
+..+|..+.++.+ +--+.++.|+||.+++|.-..
T Consensus 3 lg~~~~~~~i~~~~spl~~i~~v~k~ks~~~~~~~~~ 39 (87)
T PF03083_consen 3 LGILASVSSIIMFLSPLPQIRQVIKTKSTGSVSFPPF 39 (87)
T ss_pred eeHHHHHHHHHHHHHHHHHHHHHHhCCCCCccceehh
Confidence 3455555555333 466799999999999998754
Done!