Query 028339
Match_columns 210
No_of_seqs 21 out of 23
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 09:58:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028339.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028339hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03458 UPF0126: UPF0126 doma 77.2 5.1 0.00011 29.6 4.4 64 112-178 5-75 (80)
2 PRK10578 hypothetical protein; 65.0 12 0.00026 32.6 4.6 66 111-179 6-78 (207)
3 PF09337 zf-H2C2: His(2)-Cys(2 44.3 11 0.00025 24.9 0.9 17 178-194 21-37 (39)
4 PF06210 DUF1003: Protein of u 42.9 40 0.00087 26.7 3.9 38 134-178 7-44 (108)
5 TIGR03271 methan_mark_5 putati 40.1 12 0.00027 31.7 0.7 11 131-141 67-77 (142)
6 PF09885 DUF2112: Uncharacteri 36.8 15 0.00032 31.3 0.6 11 131-141 68-78 (143)
7 COG4327 Predicted membrane pro 30.8 34 0.00075 27.6 1.8 53 132-184 16-80 (101)
8 PRK10457 hypothetical protein; 28.2 52 0.0011 24.9 2.3 23 120-142 11-35 (82)
9 PF13085 Fer2_3: 2Fe-2S iron-s 26.6 31 0.00068 27.3 0.9 12 34-45 48-59 (110)
10 PF05915 DUF872: Eukaryotic pr 26.2 1.1E+02 0.0024 24.5 3.9 42 136-183 52-93 (115)
11 PF01102 Glycophorin_A: Glycop 24.1 76 0.0016 25.9 2.7 43 106-160 59-101 (122)
No 1
>PF03458 UPF0126: UPF0126 domain; InterPro: IPR005115 This domain is duplicated in bacterial membrane proteins of unknown function and each domain contains three transmembrane helices. The conserved glycines are suggestive of an ion channel.
Probab=77.21 E-value=5.1 Score=29.58 Aligned_cols=64 Identities=19% Similarity=0.423 Sum_probs=47.8
Q ss_pred eeehhhHHHHHHHHhhhcCCCcchhhHHHHHHH------HHHHhhhcCC-CCCCCCCCceeehhhHHHHHHHHh
Q 028339 112 EVLAGSYFSVAGALVGILKPSRMSMFGTLLVIW------GLIKEGILGK-PGNTDPSQSVYVYPTMLIAVLCAF 178 (210)
Q Consensus 112 EvlAGSYf~VaGAl~g~lkpgRmS~FGtLliiW------glvkegil~k-~~n~dp~~~v~vyPtm~iAlicAF 178 (210)
|.++=.-|++.||+.++=+ ++..||..++-. |++||-++++ |.-.- .+..|+.+++.-+++.-+
T Consensus 5 D~ig~~~fai~Ga~~A~~~--~~d~~g~~~lg~iTa~GGG~lRDvll~~~P~~~~-~~~~Y~~~a~~g~~~~~~ 75 (80)
T PF03458_consen 5 DAIGLGAFAISGALKALRA--GLDIFGAIVLGVITAVGGGILRDVLLGRTPVIFL-RDEIYATAAIIGALAYFI 75 (80)
T ss_pred HHHHHHHHHHHHHHHHHHc--CCCcHHHHHHHHHHHhhcHHHHHHHcCCCChhhc-cCchHHHHHHHHHHHHHH
Confidence 4444567899999999988 899999998876 8999999998 43222 347788877776665443
No 2
>PRK10578 hypothetical protein; Provisional
Probab=65.02 E-value=12 Score=32.61 Aligned_cols=66 Identities=23% Similarity=0.331 Sum_probs=47.0
Q ss_pred eeeehhhHHHHHHHHhhhcCCCcchhhHHHHHHH------HHHHhhhcCC-CCCCCCCCceeehhhHHHHHHHHhh
Q 028339 111 LEVLAGSYFSVAGALVGILKPSRMSMFGTLLVIW------GLIKEGILGK-PGNTDPSQSVYVYPTMLIAVLCAFS 179 (210)
Q Consensus 111 LEvlAGSYf~VaGAl~g~lkpgRmS~FGtLliiW------glvkegil~k-~~n~dp~~~v~vyPtm~iAlicAF~ 179 (210)
+|.++=.-|++.|++.+.-| +|..||..++-+ |.+|+-++|. |.. --.+..|++-+...+++--|.
T Consensus 6 ld~~g~~~FAisG~l~a~~~--~~D~~Gv~vlg~vTa~GGG~iRDill~~~P~~-~~~~~~y~~~~~~~~~~~~~~ 78 (207)
T PRK10578 6 LDIVGTAVFAISGVLLAGKL--RMDPFGVLVLGVVTAVGGGTIRDMALDNGPVF-WVKDPTDLVVAMVTSMLTIVL 78 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHc--CCCchhhHHHHHHHHhhcHHHHHHHcCCCCce-eecCccHHHHHHHHHHHHHHH
Confidence 45555567899999999876 899999999887 8999999996 431 113346666666555544333
No 3
>PF09337 zf-H2C2: His(2)-Cys(2) zinc finger; InterPro: IPR015416 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents an H2C2-type zinc finger that binds to histone upstream activating sequence (UAS) elements found in histone gene promoters []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=44.28 E-value=11 Score=24.93 Aligned_cols=17 Identities=35% Similarity=0.643 Sum_probs=14.5
Q ss_pred hhhchhhHHHhhhhcCC
Q 028339 178 FSSIKYDVKKVRRIVPA 194 (210)
Q Consensus 178 F~si~~Dv~Kv~r~~~~ 194 (210)
+-+|+.||++++|+|+.
T Consensus 21 W~gm~~~V~~~ir~C~~ 37 (39)
T PF09337_consen 21 WPGMKKDVRRVIRSCPQ 37 (39)
T ss_pred ecCHHHHHHHHHhcCcc
Confidence 45789999999999974
No 4
>PF06210 DUF1003: Protein of unknown function (DUF1003); InterPro: IPR010406 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=42.85 E-value=40 Score=26.67 Aligned_cols=38 Identities=24% Similarity=0.545 Sum_probs=25.3
Q ss_pred chhhHHHHHHHHHHHhhhcCCCCCCCCCCceeehhhHHHHHHHHh
Q 028339 134 MSMFGTLLVIWGLIKEGILGKPGNTDPSQSVYVYPTMLIAVLCAF 178 (210)
Q Consensus 134 mS~FGtLliiWglvkegil~k~~n~dp~~~v~vyPtm~iAlicAF 178 (210)
.-.|+.++++|-++--..... ...|| ||-.++.++.++
T Consensus 7 i~~~~~~~~~Wi~~N~~~~~~-~~fDp------yPFilLnl~lS~ 44 (108)
T PF06210_consen 7 IIIFTVFLAVWILLNILAPPR-PAFDP------YPFILLNLVLSL 44 (108)
T ss_pred HHHHHHHHHHHHHHHhhcccc-CCCCC------ccHHHHHHHHHH
Confidence 345788999999998877665 35788 554444444433
No 5
>TIGR03271 methan_mark_5 putative methanogenesis marker protein 5. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it.
Probab=40.06 E-value=12 Score=31.66 Aligned_cols=11 Identities=55% Similarity=1.029 Sum_probs=9.6
Q ss_pred CCcchhhHHHH
Q 028339 131 PSRMSMFGTLL 141 (210)
Q Consensus 131 pgRmS~FGtLl 141 (210)
=||||+||.|+
T Consensus 67 RGRmsl~gplI 77 (142)
T TIGR03271 67 RGRMSLFGPLI 77 (142)
T ss_pred cchhhhhhHHH
Confidence 49999999975
No 6
>PF09885 DUF2112: Uncharacterized protein conserved in archaea (DUF2112); InterPro: IPR012356 The exact function of this protein is unknown, but likely is linked to methanogenesis or a process closely connected to it.
Probab=36.83 E-value=15 Score=31.26 Aligned_cols=11 Identities=45% Similarity=0.848 Sum_probs=9.6
Q ss_pred CCcchhhHHHH
Q 028339 131 PSRMSMFGTLL 141 (210)
Q Consensus 131 pgRmS~FGtLl 141 (210)
=||||+||.|+
T Consensus 68 RGRMsl~gplI 78 (143)
T PF09885_consen 68 RGRMSLIGPLI 78 (143)
T ss_pred cchhhhhhhhH
Confidence 49999999975
No 7
>COG4327 Predicted membrane protein [Function unknown]
Probab=30.80 E-value=34 Score=27.64 Aligned_cols=53 Identities=21% Similarity=0.265 Sum_probs=29.8
Q ss_pred CcchhhHHHHHHHHHHHhh------------hcCCCCCCCCCCceeehhhHHHHHHHHhhhchhh
Q 028339 132 SRMSMFGTLLVIWGLIKEG------------ILGKPGNTDPSQSVYVYPTMLIAVLCAFSSIKYD 184 (210)
Q Consensus 132 gRmS~FGtLliiWglvkeg------------il~k~~n~dp~~~v~vyPtm~iAlicAF~si~~D 184 (210)
.|..+.+.||++|+||.=+ |+|-|.+-=-+++=-++--.++-.+-||-+=|.|
T Consensus 16 anttli~~lL~vwflVSfvvi~fa~alst~rifg~pf~ywma~QGsiitfVvlifvya~r~nkld 80 (101)
T COG4327 16 ANTTLIAALLGVWFLVSFVVILFARALSTMRIFGWPFGYWMAQQGSIITFVVLIFVYAWRMNKLD 80 (101)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhhcccEEeccchhhhhhcCCCeeehHHHHHHHHHHHhHHH
Confidence 3678899999999998644 3455544322222222222344455566554444
No 8
>PRK10457 hypothetical protein; Provisional
Probab=28.24 E-value=52 Score=24.91 Aligned_cols=23 Identities=26% Similarity=0.499 Sum_probs=19.3
Q ss_pred HHHHHHhhhcCCCc--chhhHHHHH
Q 028339 120 SVAGALVGILKPSR--MSMFGTLLV 142 (210)
Q Consensus 120 ~VaGAl~g~lkpgR--mS~FGtLli 142 (210)
.++|.+...+-||| |.+++|+++
T Consensus 11 ~iaG~lA~~i~pg~~~~G~~~tiil 35 (82)
T PRK10457 11 LIAGILAKWIMPGKDGGGFFMTIIL 35 (82)
T ss_pred HHHHHHHHHhcCCCCCcCHHHHHHH
Confidence 46888888999997 788888876
No 9
>PF13085 Fer2_3: 2Fe-2S iron-sulfur cluster binding domain; PDB: 3P4Q_N 1KFY_N 3CIR_N 3P4R_B 2B76_N 1KF6_B 3P4P_N 3P4S_B 1L0V_B 1ZOY_B ....
Probab=26.65 E-value=31 Score=27.31 Aligned_cols=12 Identities=50% Similarity=1.420 Sum_probs=8.4
Q ss_pred eeeecCCCccCC
Q 028339 34 FRIPCRAGMCST 45 (210)
Q Consensus 34 FrVpCr~G~Ctt 45 (210)
||-.||.|+|-+
T Consensus 48 fr~sCr~giCGs 59 (110)
T PF13085_consen 48 FRYSCRSGICGS 59 (110)
T ss_dssp B--SSSSSSSST
T ss_pred EEecCCCCCCCC
Confidence 799999998864
No 10
>PF05915 DUF872: Eukaryotic protein of unknown function (DUF872); InterPro: IPR008590 This entry represents several uncharacterised eukaryotic transmembrane proteins. The function of this currently unknown.
Probab=26.21 E-value=1.1e+02 Score=24.47 Aligned_cols=42 Identities=26% Similarity=0.506 Sum_probs=28.4
Q ss_pred hhHHHHHHHHHHHhhhcCCCCCCCCCCceeehhhHHHHHHHHhhhchh
Q 028339 136 MFGTLLVIWGLIKEGILGKPGNTDPSQSVYVYPTMLIAVLCAFSSIKY 183 (210)
Q Consensus 136 ~FGtLliiWglvkegil~k~~n~dp~~~v~vyPtm~iAlicAF~si~~ 183 (210)
.+|+.+++.|++..- + ..| .+.-+.+|-+++..+|-.=+.-+
T Consensus 52 i~G~~li~~g~l~~~--~---~i~-~~~~~~~~llilG~L~fIPG~Y~ 93 (115)
T PF05915_consen 52 IFGTVLIIIGLLLFF--G---HID-GDRDRGWALLILGILCFIPGFYH 93 (115)
T ss_pred HHHHHHHHHHHHHHh--c---ccC-CCCcccchHHHHHHHHHhccHHH
Confidence 578888888876553 1 112 45678899999999986555433
No 11
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=24.11 E-value=76 Score=25.88 Aligned_cols=43 Identities=19% Similarity=0.288 Sum_probs=21.1
Q ss_pred ccceeeeeehhhHHHHHHHHhhhcCCCcchhhHHHHHHHHHHHhhhcCCCCCCCC
Q 028339 106 TDLQCLEVLAGSYFSVAGALVGILKPSRMSMFGTLLVIWGLIKEGILGKPGNTDP 160 (210)
Q Consensus 106 tDlqrLEvlAGSYf~VaGAl~g~lkpgRmS~FGtLliiWglvkegil~k~~n~dp 160 (210)
-|+.+- +++|--|||..+++| +.|+||++++.-+...+.+.+|
T Consensus 59 h~fs~~-~i~~Ii~gv~aGvIg-----------~Illi~y~irR~~Kk~~~~~~p 101 (122)
T PF01102_consen 59 HRFSEP-AIIGIIFGVMAGVIG-----------IILLISYCIRRLRKKSSSDVQP 101 (122)
T ss_dssp SSSS-T-CHHHHHHHHHHHHHH-----------HHHHHHHHHHHHS---------
T ss_pred cCcccc-ceeehhHHHHHHHHH-----------HHHHHHHHHHHHhccCCCCCCC
Confidence 344444 467877777766665 4467777777665554444433
Done!