Query 033368
Match_columns 121
No_of_seqs 28 out of 30
Neff 2.0
Searched_HMMs 46136
Date Fri Mar 29 13:02:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033368.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033368hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00046 photosystem I reactio 100.0 7.5E-57 1.6E-61 341.1 3.3 115 2-119 1-115 (141)
2 TIGR03059 psaOeuk photosystem 100.0 9.1E-34 2E-38 200.2 2.2 55 65-119 1-57 (82)
3 PF07629 DUF1590: Protein of u 61.8 3.1 6.7E-05 25.6 0.3 13 102-114 16-28 (32)
4 PF03244 PSI_PsaH: Photosystem 52.2 4.7 0.0001 31.5 0.0 17 6-22 5-21 (140)
5 PF15017 AF1Q: Drug resistance 43.2 7.5 0.00016 27.9 -0.1 12 73-84 73-84 (87)
6 smart00682 G2F G2 nidogen doma 32.4 16 0.00034 30.0 0.2 42 65-108 58-100 (227)
7 PLN00170 photosystem II light- 31.3 16 0.00035 30.3 0.1 23 3-26 2-24 (255)
8 KOG1321 Protoheme ferro-lyase 29.7 31 0.00068 30.8 1.5 23 85-107 201-223 (395)
9 PLN00074 photosystem II D2 pro 21.7 37 0.00081 29.9 0.5 17 56-76 18-34 (353)
10 PF07474 G2F: G2F domain; Int 21.2 9.1 0.0002 30.4 -3.0 31 65-95 58-89 (192)
11 PF15128 T_cell_tran_alt: T-ce 20.9 9.4 0.0002 28.1 -2.8 41 55-95 13-59 (92)
12 cd00255 nidG2 Nidogen, G2 doma 20.8 33 0.00072 28.0 0.0 32 65-96 56-88 (224)
No 1
>PLN00046 photosystem I reaction center subunit O; Provisional
Probab=100.00 E-value=7.5e-57 Score=341.09 Aligned_cols=115 Identities=67% Similarity=1.045 Sum_probs=109.9
Q ss_pred ccccccCccceeccccCCCCCCCccccccCcccCcccccchhhhhccCCCeeeeeccchhccccceeeeeeeeccccCCC
Q 033368 2 AAAAFASSSPVVGLGSSSLSSPKRTALGSSFVKSPVAARNPLRVAGACGGKVTCFERDWLRTDLNVIGFGLIGWLAPSSI 81 (121)
Q Consensus 2 ~aat~~~~stv~gl~~ssls~~~~~~l~s~f~~~~V~arnpl~~a~a~~gr~t~F~rdWlr~d~~V~~~gliGW~~PSsi 81 (121)
|||+|++++||+||+++++++ +.+++|||+|++|.+|||++++.+++++++ |||||||+|++||++|||||++||+|
T Consensus 1 maa~~~a~stV~gL~~~sl~~--~~~~ss~f~~~~~~~~~~~~~~~a~~~~~t-F~rDWLr~d~~V~~~gl~GW~~PS~i 77 (141)
T PLN00046 1 MAATAATASTVSGLGSSSLSA--PRRLSSGFVKGPVTVRRRAVLARASGSKKT-FDRDWLRKDLNVIGFGLIGWLAPSSI 77 (141)
T ss_pred ChHHHHhHHHhhhccccCccc--ccccccccccCcccccchhhhhhhcccccc-cchhhhhcccceeeeeeeeeeccccc
Confidence 566778888999999999986 678999999999999999999999999998 99999999999999999999999999
Q ss_pred cccCCCchhhhhHhhhhhhhcCCCCCCCCCCceeEEee
Q 033368 82 PAINGKSLTGLFFESIGTELAHFPTPPPLTSQFWSVHF 119 (121)
Q Consensus 82 pa~~g~SL~glF~~SIG~eLAhFPtgPal~d~FWL~~~ 119 (121)
|+||||||+|+|++|||+|||||||||+|||||||||+
T Consensus 78 pa~~g~sL~glF~~sIg~~LahfPt~Pal~~~fWL~li 115 (141)
T PLN00046 78 PAIGGNSLTGLFFDSIGTELAHFPTGPALDSKFWLWLI 115 (141)
T ss_pred cccCCchhHHHHHHHHHHHHhcCCCCCCCCcchHHHHH
Confidence 99999999999999999999999999999999999985
No 2
>TIGR03059 psaOeuk photosystem I protein PsaO. Members of this family are the PsaO protein of photosystem I. This protein is found in chloroplasts but not in Cyanobacteria.
Probab=99.98 E-value=9.1e-34 Score=200.15 Aligned_cols=55 Identities=51% Similarity=1.061 Sum_probs=53.4
Q ss_pred cceeeeeeeeccccC--CCcccCCCchhhhhHhhhhhhhcCCCCCCCCCCceeEEee
Q 033368 65 LNVIGFGLIGWLAPS--SIPAINGKSLTGLFFESIGTELAHFPTPPPLTSQFWSVHF 119 (121)
Q Consensus 65 ~~V~~~gliGW~~PS--sipa~~g~SL~glF~~SIG~eLAhFPtgPal~d~FWL~~~ 119 (121)
++||++|||||++|| +||+|||+||||+|++||||||||||||||+||||||||+
T Consensus 1 ~~V~~~gliGW~~Ps~~~ip~~~g~SLtglF~~sIg~~LAhFPt~Pal~~~fWL~li 57 (82)
T TIGR03059 1 APVAAIGFVGWVLPTVLNVPLYGGKSLTGLFASSIGENLAHFPAPPALDDPFWLLLF 57 (82)
T ss_pred CCceeEeeEEeeccccccccccCCchHHHHHHHHHHHHHhcCCCCCccCCchHHHHH
Confidence 489999999999999 9999999999999999999999999999999999999985
No 3
>PF07629 DUF1590: Protein of unknown function (DUF1590); InterPro: IPR011481 These hypothetical proteins in Rhodopirellula baltica have a conserved C-terminal region.
Probab=61.77 E-value=3.1 Score=25.55 Aligned_cols=13 Identities=54% Similarity=1.058 Sum_probs=10.7
Q ss_pred cCCCCCCCCCCce
Q 033368 102 AHFPTPPPLTSQF 114 (121)
Q Consensus 102 AhFPtgPal~d~F 114 (121)
|.|||+|+....|
T Consensus 16 a~fptppaa~a~f 28 (32)
T PF07629_consen 16 ARFPTPPAARAGF 28 (32)
T ss_pred cccCCChhhhhcc
Confidence 6899999987655
No 4
>PF03244 PSI_PsaH: Photosystem I reaction centre subunit VI; InterPro: IPR004928 Photosystem I, a membrane complex found in the chloroplasts of plants and cyanobacteria uses light energy to transfer electrons from plastocyanin to ferredoxin []. The electron transfer components of the photosystem include the primary electron donor chlorophyll P-700 and 5 electron acceptors: chlorophyll (A0), phylloquinone (A1) and three 4Fe-4S iron-sulphur centres, designated Fx, Fa and Fb. The role of this protein, subunit VI or PsaH, may be in docking of the light harvesting complex I antenna to the core complex.; GO: 0015979 photosynthesis, 0009522 photosystem I, 0009538 photosystem I reaction center; PDB: 2WSF_H 2WSE_H 2WSC_H 2O01_H.
Probab=52.23 E-value=4.7 Score=31.50 Aligned_cols=17 Identities=41% Similarity=0.538 Sum_probs=0.0
Q ss_pred ccCccceeccccCCCCC
Q 033368 6 FASSSPVVGLGSSSLSS 22 (121)
Q Consensus 6 ~~~~stv~gl~~ssls~ 22 (121)
..+.++|-||++||++-
T Consensus 5 ~~~~~~~~gla~ss~~g 21 (140)
T PF03244_consen 5 VQPTAAVKGLAGSSLSG 21 (140)
T ss_dssp -----------------
T ss_pred eeccccccccccccccc
Confidence 33445799999999994
No 5
>PF15017 AF1Q: Drug resistance and apoptosis regulator
Probab=43.24 E-value=7.5 Score=27.86 Aligned_cols=12 Identities=50% Similarity=1.043 Sum_probs=9.8
Q ss_pred eeccccCCCccc
Q 033368 73 IGWLAPSSIPAI 84 (121)
Q Consensus 73 iGW~~PSsipa~ 84 (121)
=||+-||||.-|
T Consensus 73 gGWITPsNIkqi 84 (87)
T PF15017_consen 73 GGWITPSNIKQI 84 (87)
T ss_pred Cccccchhhhhh
Confidence 399999999754
No 6
>smart00682 G2F G2 nidogen domain and fibulin.
Probab=32.44 E-value=16 Score=29.95 Aligned_cols=42 Identities=33% Similarity=0.343 Sum_probs=30.8
Q ss_pred cceeeeeeeeccccCCCc-ccCCCchhhhhHhhhhhhhcCCCCCC
Q 033368 65 LNVIGFGLIGWLAPSSIP-AINGKSLTGLFFESIGTELAHFPTPP 108 (121)
Q Consensus 65 ~~V~~~gliGW~~PSsip-a~~g~SL~glF~~SIG~eLAhFPtgP 108 (121)
+.+..+|.|||+-=-.++ +.||-+|||-=|...-+ -+||++-
T Consensus 58 ~l~~ig~~igWlFA~e~~~a~NGf~lTGG~F~~~s~--v~F~~ge 100 (227)
T smart00682 58 PLVPIGGTIGWLFAKEQGGAVNGFQLTGGVFTRETE--VTFAGGE 100 (227)
T ss_pred hhhhhccceeeeEEeccCCccccEEecCeEEEEEEE--EEECCCC
Confidence 356678899999777774 78999999977766543 3566654
No 7
>PLN00170 photosystem II light-harvesting-Chl-binding protein Lhcb6 (CP24); Provisional
Probab=31.30 E-value=16 Score=30.31 Aligned_cols=23 Identities=52% Similarity=0.566 Sum_probs=15.4
Q ss_pred cccccCccceeccccCCCCCCCcc
Q 033368 3 AAAFASSSPVVGLGSSSLSSPKRT 26 (121)
Q Consensus 3 aat~~~~stv~gl~~ssls~~~~~ 26 (121)
|.++ +++..+||+++.++-.+|.
T Consensus 2 a~s~-s~a~~~~~~ssf~~g~~~~ 24 (255)
T PLN00170 2 AAAT-SGAVLNGLGSSFLTGGKRS 24 (255)
T ss_pred chhh-hHHHHhhccCcccccchhh
Confidence 3334 3456899999999855544
No 8
>KOG1321 consensus Protoheme ferro-lyase (ferrochelatase) [Coenzyme transport and metabolism]
Probab=29.68 E-value=31 Score=30.76 Aligned_cols=23 Identities=39% Similarity=0.637 Sum_probs=20.3
Q ss_pred CCCchhhhhHhhhhhhhcCCCCC
Q 033368 85 NGKSLTGLFFESIGTELAHFPTP 107 (121)
Q Consensus 85 ~g~SL~glF~~SIG~eLAhFPtg 107 (121)
-...|-..|++.|-+||.|||.+
T Consensus 201 t~~glIkafA~~I~keL~~F~~~ 223 (395)
T KOG1321|consen 201 TREGLIKAFAENIEKELQTFPEP 223 (395)
T ss_pred ccchHHHHHHHHHHHHHHhcCCc
Confidence 45668899999999999999987
No 9
>PLN00074 photosystem II D2 protein (PsbD); Provisional
Probab=21.66 E-value=37 Score=29.95 Aligned_cols=17 Identities=47% Similarity=1.032 Sum_probs=12.2
Q ss_pred eccchhccccceeeeeeeecc
Q 033368 56 FERDWLRTDLNVIGFGLIGWL 76 (121)
Q Consensus 56 F~rdWlr~d~~V~~~gliGW~ 76 (121)
--|||||+|--| .|||.
T Consensus 18 ~~dd~~~~drf~----yiGw~ 34 (353)
T PLN00074 18 IMDDWLRRDRFV----FVGWS 34 (353)
T ss_pred hhhhhhhhccEE----EechH
Confidence 348999999755 45664
No 10
>PF07474 G2F: G2F domain; InterPro: IPR006605 Basement membranes are sheet-like extracellular matrices found at the basal surfaces of epithelia and condensed mesenchyma. By preventing cell mixing and providing a cell-adhesive substrate, they play crucial roles in tissue development and function. Basement menbranes are composed of an evolutionarily ancient set of large glycoproteins, which includes members of the laminin family, collagen IV, perlecan and nidogen/entactin. Nidogen/entactin is an important basement membrane component, which promotes cell attachment, neutrophil chemotaxis, trophoblast outgrowth, and angiogenesis. It consists of three globular regions, G1-G3. G1 and G2 are connected by a thread-like structure, whereas that between G2 and G3 is rod-like [, ]. The nidogen G2 region binds to collagen IV and perlecan. The nidogen G2 structure is composed of two domains, an N-terminal EGF-like domain and a much larger beta-barrel domain of ~230 residues. The nidogen G2 beta-barrel consists of an 11-stranded beta-barrel of complex topology, the interior of which is traversed by the hydrophobic, predominantly alpha helical segment connecting strands C and D. The N-terminal half of the barrel comprises two beta-meanders (strands A-C and D-F) linked by the buried alpha-helical segment. The polypeptide chain then crosses the bottom of the barrel and forms a five-stranded Greek key motif in the C- terminal half of the domain. Helix alpha3 caps the top of the barrel and forms the interface to the EGF-like domain. The nidogen G2 beta-barrel domain has unexpected structural similarity to green fluorescent protein, suggesting that they derive from a common ancestor. A large surface patch on the barrel surface is strikingly conserved in all metazoan nidogens. Site-directed mutagenesis demonstrates that the conserved residues in the conserved patch are involved in the binding of perlecan, and possibly also of collagen IV [].; PDB: 1GL4_A 1H4U_A.
Probab=21.21 E-value=9.1 Score=30.35 Aligned_cols=31 Identities=45% Similarity=0.390 Sum_probs=19.2
Q ss_pred cceeeeeeeeccccCCCc-ccCCCchhhhhHh
Q 033368 65 LNVIGFGLIGWLAPSSIP-AINGKSLTGLFFE 95 (121)
Q Consensus 65 ~~V~~~gliGW~~PSsip-a~~g~SL~glF~~ 95 (121)
+.+...+.|||+-=-.+| +.||-||||-=|.
T Consensus 58 ~L~~ig~~igWlfA~e~~~a~NGfslTGG~F~ 89 (192)
T PF07474_consen 58 PLVPIGGPIGWLFAKEQGGAQNGFSLTGGEFN 89 (192)
T ss_dssp T-THHHHHHHHHT-EE-TT---HHHHHTTEEE
T ss_pred HHHHhhhheeeeEEeccCCccCceeeeccEEE
Confidence 355678999999766665 8899999986443
No 11
>PF15128 T_cell_tran_alt: T-cell leukemia translocation-altered
Probab=20.90 E-value=9.4 Score=28.10 Aligned_cols=41 Identities=29% Similarity=0.708 Sum_probs=32.1
Q ss_pred eeccchhccccceeeee-eeeccccCCCc-----ccCCCchhhhhHh
Q 033368 55 CFERDWLRTDLNVIGFG-LIGWLAPSSIP-----AINGKSLTGLFFE 95 (121)
Q Consensus 55 ~F~rdWlr~d~~V~~~g-liGW~~PSsip-----a~~g~SL~glF~~ 95 (121)
.|.+||+-.|..|..|= |+||++=|-+- -+-|++.+++|-.
T Consensus 13 ef~~dW~a~Dmrv~ifkllL~WlvlsLl~I~lAWk~yG~TV~dmyyR 59 (92)
T PF15128_consen 13 EFVDDWEANDMRVQIFKLLLGWLVLSLLAIHLAWKVYGNTVNDMYYR 59 (92)
T ss_pred HHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccceeC
Confidence 49999999999998875 57999887663 2367788887753
No 12
>cd00255 nidG2 Nidogen, G2 domain; Nidogen is an important component of the basement membrane, an extracellular sheet-like matrix. Nidogen is a multifunctional protein that interacts with many other basement membrane proteins, like collagen, perlecan, lamin, and has a potential role in the assembly and connection of networks. Nidogen consists of 3 globular domains (G1-G3), G3 is the lamin-binding domain, while G2 binds collagen IV and perlecan. Also found in hemicentin, a protein which functions at various cell-cell and cell-matrix junctions and might assist in refining broad regions of cell contact into oriented, line-shaped junctions. Nidogen G2 consists of an N-terminal EGF-like domain (excluded from this alignment model) and an 11-stranded beta-barrel with a central helix, a topology that exhibits high structural similarity to the green flourescent proteins of Cnidaria.
Probab=20.84 E-value=33 Score=27.99 Aligned_cols=32 Identities=41% Similarity=0.317 Sum_probs=24.1
Q ss_pred cceeeeeeeeccccCCCc-ccCCCchhhhhHhh
Q 033368 65 LNVIGFGLIGWLAPSSIP-AINGKSLTGLFFES 96 (121)
Q Consensus 65 ~~V~~~gliGW~~PSsip-a~~g~SL~glF~~S 96 (121)
+.+...|.|||+-=-.+| +.||=||||-=|..
T Consensus 56 ~l~~ig~~igWlFA~e~~~~~NGfslTGG~F~~ 88 (224)
T cd00255 56 PLAPIGGTIGWLFALEQGGAKNGFSLTGGEFTR 88 (224)
T ss_pred hhhhhcCceeeEEEeecCCccCcEeccCceEEE
Confidence 356678999999755555 77999999865543
Done!