Query psy2035
Match_columns 141
No_of_seqs 119 out of 554
Neff 3.5
Searched_HMMs 46136
Date Fri Aug 16 22:36:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2035.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2035hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02412 TSP_3: Thrombospondin 99.3 5.8E-13 1.3E-17 82.5 1.1 36 13-48 1-36 (36)
2 PF02412 TSP_3: Thrombospondin 98.0 3.2E-06 6.9E-11 52.4 1.7 33 27-75 2-34 (36)
3 KOG4231|consensus 31.2 30 0.00066 33.5 1.8 52 56-115 523-583 (763)
4 PRK08351 DNA-directed RNA poly 27.9 52 0.0011 22.7 2.1 26 68-94 17-42 (61)
5 KOG2843|consensus 27.7 36 0.00079 30.8 1.6 35 84-118 299-333 (420)
6 PF05901 Excalibur: Excalibur 25.9 41 0.00089 20.4 1.2 10 12-21 26-35 (37)
7 PF11154 DUF2934: Protein of u 23.5 52 0.0011 20.5 1.3 18 99-116 19-36 (40)
8 PRK06393 rpoE DNA-directed RNA 18.3 84 0.0018 21.9 1.6 27 67-94 18-44 (64)
9 PF11028 DUF2723: Protein of u 14.2 73 0.0016 25.5 0.5 21 97-117 86-106 (178)
10 COG2093 DNA-directed RNA polym 13.3 1.3E+02 0.0027 21.2 1.5 26 69-95 21-46 (64)
No 1
>PF02412 TSP_3: Thrombospondin type 3 repeat; InterPro: IPR003367 Thrombospondins are multimeric multidomain glycoproteins that function at cell surfaces and in the extracellular matrix milieu. They act as regulators of cell interactions in vertebrates. They are divided into two subfamilies, A and B, according to their overall molecular organisation. The subgroup A proteins TSP-1 and -2 contain an N-terminal domain, a VWFC domain, three TSP1 repeats, three EGF-like domains, TSP3 repeats and a C-terminal domain. They are assembled as trimer. The subgroup B thrombospondins, designated TSP-3, -4, and COMP (cartilage oligomeric matrix protein, also designated TSP-5) are distinct in that they contain unique N-terminal regions, lack the VWFC domain and TSP1 repeats, contain four copies of EGF-like domains, and are assembled as pentamers []. EGF, TSP3 repeats and the C-terminal domain are thus the hallmark of a thrombospondin. This entry represents the type 3 thrombospondin repeat, and related repeats present in other types of protein.; GO: 0005509 calcium ion binding, 0007155 cell adhesion; PDB: 1UX6_A 3FBY_C 1YO8_A 2RHP_A.
Probab=99.30 E-value=5.8e-13 Score=82.50 Aligned_cols=36 Identities=56% Similarity=0.957 Sum_probs=31.1
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy2035 13 LDNDRDGKGDECDPDLDGDGISNDEDNCRLIYNPNQ 48 (141)
Q Consensus 13 ~DtD~DGiGDaCD~D~DgDGI~D~~DnCP~v~Np~Q 48 (141)
.|+|+|||||+|+.|.|+|||+|..||||+++|+.|
T Consensus 1 ~D~D~dg~GD~C~~D~D~Dgi~d~~DnCP~~~n~~Q 36 (36)
T PF02412_consen 1 EDSDGDGIGDACDDDSDGDGIPDACDNCPNVPNPDQ 36 (36)
T ss_dssp --TTSSSS-GGGSSSTTSSSS-GGGHSSTTSTTTTS
T ss_pred CcccCCCCCcccccCCCCCcccCcccCCCCCCCCCC
Confidence 489999999999999999999999999999999986
No 2
>PF02412 TSP_3: Thrombospondin type 3 repeat; InterPro: IPR003367 Thrombospondins are multimeric multidomain glycoproteins that function at cell surfaces and in the extracellular matrix milieu. They act as regulators of cell interactions in vertebrates. They are divided into two subfamilies, A and B, according to their overall molecular organisation. The subgroup A proteins TSP-1 and -2 contain an N-terminal domain, a VWFC domain, three TSP1 repeats, three EGF-like domains, TSP3 repeats and a C-terminal domain. They are assembled as trimer. The subgroup B thrombospondins, designated TSP-3, -4, and COMP (cartilage oligomeric matrix protein, also designated TSP-5) are distinct in that they contain unique N-terminal regions, lack the VWFC domain and TSP1 repeats, contain four copies of EGF-like domains, and are assembled as pentamers []. EGF, TSP3 repeats and the C-terminal domain are thus the hallmark of a thrombospondin. This entry represents the type 3 thrombospondin repeat, and related repeats present in other types of protein.; GO: 0005509 calcium ion binding, 0007155 cell adhesion; PDB: 1UX6_A 3FBY_C 1YO8_A 2RHP_A.
Probab=97.99 E-value=3.2e-06 Score=52.38 Aligned_cols=33 Identities=33% Similarity=0.458 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCCcCCCCCCCCCc
Q psy2035 27 DLDGDGISNDEDNCRLIYNPNQDDSDAHYNADLILMRQVMAWAMYVTKI 75 (141)
Q Consensus 27 D~DgDGI~D~~DnCP~v~Np~Q~DsD~DGDgDGV~~~D~~D~CP~~~~~ 75 (141)
|.|+|||.+ .| +.|.|+|||+ |..|+||.++++
T Consensus 2 D~D~dg~GD---~C-----------~~D~D~Dgi~--d~~DnCP~~~n~ 34 (36)
T PF02412_consen 2 DSDGDGIGD---AC-----------DDDSDGDGIP--DACDNCPNVPNP 34 (36)
T ss_dssp -TTSSSS-G---GG-----------SSSTTSSSS---GGGHSSTTSTTT
T ss_pred cccCCCCCc---cc-----------ccCCCCCccc--CcccCCCCCCCC
Confidence 778999976 44 2234668899 999999999997
No 3
>KOG4231|consensus
Probab=31.15 E-value=30 Score=33.52 Aligned_cols=52 Identities=25% Similarity=0.469 Sum_probs=36.0
Q ss_pred CCCccccCCcCCCCCCCCCcccccc---------ccCCceEEeccCCcchhhhhhccccchhhHHHHhh
Q psy2035 56 NADLILMRQVMAWAMYVTKISTKME---------LRTYQMCVLTILSSTELTSGFMAGFSHSYWTQAQR 115 (141)
Q Consensus 56 DgDGV~~~D~~D~CP~~~~~~~~tD---------fr~yQ~V~Ldp~~~~~l~~~~~~~~~~~~~~~~~~ 115 (141)
|+|-|. .-+.-+||.++.+|+... ||+|| .|.+. -|-||||--|-.|+..+.
T Consensus 523 d~~mi~-tsr~~~~PkvavVStiVn~~pT~qpfIFRNY~----hp~G~---~Shy~Ggc~h~~WqAIrA 583 (763)
T KOG4231|consen 523 DGDMII-TSRVKNVPKVAVVSTIVNVMPTAQPFIFRNYQ----HPVGT---QSHYMGGCKHQVWQAIRA 583 (763)
T ss_pred hhhHHH-hhccCCCCceeehhhhhhcCCCccceeeeccC----CCCCc---chhhcccchHHHHHHHHh
Confidence 444444 236678888877654333 89998 45554 688999999999976543
No 4
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=27.92 E-value=52 Score=22.67 Aligned_cols=26 Identities=8% Similarity=-0.046 Sum_probs=17.3
Q ss_pred CCCCCCCccccccccCCceEEeccCCc
Q psy2035 68 WAMYVTKISTKMELRTYQMCVLTILSS 94 (141)
Q Consensus 68 ~CP~~~~~~~~tDfr~yQ~V~Ldp~~~ 94 (141)
.||.=......+++.+ .+|+|||+.|
T Consensus 17 ~CP~Cgs~~~T~~W~G-~viI~dPe~S 42 (61)
T PRK08351 17 RCPVCGSRDLSDEWFD-LVIIIDVENS 42 (61)
T ss_pred cCCCCcCCcccccccc-EEEEeCCcHh
Confidence 5776665523556888 4567999965
No 5
>KOG2843|consensus
Probab=27.69 E-value=36 Score=30.76 Aligned_cols=35 Identities=23% Similarity=0.213 Sum_probs=27.1
Q ss_pred CceEEeccCCcchhhhhhccccchhhHHHHhhccc
Q psy2035 84 YQMCVLTILSSTELTSGFMAGFSHSYWTQAQRNKK 118 (141)
Q Consensus 84 yQ~V~Ldp~~~~~l~~~~~~~~~~~~~~~~~~~~~ 118 (141)
--.|.|.|++.+|-..=-..-|-|-|||-.|.-..
T Consensus 299 NL~Vslkpeg~~~~a~icKsNFKhlYWT~lQQlaH 333 (420)
T KOG2843|consen 299 NLEVSLKPEGQNEDALICKSNFKHLYWTPLQQLAH 333 (420)
T ss_pred eeEEEeccCCccccceeecccchhhhhhHHHHhhh
Confidence 35678999988886666677899999998886543
No 6
>PF05901 Excalibur: Excalibur calcium-binding domain; InterPro: IPR008613 Extracellular Ca2+-dependent nuclease YokF from Bacillus subtilis and several other surface-exposed proteins from diverse bacteria are encoded in the genomes in two paralogous forms that differ by a ~45 amino acid fragment, which comprises a novel conserved domain. Sequence analysis of this domain revealed a conserved DxDxDGxxCE motif, which is strikingly similar to the Ca2+-binding loop of the calmodulin-like EF-hand domains, suggesting an evolutionary relationship between them. Functions of many of the other proteins in which the novel domain, named Excalibur (extracellular calcium-binding region), is found, as well as a structural model of its conserved motif are consistent with the notion that the Excalibur domain binds calcium. This domain is but one more example of the diversity of structural contexts surrounding the EF-hand-like calcium-binding loop in bacteria. This loop is thus more widespread than hitherto recognised and the evolution of EF-hand-like domains is probably more complex than previously appreciated [].
Probab=25.90 E-value=41 Score=20.44 Aligned_cols=10 Identities=50% Similarity=0.797 Sum_probs=7.0
Q ss_pred CCCCCCCCCC
Q psy2035 12 QLDNDRDGKG 21 (141)
Q Consensus 12 Q~DtD~DGiG 21 (141)
.+|.|+|||+
T Consensus 26 ~LDrD~DGia 35 (37)
T PF05901_consen 26 KLDRDGDGIA 35 (37)
T ss_pred cccCCCCCCc
Confidence 5777777773
No 7
>PF11154 DUF2934: Protein of unknown function (DUF2934); InterPro: IPR021327 This bacterial family of proteins has no known function.
Probab=23.51 E-value=52 Score=20.45 Aligned_cols=18 Identities=28% Similarity=0.497 Sum_probs=15.4
Q ss_pred hhhccccchhhHHHHhhc
Q psy2035 99 SGFMAGFSHSYWTQAQRN 116 (141)
Q Consensus 99 ~~~~~~~~~~~~~~~~~~ 116 (141)
.|+..|-.+.||.+|.+.
T Consensus 19 ~G~p~G~~~~~W~~AE~e 36 (40)
T PF11154_consen 19 RGRPEGRDEEDWLEAERE 36 (40)
T ss_pred cCCCCCCcHHHHHHHHHH
Confidence 588889999999999764
No 8
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=18.25 E-value=84 Score=21.92 Aligned_cols=27 Identities=11% Similarity=-0.130 Sum_probs=17.8
Q ss_pred CCCCCCCCccccccccCCceEEeccCCc
Q psy2035 67 AWAMYVTKISTKMELRTYQMCVLTILSS 94 (141)
Q Consensus 67 D~CP~~~~~~~~tDfr~yQ~V~Ldp~~~ 94 (141)
+.||.=....+..+|.+|-.| +||+.|
T Consensus 18 ~~Cp~Cgs~~~S~~w~G~v~i-~dPe~S 44 (64)
T PRK06393 18 KTCPVHGDEKTTTEWFGFLII-TEPEGS 44 (64)
T ss_pred CcCCCCCCCcCCcCcceEEEE-ECCchh
Confidence 356665555346678887655 799965
No 9
>PF11028 DUF2723: Protein of unknown function (DUF2723); InterPro: IPR021280 This family is conserved in bacteria. The function is not known.
Probab=14.21 E-value=73 Score=25.51 Aligned_cols=21 Identities=33% Similarity=0.607 Sum_probs=15.3
Q ss_pred hhhhhccccchhhHHHHhhcc
Q psy2035 97 LTSGFMAGFSHSYWTQAQRNK 117 (141)
Q Consensus 97 l~~~~~~~~~~~~~~~~~~~~ 117 (141)
|..++.-+||.++|.||-..+
T Consensus 86 lv~al~fafS~sfW~~Av~aE 106 (178)
T PF11028_consen 86 LVGALAFAFSDSFWFQAVEAE 106 (178)
T ss_pred HHHHHHHHhhHHHHHHHHHHH
Confidence 444566679999999986543
No 10
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=13.30 E-value=1.3e+02 Score=21.24 Aligned_cols=26 Identities=8% Similarity=-0.109 Sum_probs=16.4
Q ss_pred CCCCCCccccccccCCceEEeccCCcc
Q psy2035 69 AMYVTKISTKMELRTYQMCVLTILSST 95 (141)
Q Consensus 69 CP~~~~~~~~tDfr~yQ~V~Ldp~~~~ 95 (141)
||.=...+...++++|- |++||+.|+
T Consensus 21 CP~Cgs~~~te~W~G~~-iIidpe~Se 46 (64)
T COG2093 21 CPVCGSTDLTEEWFGLL-IIIDPEKSE 46 (64)
T ss_pred CCCCCCcccchhhccEE-EEEcCcHHH
Confidence 77655543345567764 459998753
Done!