Query psy4124
Match_columns 99
No_of_seqs 111 out of 499
Neff 6.0
Searched_HMMs 46136
Date Fri Aug 16 17:35:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4124.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4124hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2104|consensus 100.0 3.4E-36 7.4E-41 205.2 9.2 92 4-98 1-126 (126)
2 cd00780 NTF2 Nuclear transport 99.9 3.4E-27 7.4E-32 158.4 10.1 85 8-95 1-119 (119)
3 KOG0116|consensus 99.9 5.2E-25 1.1E-29 176.3 8.2 90 3-95 7-134 (419)
4 PF02136 NTF2: Nuclear transpo 99.9 2.9E-23 6.3E-28 137.2 6.8 80 12-93 1-118 (118)
5 KOG4353|consensus 99.8 2.1E-20 4.5E-25 129.5 4.6 86 7-95 10-136 (139)
6 cd00531 NTF2_like Nuclear tran 98.2 1.9E-05 4.1E-10 49.6 7.8 78 14-93 2-123 (124)
7 TIGR02246 conserved hypothetic 96.7 0.034 7.5E-07 35.9 9.2 48 12-61 5-53 (128)
8 PF10429 Mtr2: Nuclear pore RN 96.6 0.0016 3.5E-08 47.1 2.4 50 11-61 5-57 (166)
9 PF13474 SnoaL_3: SnoaL-like d 96.5 0.017 3.7E-07 36.8 6.8 74 14-89 2-114 (121)
10 KOG3763|consensus 95.3 0.1 2.2E-06 44.1 7.7 38 6-45 334-371 (585)
11 PF12680 SnoaL_2: SnoaL-like d 95.1 0.02 4.2E-07 34.8 2.5 43 17-61 1-43 (102)
12 PF14534 DUF4440: Domain of un 94.0 0.31 6.8E-06 29.9 6.0 45 15-61 3-47 (107)
13 cd00781 ketosteroid_isomerase 93.7 0.97 2.1E-05 29.0 8.2 47 13-61 5-53 (122)
14 PF15008 DUF4518: Domain of un 89.8 1.7 3.8E-05 33.6 6.8 86 7-94 125-259 (262)
15 COG4875 Uncharacterized protei 86.6 9.3 0.0002 27.0 8.8 81 6-89 33-147 (156)
16 PF13577 SnoaL_4: SnoaL-like d 86.0 1.8 3.9E-05 27.6 4.3 48 12-61 8-58 (127)
17 PF08332 CaMKII_AD: Calcium/ca 82.6 9.5 0.00021 26.3 6.9 50 10-61 3-54 (128)
18 TIGR02096 conserved hypothetic 80.6 3.4 7.3E-05 26.6 3.9 44 16-61 3-48 (129)
19 COG4319 Ketosteroid isomerase 80.4 6.9 0.00015 27.6 5.6 62 28-89 26-127 (137)
20 PF07080 DUF1348: Protein of u 77.2 2.4 5.2E-05 30.0 2.5 54 6-61 5-58 (143)
21 PF11533 DUF3225: Protein of u 73.5 28 0.0006 24.2 8.6 51 9-61 9-60 (125)
22 PRK09636 RNA polymerase sigma 52.0 32 0.0007 25.9 4.5 48 12-61 172-227 (293)
23 PRK08241 RNA polymerase factor 49.7 32 0.00069 26.3 4.3 49 11-61 214-264 (339)
24 PF12893 Lumazine_bd_2: Putati 45.9 60 0.0013 20.8 4.6 76 14-91 7-115 (116)
25 TIGR02960 SigX5 RNA polymerase 42.2 45 0.00099 25.1 4.0 48 12-61 205-254 (324)
26 COG3558 Uncharacterized protei 41.8 25 0.00054 24.7 2.3 54 6-61 7-60 (154)
27 COG2827 Predicted endonuclease 35.5 14 0.00031 24.5 0.3 26 74-99 7-35 (95)
28 PF07366 SnoaL: SnoaL-like pol 30.1 52 0.0011 21.0 2.3 42 18-61 5-47 (126)
29 PF09053 CagZ: CagZ; InterPro 29.9 72 0.0016 22.9 3.1 31 3-33 18-48 (199)
30 PF12636 DUF3781: Protein of u 27.4 10 0.00022 24.0 -1.4 44 52-95 13-62 (73)
31 PF12642 TpcC: Conjugative tra 27.1 26 0.00056 25.4 0.5 25 12-38 2-31 (232)
32 PF06851 DUF1247: Protein of u 21.7 53 0.0012 23.4 1.2 13 15-27 93-105 (148)
33 PF08804 gp32: gp32 DNA bindin 20.7 47 0.001 22.0 0.7 33 56-88 17-50 (94)
No 1
>KOG2104|consensus
Probab=100.00 E-value=3.4e-36 Score=205.21 Aligned_cols=92 Identities=49% Similarity=0.881 Sum_probs=88.1
Q ss_pred CCCccHHHHHHHHHHHHHHhccCCCChhhhhhhccCCCceeeEcCceeccHHHHHhhh----------------------
Q psy4124 4 QLNPAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGIQLQGAVKIMEKF---------------------- 61 (99)
Q Consensus 4 ~~~p~~~~ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~eg~~~~G~~~I~~kl---------------------- 61 (99)
+++|.+++||++||+|||++|| .+|..|..+|.++ |+|||||++++|+++|+|||
T Consensus 1 ~~d~~~e~v~~~FvqhYY~~FD--~dR~ql~~lY~~~-S~LTfEGqq~qG~~~IveKl~sLpFqkiqh~IttvD~QPt~~ 77 (126)
T KOG2104|consen 1 SLDPVYEAVAKAFVQHYYSLFD--NDRSQLGALYIDT-SMLTFEGQQIQGKDAIVEKLTSLPFQKIQHSITTVDSQPTPD 77 (126)
T ss_pred CCCccHHHHHHHHHHHHHHHhc--CchhHhhhhhccc-ceeeEcchhhcchHHHHHHHhcCChhhhhceeeecccccCCC
Confidence 4678999999999999999999 9999999999999 99999999999999999999
Q ss_pred -----------hcCCCCCeeEEEEEEEEee-CCEEEEEcceEeeecCCC
Q psy4124 62 -----------NCDDDPPHAYSQIFVLKPL-GASFYCQHDIFRLGIHDT 98 (99)
Q Consensus 62 -----------~~d~~~~~~F~QtF~L~~~-~~~y~v~NDifR~~~~n~ 98 (99)
++||+||.+|+|+|+|.|. +|+|||.||||||.+||+
T Consensus 78 g~ilv~V~G~Lk~dEd~~~~FsQvF~L~~n~~~~~~v~ndiFRLn~~n~ 126 (126)
T KOG2104|consen 78 GGILVMVVGQLKLDEDPILRFSQVFLLKPNIQGSYYVFNDIFRLNLHNS 126 (126)
T ss_pred CcEEEEEeeeeeeccCCccceeeEEEEeEcCCCCEEEEeeeEEEecccC
Confidence 7889999999999999988 499999999999999996
No 2
>cd00780 NTF2 Nuclear transport factor 2 (NTF2) domain plays an important role in the trafficking of macromolecules, ions and small molecules between the cytoplasm and nucleus. This bi-directional transport of macromolecules across the nuclear envelope requires many soluble factors that includes GDP-binding protein Ran (RanGDP). RanGDP is required for both import and export of proteins and poly(A) RNA. RanGDP also has been implicated in cell cycle control, specifically in mitotic spindle assembly. In interphase cells, RanGDP is predominately nuclear and thought to be GTP bound, but it is also present in the cytoplasm, probably in the GDP-bound state. NTF2 mediates the nuclear import of RanGDP. NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins.
Probab=99.95 E-value=3.4e-27 Score=158.36 Aligned_cols=85 Identities=40% Similarity=0.737 Sum_probs=79.2
Q ss_pred cHHHHHHHHHHHHHHhccCCCChhhhhhhccCCCceeeEcC-ceeccHHHHHhhh-------------------------
Q psy4124 8 AYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEG-IQLQGAVKIMEKF------------------------- 61 (99)
Q Consensus 8 ~~~~ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~eg-~~~~G~~~I~~kl------------------------- 61 (99)
.+++||++||++||++|+ ++|+.|++||.++ |+++|+| ..+.|.++|.++|
T Consensus 1 ~~~~v~~~Fv~~YY~~l~--~~~~~L~~fY~~~-s~~~~~~~~~~~g~~~I~~~l~~lp~~~~~~~i~~~d~q~~~~~~i 77 (119)
T cd00780 1 SAEDVAKAFVQQYYSIFD--NNREGLHRLYGDT-SMLSREGMKQVTGRDAIVEKLSSLPFQKTKHKITTVDSQPTPSGGV 77 (119)
T ss_pred CHHHHHHHHHHHHHHHHh--cCHHHHHhhcCCC-cEEEECCceEecCHHHHHHHHHhCCCcceEEEEEEEeeeEcCCCCE
Confidence 368999999999999999 9999999999999 9999999 9999999999988
Q ss_pred --------hcCCCCCeeEEEEEEEEeeCCEEEEEcceEeeec
Q psy4124 62 --------NCDDDPPHAYSQIFVLKPLGASFYCQHDIFRLGI 95 (99)
Q Consensus 62 --------~~d~~~~~~F~QtF~L~~~~~~y~v~NDifR~~~ 95 (99)
+.+++++++|+|+|+|++++++|+|.|||||++.
T Consensus 78 li~V~G~~~~~~~~~~~F~q~F~L~~~~~~~~I~nD~fr~~~ 119 (119)
T cd00780 78 IVMVTGSLKLDEQPPRKFSQTFVLAPQNGGYFVLNDIFRFVD 119 (119)
T ss_pred EEEEEEEEEECCCCceeEeEEEEEEecCCeEEEEeeEEEecC
Confidence 3345789999999999999999999999999973
No 3
>KOG0116|consensus
Probab=99.92 E-value=5.2e-25 Score=176.30 Aligned_cols=90 Identities=30% Similarity=0.541 Sum_probs=82.0
Q ss_pred CCCCccHHHHHHHHHHHHHHhccCCCChhhhhhhccCCCceeeEcCc-----eeccHHHHHhhh----------------
Q psy4124 3 SQLNPAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGI-----QLQGAVKIMEKF---------------- 61 (99)
Q Consensus 3 ~~~~p~~~~ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~eg~-----~~~G~~~I~~kl---------------- 61 (99)
.++.|+++.||++||++||++|. +.|+.||+||.++ |.||+.|. .+.|.++|++++
T Consensus 7 ~~~~~~~~~vg~~Fv~qYY~~L~--~~P~~lhrfY~~~-S~ltr~~~dg~m~s~t~~~~I~~~i~sld~~~~s~eI~tvd 83 (419)
T KOG0116|consen 7 LSPVPTPQLVGNEFVRQYYNVLQ--NSPSKLHRFYMDD-SVLTRPGLDGKMVSVTGLEAIHEKIMSLDYEVCSVEISTVD 83 (419)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHh--hChHHHHHHhhcc-ceeeccCCCCceEEEecHHHhhhheeecCCCceeEEEEEEe
Confidence 35678999999999999999999 9999999999999 99999773 689999999988
Q ss_pred -----------------hcCCCCCeeEEEEEEEEeeCCEEEEEcceEeeec
Q psy4124 62 -----------------NCDDDPPHAYSQIFVLKPLGASFYCQHDIFRLGI 95 (99)
Q Consensus 62 -----------------~~d~~~~~~F~QtF~L~~~~~~y~v~NDifR~~~ 95 (99)
...+.+.|+|+|||+|+|++++|||+||||||+.
T Consensus 84 sQ~S~~~GvvI~VtG~lt~~~~~rRkF~QtFfLapq~~~yfVlNDiFRfvd 134 (419)
T KOG0116|consen 84 SQASLEKGVVIMVTGYLTNKDGPRRKFSQTFFLAPQEKGYFVLNDIFRFVD 134 (419)
T ss_pred hhhhccCCeEEEEEEEEEeCCCcceEEEEEEEEeecCCceEEEechhhhcc
Confidence 3345778899999999999999999999999998
No 4
>PF02136 NTF2: Nuclear transport factor 2 (NTF2) domain; InterPro: IPR002075 Nuclear transport factor 2 (NTF2) is a homodimer which stimulates efficient nuclear import of a cargo protein. NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins. NTF2 folds into a cone with a deep hydrophobic cavity, the opening of which is surrounded by several negatively charged residues. RanGDP binds to NTF2 by inserting a conserved phenylalanine residue into the hydrophobic pocket of NTF2 and making electrostatic interactions with the conserved negatively charged residues that surround the cavity []. This entry represent the main structural domain of NTF2 and related domains which are found in other nuclear import proteins.; GO: 0006810 transport, 0005622 intracellular; PDB: 3UJM_B 1JKG_B 1JN5_B 1M98_A 3MG1_A 3MG2_A 3MG3_B 2Z76_A 2Z7A_D 2Z77_A ....
Probab=99.89 E-value=2.9e-23 Score=137.21 Aligned_cols=80 Identities=43% Similarity=0.827 Sum_probs=71.5
Q ss_pred HHHHHHHHHHHhccCCC-ChhhhhhhccCCCceeeEcCc-eeccHHHHHhhh----------------------------
Q psy4124 12 IGKGFVQQYYALFDDPA-QRPNLINMYNTETSFMTFEGI-QLQGAVKIMEKF---------------------------- 61 (99)
Q Consensus 12 ig~~FV~~YY~~~d~~~-~r~~L~~~Y~~~~S~lt~eg~-~~~G~~~I~~kl---------------------------- 61 (99)
||+.||++||+.|| + +|+.|++||.+++|.++|+|+ .+.|.++|.+++
T Consensus 1 v~~~Fv~~Yy~~~d--~~~~~~L~~~Y~~~~s~~~~~~~~~~~G~~~I~~~~~~l~~~~~~~~i~~~d~qp~~~~~~~i~ 78 (118)
T PF02136_consen 1 VANSFVQQYYQLFD--SGDREGLHKLYHDDASFLTWNGNRPVVGREAIQEFFQSLPATGVQHRITSVDCQPSPSSDGSIL 78 (118)
T ss_dssp HHHHHHHHHHHHHH--HTHGGGGGGGEEEEEEEEEETTECEEESHHHHHHHHHHHTTSSEEEEEEEEEEEEEEECCSEEE
T ss_pred CHHHHHHHHHHHHc--cCCHHHHHHHHcCCCeeecCCCchhhhhHHHHHHHHhcCCCcccEEEecccccccccccCCcEE
Confidence 79999999999999 7 999999999444499999999 999999999998
Q ss_pred -------hcCCCC-CeeEEEEEEEEeeCCEEEEEcceEee
Q psy4124 62 -------NCDDDP-PHAYSQIFVLKPLGASFYCQHDIFRL 93 (99)
Q Consensus 62 -------~~d~~~-~~~F~QtF~L~~~~~~y~v~NDifR~ 93 (99)
+.++.+ +++|+|+|+|.|.+++|+|.||||||
T Consensus 79 i~v~G~~~~~~~~~~~~F~q~FvL~~~~~~~~I~nd~~r~ 118 (118)
T PF02136_consen 79 ITVTGQFKEDDNPNPRRFSQTFVLVPQNNGYFIANDIFRF 118 (118)
T ss_dssp EEEEEEEEETTSEEEEEEEEEEEEEEETTEEEEEEEEEEE
T ss_pred EEEEeEEEecCCCcccEEEEEEEEEEcCCEEEEEeeEEEC
Confidence 233343 68999999999999999999999997
No 5
>KOG4353|consensus
Probab=99.81 E-value=2.1e-20 Score=129.48 Aligned_cols=86 Identities=22% Similarity=0.415 Sum_probs=79.1
Q ss_pred ccHHHHHHHHHHHHHHhccCCCChhhhhhhccCCCceeeEcCceeccHHHHHhhh-------------------------
Q psy4124 7 PAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGIQLQGAVKIMEKF------------------------- 61 (99)
Q Consensus 7 p~~~~ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~eg~~~~G~~~I~~kl------------------------- 61 (99)
.++...|++||+.||..+| ++|..|.+||.++ |.+.|||++++|.+.|.+.+
T Consensus 10 es~cr~A~eFv~~YY~smD--~rR~~i~rlY~~~-atlvWNGn~v~g~esls~ff~~LPsS~~qi~~lD~Qpv~dqat~~ 86 (139)
T KOG4353|consen 10 ESACRAAEEFVNVYYSSMD--KRRRGIGRLYLDN-ATLVWNGNPVSGTESLSEFFNMLPSSEFQINDLDCQPVHDQATGS 86 (139)
T ss_pred HHHHHHHHHHHHHHHHHHH--HHHHHhHHHhhcc-ceEEEcCCcchhHHHHHHHHHhCCCccccccccccccchhhcccc
Confidence 4677889999999999999 9999999999999 99999999999999999887
Q ss_pred ------------hcCCCCCeeEEEEEEEEeeCCEEE----EEcceEeeec
Q psy4124 62 ------------NCDDDPPHAYSQIFVLKPLGASFY----CQHDIFRLGI 95 (99)
Q Consensus 62 ------------~~d~~~~~~F~QtF~L~~~~~~y~----v~NDifR~~~ 95 (99)
+.|++.+|.|.|||+|..+++.|- |.+||||+..
T Consensus 87 q~~vLvvvsGtVkFdG~k~r~F~qt~ll~~e~~~~k~~~~v~Sd~fr~~d 136 (139)
T KOG4353|consen 87 QTTVLVVVSGTVKFDGNKQRVFNQTFLLTAEDPPFKTVWKVASDCFRFQD 136 (139)
T ss_pred cceEEEEEeeeEEEcCCccccccceeEEeecCCccchhhhhhhhhhhhhh
Confidence 567788999999999999987766 9999999864
No 6
>cd00531 NTF2_like Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of divergent evolution wherein the proteins have many common structural details but diverge greatly in their function. For example, nuclear transport factor 2 (NTF2) mediates the nuclear import of RanGDP and binds to both RanGDP and FxFG repeat-containing nucleoporins while Ketosteroid isomerases catalyze the isomerization of delta-5-3-ketosteroid to delta-4-3-ketosteroid, by intramolecular transfer of the C4-beta proton to the C6-beta position. While the function of the beta sub-unit of the Ring hydroxylating dioxygenases is not known, Scytalone Dehydratases catalyzes two reactions in the biosynthetic pathway that produces fungal melanin. Members of the NTF2-like superfamily are widely distributed among bacteria, archaea
Probab=98.15 E-value=1.9e-05 Score=49.56 Aligned_cols=78 Identities=26% Similarity=0.395 Sum_probs=62.7
Q ss_pred HHHHHHHHHhccCCCChhhhhhhccCCCceeeEcC-----ceeccHHHHHhhh---------------------------
Q psy4124 14 KGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEG-----IQLQGAVKIMEKF--------------------------- 61 (99)
Q Consensus 14 ~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~eg-----~~~~G~~~I~~kl--------------------------- 61 (99)
++|+.+||..+| ..+++.|..||.++ +.+++.+ ....|.++|.+.+
T Consensus 2 ~~l~~~y~~~ld-~~~~~~l~~~~~~d-~~~~~~~~~~~~~~~~g~~~i~~~~~~~~~~~~~~~h~~~~~~~~~~~~~~~ 79 (124)
T cd00531 2 EQFLYRYARLLD-AGDREWLALLYADD-AYFEPPGGDGLIYPDDGREAIEDRVRRLPFGPSRTRHLVSNVDVQPGDDGEG 79 (124)
T ss_pred HHHHHHHHHHhC-CchHHHHHhhCcCc-EEEEEccCCEEEEcCChHHHHHHHHHhcCCCCCceEEEEEeEEEEeCCCCEE
Confidence 589999999999 46789999999998 9999887 5678998998876
Q ss_pred ---------hcCC---CCCeeEEEEEEEEeeCCEEEEEcceEee
Q psy4124 62 ---------NCDD---DPPHAYSQIFVLKPLGASFYCQHDIFRL 93 (99)
Q Consensus 62 ---------~~d~---~~~~~F~QtF~L~~~~~~y~v~NDifR~ 93 (99)
.... ...+.+.+++.+.+.+++|.|.+..+++
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~w~i~~~~~~~ 123 (124)
T cd00531 80 VVVSVFGVLRTRGDGEQDVFAGGQTFVLRPQGGGGKIANRRFRL 123 (124)
T ss_pred EEEEEEEEEEEccCCceeEEEEEEEEEEEEeCCEEEEEEEEEec
Confidence 0111 2244588888888889999999988876
No 7
>TIGR02246 conserved hypothetical protein. This family consists of uncharacterized proteins found in a number of genera and species, including Streptomyces, Xanthomonas, Oceanobacillus iheyensis, Caulobacter crescentus CB15, and Xylella fastidiosa. The function is unknown.
Probab=96.70 E-value=0.034 Score=35.86 Aligned_cols=48 Identities=10% Similarity=0.253 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHhccCCCChhhhhhhccCCCceee-EcCceeccHHHHHhhh
Q psy4124 12 IGKGFVQQYYALFDDPAQRPNLINMYNTETSFMT-FEGIQLQGAVKIMEKF 61 (99)
Q Consensus 12 ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt-~eg~~~~G~~~I~~kl 61 (99)
--++.++.|+..++. .+++.+..+|.++ +.+. ..|..+.|.++|.+.+
T Consensus 5 ~i~~l~~~~~~a~~~-~D~~~~~~~~~~D-a~~~~~~g~~~~G~~~i~~~~ 53 (128)
T TIGR02246 5 AIRALVATWEAAWAA-GDAEGFADLFTPD-GVFVTVPGQVWKGREAIAAAH 53 (128)
T ss_pred HHHHHHHHHHHHHHc-CCHHHHHHhhCCC-ceEECCCCCeecCHHHHHHHH
Confidence 346788889999984 4889999999999 6665 6777889999999876
No 8
>PF10429 Mtr2: Nuclear pore RNA shuttling protein Mtr2; InterPro: IPR019488 Mtr2 is a monomeric, dual-action, RNA-shuttle protein found in yeasts. Transport across the nuclear-cytoplasmic membrane is via the macro-molecular membrane-spanning nuclear pore complex, NPC. The pore is lined by a subset of NPC members called nucleoporins that present FG (Phe-Gly) receptors, characteristically GLFG and FXFG motifs, for shuttling RNAs and proteins. RNA cargo is bound to soluble transport proteins (nuclear export factors) such as Mex67 in yeasts, and TAP in metazoa, which pass along the pore by binding to successive FG receptors. Mtr2 when bound to Mex67 maximises this FG-binding. Mtr2 also acts independently of Mex67 in transporting the large ribosomal RNA subunit through the pore []. ; PDB: 1Q40_A 1Q42_A 1OF5_B.
Probab=96.58 E-value=0.0016 Score=47.10 Aligned_cols=50 Identities=16% Similarity=0.315 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHhccC---CCChhhhhhhccCCCceeeEcCceeccHHHHHhhh
Q psy4124 11 AIGKGFVQQYYALFDD---PAQRPNLINMYNTETSFMTFEGIQLQGAVKIMEKF 61 (99)
Q Consensus 11 ~ig~~FV~~YY~~~d~---~~~r~~L~~~Y~~~~S~lt~eg~~~~G~~~I~~kl 61 (99)
++.+.||+.||..+|+ ++-++.|..||.++ |.++|||+++.+..+-.+++
T Consensus 5 q~~E~FvKk~la~LD~~~~~~l~~~l~~F~~~~-~~II~Ng~Pi~~~~~F~~~w 57 (166)
T PF10429_consen 5 QIIETFVKKILAHLDEQDPPNLNSFLTQFLPPN-CKIIWNGTPIAQPTAFQQTW 57 (166)
T ss_dssp CCHHHHHHHHHHHHCT-SS--HHHHHTTCECCE-EEEEETTEEES-HHHHHHHH
T ss_pred hhHHHHHHHHHHHhcCcchHHHHHHhHhhcCCC-cEEEECCccCCCHHHHHHHH
Confidence 4678999999999995 33456777889988 99999999999998888888
No 9
>PF13474 SnoaL_3: SnoaL-like domain; PDB: 2GXF_A 3KSP_A 3KE7_A 3BB9_E 3CNX_A 3F7S_A 3GWR_B.
Probab=96.53 E-value=0.017 Score=36.75 Aligned_cols=74 Identities=14% Similarity=0.248 Sum_probs=55.2
Q ss_pred HHHHHHHHHhccCCCChhhhhhhccCCCceeeEc--CceeccHHHHHhhh------------------------------
Q psy4124 14 KGFVQQYYALFDDPAQRPNLINMYNTETSFMTFE--GIQLQGAVKIMEKF------------------------------ 61 (99)
Q Consensus 14 ~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~e--g~~~~G~~~I~~kl------------------------------ 61 (99)
.++++.|++.+.. .+.+.+..+|.++ ..+... +..+.|.++|.+.+
T Consensus 2 ~~~~~~~~~a~~~-~D~~~~~~~~~~d-~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~a~~~~ 79 (121)
T PF13474_consen 2 EALLEEWIEAFER-GDIDALLSLFSDD-FVFFGTGPGEIWRGREAIRAYFERDFESFRPISIEFEDVQVSVSGDVAVVTG 79 (121)
T ss_dssp HHHHHHHHHHHHC-T-HHHHHHHEEEE-EEEEETTSSSEEESHHHHHHHHHHHHHTHSEEEEEEEEEEEEEETTEEEEEE
T ss_pred HHHHHHHHHHHHh-CCHHHHHHhhCCC-EEEEcCCCCceECCHHHHHHHHHHHhhhCceEEEEEEEEEEEECCCEEEEEE
Confidence 4678888988884 5679999999988 666553 45778999998877
Q ss_pred ------hcCCCC-CeeEEEEEEEEeeCCEEEEEcc
Q psy4124 62 ------NCDDDP-PHAYSQIFVLKPLGASFYCQHD 89 (99)
Q Consensus 62 ------~~d~~~-~~~F~QtF~L~~~~~~y~v~ND 89 (99)
..++.+ ...+..|+++++.+++|.|...
T Consensus 80 ~~~~~~~~~~~~~~~~~r~t~v~~k~~~~Wki~h~ 114 (121)
T PF13474_consen 80 EFRLRFRNDGEEIEMRGRATFVFRKEDGGWKIVHI 114 (121)
T ss_dssp EEEEEEECTTCEEEEEEEEEEEEEEETTEEEEEEE
T ss_pred EEEEEEecCCccceeeEEEEEEEEEECCEEEEEEE
Confidence 112222 4568999999999999998754
No 10
>KOG3763|consensus
Probab=95.26 E-value=0.1 Score=44.13 Aligned_cols=38 Identities=24% Similarity=0.493 Sum_probs=29.4
Q ss_pred CccHHHHHHHHHHHHHHhccCCCChhhhhhhccCCCceee
Q psy4124 6 NPAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMT 45 (99)
Q Consensus 6 ~p~~~~ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt 45 (99)
++...++-.+|+++||..+|+ .++..+-..|.++ |+.+
T Consensus 334 ~~~l~~LV~~Fl~~y~~~yD~-~d~q~~~~~y~dn-s~FS 371 (585)
T KOG3763|consen 334 SEELKQLVLQFLQQYYKIYDN-NDGQLLLYAYHDN-STFS 371 (585)
T ss_pred chHHHHHHHHHHHHHHHhhcC-chhhhHHhhcCcc-ceeE
Confidence 456678889999999999995 3556666677777 8876
No 11
>PF12680 SnoaL_2: SnoaL-like domain; PDB: 3F40_A 3RGA_A 3G8Z_A 3DMC_A 3FH1_A 1TUH_A 3F14_A 3ER7_A 1Z1S_A 3F7X_A ....
Probab=95.14 E-value=0.02 Score=34.84 Aligned_cols=43 Identities=16% Similarity=0.386 Sum_probs=37.9
Q ss_pred HHHHHHhccCCCChhhhhhhccCCCceeeEcCceeccHHHHHhhh
Q psy4124 17 VQQYYALFDDPAQRPNLINMYNTETSFMTFEGIQLQGAVKIMEKF 61 (99)
Q Consensus 17 V~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~eg~~~~G~~~I~~kl 61 (99)
|+.||..+++ .+.+.+..+|.++ ..+..++.+..|.++|.+.+
T Consensus 1 V~~~~~a~~~-~d~~~i~~~~~~d-~~~~~~~~~~~g~~~~~~~~ 43 (102)
T PF12680_consen 1 VRRFFEAWNA-GDLDAIAALFAPD-AVFHDPGGTLRGREAIREFF 43 (102)
T ss_dssp HHHHHHHHHT-THHHHHHHTEEEE-EEEEETTSEEESHHHHHHHH
T ss_pred CHHHHHHHHc-CCHHHHHHHcCCC-EEEEeCCCcccCHHHHHHHH
Confidence 6889999984 4679999999999 88888887899999999988
No 12
>PF14534 DUF4440: Domain of unknown function (DUF4440); PDB: 3HX8_A 3SOY_A 3ROB_B 3GZR_A 3B7C_A 3CU3_A 3FSD_A 2R4I_C 1TP6_A.
Probab=93.96 E-value=0.31 Score=29.85 Aligned_cols=45 Identities=20% Similarity=0.345 Sum_probs=35.7
Q ss_pred HHHHHHHHhccCCCChhhhhhhccCCCceeeEcCceeccHHHHHhhh
Q psy4124 15 GFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGIQLQGAVKIMEKF 61 (99)
Q Consensus 15 ~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~eg~~~~G~~~I~~kl 61 (99)
+.++.|...+.+ .+.+.+.++|.|+ ..+...+..+.|.+++++.+
T Consensus 3 a~~~~~~~A~~~-~D~~~~~~~~~~d-~~~~~~~g~~~~~~~~l~~~ 47 (107)
T PF14534_consen 3 ALEEQYEDAFNA-GDIDALASLYADD-FVFVGPGGTILGKEAILAAF 47 (107)
T ss_dssp HHHHHHHHHHHT-THHHHHHTTEEEE-EEEEETTSEEEEHHHHHHHH
T ss_pred HHHHHHHHHHHh-CCHHHHHhhhCCC-EEEECCCCCEeCHHHHHHHH
Confidence 456777777763 5789999999998 77777666667999999888
No 13
>cd00781 ketosteroid_isomerase ketosteroid isomerase: Many biological reactions proceed by enzymatic cleavage of a C-H bond adjacent to carbonyl or a carboxyl group, leading to an enol or a enolate intermediate that is subsequently re-protonated at the same or an adjacent carbon. Ketosteroid isomerases are important members of this class of enzymes which are the most proficient of all enzymes known and have served as a paradigm for enzymatic enolizations since its discovery in 1954. This CD includes members of this class that calalyze the isomerization of various beta,gamma-unsaturated isomers at nearly a diffusion-controlled rate. These enzymes are widely distributed in bacteria.
Probab=93.68 E-value=0.97 Score=29.02 Aligned_cols=47 Identities=13% Similarity=0.222 Sum_probs=38.3
Q ss_pred HHHHHHHHHHhccCCCChhhhhhhccCCCceeeEc--CceeccHHHHHhhh
Q psy4124 13 GKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFE--GIQLQGAVKIMEKF 61 (99)
Q Consensus 13 g~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~e--g~~~~G~~~I~~kl 61 (99)
-++.|+.||..++. .+.+.|..+|.++ ..+.+. +.++.|.++|.+.+
T Consensus 5 ~~~~v~~~~~a~~~-~D~~~~~~l~aed-~~~~~p~~~~~~~G~~~i~~~~ 53 (122)
T cd00781 5 MKAAVQRYVEAVNA-GDPEGIVALFADD-ATVEDPVGSPPRSGRAAIAAFY 53 (122)
T ss_pred HHHHHHHHHHHHHC-CCHHHHHHHcCCC-eEEeCCCCCCCccCHHHHHHHH
Confidence 35678889999985 4789999999998 777664 34689999999887
No 14
>PF15008 DUF4518: Domain of unknown function (DUF4518)
Probab=89.76 E-value=1.7 Score=33.55 Aligned_cols=86 Identities=13% Similarity=0.231 Sum_probs=59.1
Q ss_pred ccHHHHHHHHHHHHHHhccCCCChhhhhhhccCCCceeeE---cC--c---eeccHHHHHhhh-----------------
Q psy4124 7 PAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTF---EG--I---QLQGAVKIMEKF----------------- 61 (99)
Q Consensus 7 p~~~~ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~---eg--~---~~~G~~~I~~kl----------------- 61 (99)
.++..+|++|.+.||..+++|.+-=...-|+.| +.|.+ .+ . .+.|++.++.+|
T Consensus 125 ~~~~~L~~~F~~WFf~llNs~~~~wgpqhFW~D--a~L~~~~~~~~~~~e~~~~Ga~~vs~~Llsl~~e~~l~fnPNl~~ 202 (262)
T PF15008_consen 125 YPIHLLAEEFCEWFFELLNSPQDDWGPQHFWPD--AKLKLYYSTSEQNVEEYCEGAEEVSLRLLSLVKEERLFFNPNLDS 202 (262)
T ss_pred CCHHHHHHHHHHHHHHHhcccccccChhhccCC--CeEEEEEEcCCCceeEEecCHHHHHHHHHHHhhcccEEECCCCCC
Confidence 468999999999999999943355555668885 45543 12 1 248999999888
Q ss_pred -------------------hc-CCCCCee-EEEEEEEEeeC---CEEEEEcceEeee
Q psy4124 62 -------------------NC-DDDPPHA-YSQIFVLKPLG---ASFYCQHDIFRLG 94 (99)
Q Consensus 62 -------------------~~-d~~~~~~-F~QtF~L~~~~---~~y~v~NDifR~~ 94 (99)
++ .++.-.+ |=|+|=|...+ +.|.|-+==+|+.
T Consensus 203 ~G~k~~~~phGlV~V~v~GTvH~~~~ClGiFEq~FGLiRdP~~~N~WKiK~~~l~i~ 259 (262)
T PF15008_consen 203 DGVKGRISPHGLVLVAVCGTVHRDNTCLGIFEQIFGLIRDPFAENNWKIKFVNLRIR 259 (262)
T ss_pred CCcceEEcCCCcEEEEEeeeEecCCceEeehhhhhhcccCccccCceeEEEEEEEEE
Confidence 11 1122233 99999998765 8898876555543
No 15
>COG4875 Uncharacterized protein conserved in bacteria with a cystatin-like fold [Function unknown]
Probab=86.56 E-value=9.3 Score=27.01 Aligned_cols=81 Identities=12% Similarity=0.137 Sum_probs=56.6
Q ss_pred CccHHHHHHHHHHHHHHhccCCCChhhhhhhccCCCcee--eEcCceeccHHHHHhhh----------------------
Q psy4124 6 NPAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFM--TFEGIQLQGAVKIMEKF---------------------- 61 (99)
Q Consensus 6 ~p~~~~ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~l--t~eg~~~~G~~~I~~kl---------------------- 61 (99)
++.-.+||.-|=+.==.+.- -+|+++...|.++ .+| |...+.-..+.+|...+
T Consensus 33 ~~t~~~vAaLFdrWN~~L~T--GdP~kV~anyApD-aVLLPT~Sn~vR~s~~ei~DYF~~FLk~KPqG~IdsR~i~~gcN 109 (156)
T COG4875 33 NVTEREVAALFDRWNAALTT--GDPNKVAANYAPD-AVLLPTMSNQVRSSRSEILDYFSHFLKLKPQGYIDSRKITLGCN 109 (156)
T ss_pred CccHHHHHHHHHHHHhhhhc--CChHHHHhhcCCc-eEeecccccccccCHHHHHHHHHHHhccCCcceecceeEEeccc
Confidence 46778899888777777777 8999999999999 666 45555666777887655
Q ss_pred ----------hcCCCCCeeEEEEEEEEeeCCEEEEEcc
Q psy4124 62 ----------NCDDDPPHAYSQIFVLKPLGASFYCQHD 89 (99)
Q Consensus 62 ----------~~d~~~~~~F~QtF~L~~~~~~y~v~ND 89 (99)
+..|+....=.=||.-..++|.|.|.|.
T Consensus 110 ~AlD~GtYTF~f~DGs~v~ARYtftY~w~~g~WlI~~H 147 (156)
T COG4875 110 NALDAGTYTFIFTDGSNVQARYTFTYSWIDGTWLIVNH 147 (156)
T ss_pred cccccceEEEEEcCCcceeEEEEEEEEecCCeEEEEec
Confidence 1122222222236777788899998874
No 16
>PF13577 SnoaL_4: SnoaL-like domain; PDB: 3S5C_B 3EJV_A 2RFR_A 3B8L_F 2CHC_A 3A76_A 3EF8_B.
Probab=86.03 E-value=1.8 Score=27.58 Aligned_cols=48 Identities=13% Similarity=0.348 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHhccCCCChhhhhhhccCCCceeeEcCc---eeccHHHHHhhh
Q psy4124 12 IGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGI---QLQGAVKIMEKF 61 (99)
Q Consensus 12 ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~eg~---~~~G~~~I~~kl 61 (99)
--.+++..|...+|. .+.+.+..++.++ ..+.+.+. .+.|.++|.+.+
T Consensus 8 ~I~~l~~~~~~~~D~-~~~~~~~~lft~d-~~~~~~~~~~~~~~G~~~i~~~~ 58 (127)
T PF13577_consen 8 AIRDLIARYARALDT-GDWEEWADLFTED-AVFDFPGFGFGRYRGRDAIRAFL 58 (127)
T ss_dssp HHHHHHHHHHHHHHT-T-HHHHHTTEEEE-EEEEETTTCEEEEESHHHHHHHH
T ss_pred HHHHHHHHHHHHhhC-CCHHHHHhccCCc-EEEEEeCccccccCCHHHHHHHH
Confidence 345778888888884 5678999999998 99988874 799999999988
No 17
>PF08332 CaMKII_AD: Calcium/calmodulin dependent protein kinase II Association; InterPro: IPR013543 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain is found at the C terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (IPR000719 from INTERPRO) at their N terminus []. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers [] and is a prominent kinase in the central nervous system that may function in long-term potentiation and neurotransmitter release. ; GO: 0004683 calmodulin-dependent protein kinase activity, 0005516 calmodulin binding, 0006468 protein phosphorylation; PDB: 2W2C_F 3H51_B 3SOA_A 2UX0_A 1HKX_M 2F86_B.
Probab=82.59 E-value=9.5 Score=26.27 Aligned_cols=50 Identities=12% Similarity=0.065 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHhccCCCChhhhhhhccCCCceeeE--cCceeccHHHHHhhh
Q psy4124 10 EAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTF--EGIQLQGAVKIMEKF 61 (99)
Q Consensus 10 ~~ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~--eg~~~~G~~~I~~kl 61 (99)
+||+..|-+.==.+-. .+++...++|.++.+++.+ -|+.+.|.+.|...+
T Consensus 3 ~eI~~l~~~w~~ai~t--gD~~~~~~ly~~d~av~~Pt~s~~~~~g~~~~~~YF 54 (128)
T PF08332_consen 3 QEIAALFDRWNDAIQT--GDPETYAKLYAPDVAVFEPTVSNQLREGLEFHKFYF 54 (128)
T ss_dssp HHHHHHHHHHHHHHHH--T-HHHHHHHEEEEEEEEEGGGTTSEEESCHHHHHHH
T ss_pred HHHHHHHHHHHHHHHc--CCHHHHhhhcCCCeeEeccccCCceecChHHHHHHH
Confidence 4666666555555555 7899999999987556644 477889998887655
No 18
>TIGR02096 conserved hypothetical protein, steroid delta-isomerase-related. This family of proteins about 135 amino acids in length largely restricted to the Proteobacteria. This family and a delta5-3-ketosteroid isomerase from Pseudomonas testosteroni appear homologous, especially toward their respective N-termini. Members, therefore, probably are enzymes.
Probab=80.65 E-value=3.4 Score=26.55 Aligned_cols=44 Identities=9% Similarity=0.225 Sum_probs=33.4
Q ss_pred HHHHHHHhccCCCChhhhhhhccCCCceeeEcC--ceeccHHHHHhhh
Q psy4124 16 FVQQYYALFDDPAQRPNLINMYNTETSFMTFEG--IQLQGAVKIMEKF 61 (99)
Q Consensus 16 FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~eg--~~~~G~~~I~~kl 61 (99)
-|+.||+.++. .+.+.+..+|.++ ......+ ....|.++|.+.+
T Consensus 3 iv~~~~~a~~~-~d~~~~~~~~~~d-~~~~~~~~~~~~~G~~~~~~~~ 48 (129)
T TIGR02096 3 LAQHWIEAFNR-GDMDAVLALLAED-VLYDDNQGGRVLGGKAQLARFL 48 (129)
T ss_pred HHHHHHHHHHC-CCHHHHHHhcCCC-eEEEcCCCCcEeccHHHHHHHH
Confidence 46788888883 4789999999998 7666543 3567799987655
No 19
>COG4319 Ketosteroid isomerase homolog [Function unknown]
Probab=80.41 E-value=6.9 Score=27.56 Aligned_cols=62 Identities=19% Similarity=0.362 Sum_probs=46.0
Q ss_pred CChhhhhhhccCCCceeeEcCceeccHHHHHhhh-----------------------------------hc--CCCC--C
Q psy4124 28 AQRPNLINMYNTETSFMTFEGIQLQGAVKIMEKF-----------------------------------NC--DDDP--P 68 (99)
Q Consensus 28 ~~r~~L~~~Y~~~~S~lt~eg~~~~G~~~I~~kl-----------------------------------~~--d~~~--~ 68 (99)
.+-+.+..+|.++.-.+.-.|.++.|+++|.+-+ .. ++++ +
T Consensus 26 ~D~~av~~~YtdDav~f~~~~~~~~Gk~~i~k~~~~~~~~~~~~~~f~~~el~v~~~GD~a~~~~~~~~~~~~~dg~~~~ 105 (137)
T COG4319 26 KDADAVADFYTDDAVVFPPPGLQRKGKAAIRKAFEGIFAMGIGPLKFTLEELQVHESGDVAFVTALLLLTGTKKDGPPAD 105 (137)
T ss_pred ccHHHHHHhcCCceEEecCCCCcccCHHHHHHHHHHHHHhccCCCcceeeeeeeeccCCEEEEEEeeeeeccCCCCcchh
Confidence 6778999999999333334589999999998877 11 2333 3
Q ss_pred eeEEEEEEEEeeC-CEEEEEcc
Q psy4124 69 HAYSQIFVLKPLG-ASFYCQHD 89 (99)
Q Consensus 69 ~~F~QtF~L~~~~-~~y~v~ND 89 (99)
+.-.=|.+++++. |+|.|.-|
T Consensus 106 ~~~Rat~v~rK~~dg~Wk~~~d 127 (137)
T COG4319 106 LAGRATYVFRKEADGGWKLAHD 127 (137)
T ss_pred heeeeEEEEEEcCCCCEEEEEe
Confidence 4677888899887 49998877
No 20
>PF07080 DUF1348: Protein of unknown function (DUF1348); InterPro: IPR009783 This family consists of several highly conserved hypothetical proteins of around 150 residues in length. The function of this family is unknown.; PDB: 2IMJ_B.
Probab=77.20 E-value=2.4 Score=30.04 Aligned_cols=54 Identities=13% Similarity=0.100 Sum_probs=36.2
Q ss_pred CccHHHHHHHHHHHHHHhccCCCChhhhhhhccCCCceeeEcCceeccHHHHHhhh
Q psy4124 6 NPAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGIQLQGAVKIMEKF 61 (99)
Q Consensus 6 ~p~~~~ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~eg~~~~G~~~I~~kl 61 (99)
.|--.+.|.+=|+.==..-+ ..+|+.++.-|+++ |.-.=-..-++|.++|+++|
T Consensus 5 PPFt~etA~~KVr~AEdaWN-srdP~~ValaYT~D-s~WRNR~eF~~GR~~I~~FL 58 (143)
T PF07080_consen 5 PPFTRETAIQKVRAAEDAWN-SRDPEKVALAYTPD-SVWRNRDEFLTGREEIVAFL 58 (143)
T ss_dssp SS--HHHHHHHHHHHHHHHT-TT-HHHHHTTEEEE-EEEEETTEEE-SHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHhccc-cCChhHheeccCCC-CcccCcccccCcHHHHHHHH
Confidence 34444555555554434444 26899999999998 77765667899999999999
No 21
>PF11533 DUF3225: Protein of unknown function (DUF3225); InterPro: IPR024507 This family of proteins has no known function.; PDB: 2OWP_A 2RCD_B.
Probab=73.50 E-value=28 Score=24.20 Aligned_cols=51 Identities=16% Similarity=0.141 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHHhccCCCChhhhhhhccCCCceeeEc-CceeccHHHHHhhh
Q psy4124 9 YEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFE-GIQLQGAVKIMEKF 61 (99)
Q Consensus 9 ~~~ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~e-g~~~~G~~~I~~kl 61 (99)
..+|...|-...=.++. ++-+.|-.|+-+....+.++ |....|.++|.++-
T Consensus 9 ~aev~aaf~~YE~AL~~--nDv~~Ld~lFw~~p~TvRyg~~E~LyG~~aI~aFR 60 (125)
T PF11533_consen 9 VAEVTAAFDRYERALMA--NDVDALDALFWDDPRTVRYGAGENLYGHDAIRAFR 60 (125)
T ss_dssp HHHHHHHHHHHHHHHHC--T-HHHHHHCB--STT-EEEETTEEEESHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhh--CCHHHHHHHhccCCceEEECCCccccCHHHHHHHH
Confidence 34677788777777777 88899999887776889998 67899999999766
No 22
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=51.99 E-value=32 Score=25.87 Aligned_cols=48 Identities=19% Similarity=0.393 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHhccCCCChhhhhhhccCCCceeeEcC--------ceeccHHHHHhhh
Q psy4124 12 IGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEG--------IQLQGAVKIMEKF 61 (99)
Q Consensus 12 ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~eg--------~~~~G~~~I~~kl 61 (99)
...+-|+.|+..+.. .+.+.|..++.++ ..++-+| .++.|.++|...+
T Consensus 172 ~~~~~v~~f~~A~~~-gD~~~l~~Lla~D-v~~~~dggg~~~~~~~~~~G~~~v~~~l 227 (293)
T PRK09636 172 EGAELVEAFFAALAS-GDLDALVALLAPD-VVLHADGGGKVPTALRPIYGADKVARFF 227 (293)
T ss_pred HHHHHHHHHHHHHHh-CCHHHHHHHHhhC-eEEEecCCCccCCCCccccCHHHHHHHH
Confidence 456789999999985 4889999999999 8887665 2368999998888
No 23
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=49.74 E-value=32 Score=26.27 Aligned_cols=49 Identities=12% Similarity=0.234 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHhccCCCChhhhhhhccCCCceeeEcCc--eeccHHHHHhhh
Q psy4124 11 AIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGI--QLQGAVKIMEKF 61 (99)
Q Consensus 11 ~ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~eg~--~~~G~~~I~~kl 61 (99)
+.-.+-|+.||..+.. .+.+.|..++.++ ...++.+. .+.|.++|.+.+
T Consensus 214 ~~~~~~v~~~~~A~~~-gD~~~l~~lla~D-v~~~~p~~~~~~~G~~~v~~~~ 264 (339)
T PRK08241 214 PEERALLARYVAAFEA-YDVDALVALLTED-ATWSMPPFPLWYRGRDAIAAFL 264 (339)
T ss_pred hHHHHHHHHHHHHHhc-CCHHHHHHHhcCC-EEEEcCCCCCcccCHHHHHHHH
Confidence 5667889999999985 4789999999999 77776653 499999998877
No 24
>PF12893 Lumazine_bd_2: Putative lumazine-binding; PDB: 3BLZ_C 3DUK_F 3FKA_C.
Probab=45.86 E-value=60 Score=20.82 Aligned_cols=76 Identities=12% Similarity=0.262 Sum_probs=48.5
Q ss_pred HHHHHHHHHhccCCCChhhhhhhccCCCcee-eEc-Cc-eeccHHHHHhhh--------------------hcCC-----
Q psy4124 14 KGFVQQYYALFDDPAQRPNLINMYNTETSFM-TFE-GI-QLQGAVKIMEKF--------------------NCDD----- 65 (99)
Q Consensus 14 ~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~l-t~e-g~-~~~G~~~I~~kl--------------------~~d~----- 65 (99)
.+=|+.|..-+.+ .+.+.|.+.+.|+ ..+ +.. |. .....++-.+.+ .+++
T Consensus 7 ~~~v~~Y~dg~~~-gD~~~l~~~f~~~-a~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~i~~i~i~g~~A~a 84 (116)
T PF12893_consen 7 EATVQDYFDGLYN-GDSEKLRSAFHPD-ARLQGVRKGKLRTMPIEEFIARVKSRVSPKPPGQERKESILSIDIDGDVASA 84 (116)
T ss_dssp HHHHHHHHHHHHH-T-HHHHGGGEEEE-EEEEEEETTEEEEEETHHHHHHHHHC---H-SSTT-EEEEEEEEEETTEEEE
T ss_pred HHHHHHHHHHHHh-cCHHHHHHhhCCC-cEEEEEcCCceEEeCHHHHHHHHHhhccccCCCCCceeEEEEEEEECCEEEE
Confidence 4567778888775 4889999999998 555 443 32 122222222222 1111
Q ss_pred -----CCCeeEEEEEEEEeeCCEEEEEcceE
Q psy4124 66 -----DPPHAYSQIFVLKPLGASFYCQHDIF 91 (99)
Q Consensus 66 -----~~~~~F~QtF~L~~~~~~y~v~NDif 91 (99)
-+...|.-.|.|.+.+|+|-|.|=+|
T Consensus 85 ~v~~~~~~~~~~d~~~L~K~dg~WkIv~k~~ 115 (116)
T PF12893_consen 85 KVEYEFPGFWFVDYFTLVKTDGGWKIVSKVY 115 (116)
T ss_dssp EEEEEEETEEEEEEEEEEEETTEEEEEEEEE
T ss_pred EEEEEECCCceEEEEEEEEECCEEEEEEEec
Confidence 12457999999999999999998766
No 25
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=42.20 E-value=45 Score=25.10 Aligned_cols=48 Identities=15% Similarity=0.268 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHhccCCCChhhhhhhccCCCceeeEcC--ceeccHHHHHhhh
Q psy4124 12 IGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEG--IQLQGAVKIMEKF 61 (99)
Q Consensus 12 ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~eg--~~~~G~~~I~~kl 61 (99)
...+-|+.||..+.. .+.+.|..++.++ ..++... .++.|.++|...+
T Consensus 205 ~~~~~v~~~~~a~~~-gD~~~l~~Lla~D-v~~~~p~~~~~~~G~~~v~~~~ 254 (324)
T TIGR02960 205 EEQDLLERYIAAFES-YDLDALTALLHED-AIWEMPPYTLWYQGRPAIVGFI 254 (324)
T ss_pred HHHHHHHHHHHHHHc-CCHHHHHHHhcCC-eEEEcCCCCcceeCHHHHHHHH
Confidence 446789999999985 5789999999999 8777653 5799999998877
No 26
>COG3558 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.81 E-value=25 Score=24.74 Aligned_cols=54 Identities=19% Similarity=0.164 Sum_probs=40.6
Q ss_pred CccHHHHHHHHHHHHHHhccCCCChhhhhhhccCCCceeeEcCceeccHHHHHhhh
Q psy4124 6 NPAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGIQLQGAVKIMEKF 61 (99)
Q Consensus 6 ~p~~~~ig~~FV~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~eg~~~~G~~~I~~kl 61 (99)
.|-..++|-+=|+.==...++ .+|++++--|.++ |...=....++|.++|.++|
T Consensus 7 ppft~eta~~kvr~aed~wns-rdp~kv~layt~d-s~wrnraef~~gre~i~~fl 60 (154)
T COG3558 7 PPFTAETAIQKVRMAEDAWNS-RDPAKVALAYTED-SFWRNRAEFFQGREKIQEFL 60 (154)
T ss_pred CCchHHHHHHHHHHhHhcccc-CChhheeeeeccc-hhhhhHHHHHccHHHHHHHH
Confidence 445557777777665555553 6889999999998 76655556799999999998
No 27
>COG2827 Predicted endonuclease containing a URI domain [DNA replication, recombination, and repair]
Probab=35.54 E-value=14 Score=24.45 Aligned_cols=26 Identities=23% Similarity=0.585 Sum_probs=19.1
Q ss_pred EEEEEeeCCEEE--EEcceE-eeecCCCC
Q psy4124 74 IFVLKPLGASFY--CQHDIF-RLGIHDTA 99 (99)
Q Consensus 74 tF~L~~~~~~y~--v~NDif-R~~~~n~~ 99 (99)
+++|+-.+|.+| |++|+- |+..||.|
T Consensus 7 vYil~c~dgtlY~GvT~D~~rR~~~H~~G 35 (95)
T COG2827 7 VYILRCADGTLYTGVTTDLERRLAEHNSG 35 (95)
T ss_pred EEEEEeCCCCEEEEecCCHHHHHHHHhcc
Confidence 567877788888 577776 67777764
No 28
>PF07366 SnoaL: SnoaL-like polyketide cyclase; InterPro: IPR009959 This domain is found in SnoaL [] a polyketide cyclase involved in nogalamycin biosynthesis. This domain was formerly known as DUF1486. It adopts a distorted alpha-beta barrel fold []. Structural data together with site-directed mutagenesis experiments have shown that SnoaL has a different mechanism to that of the classical aldolase for catalysing intramolecular aldol condensation [].; PDB: 2GEY_C 3F9S_A 2GEX_A 3EHC_B 2F99_D 2F98_D 1SJW_A 3K0Z_B.
Probab=30.11 E-value=52 Score=21.01 Aligned_cols=42 Identities=12% Similarity=0.107 Sum_probs=29.8
Q ss_pred HHHHHhccCCCChhhhhhhccCCCceeeEcC-ceeccHHHHHhhh
Q psy4124 18 QQYYALFDDPAQRPNLINMYNTETSFMTFEG-IQLQGAVKIMEKF 61 (99)
Q Consensus 18 ~~YY~~~d~~~~r~~L~~~Y~~~~S~lt~eg-~~~~G~~~I~~kl 61 (99)
+.|...++. .+.+.+.++|.++ ......+ ....|.+++.+.+
T Consensus 5 ~~~~~~~n~-~d~~~~~~~~~~d-~~~~~~~~~~~~G~~~~~~~~ 47 (126)
T PF07366_consen 5 RFYEEVWNR-GDLDALDELVAPD-VVFHDPGPGPPVGREGFKEFL 47 (126)
T ss_dssp HHHHHHHHT-T-GCHHHGTEEEE-EEEEGCTTTEEEHHHHHHHHH
T ss_pred HHHHHHHhC-CCHHHHHHhcCCC-EEEEecCCCCCCCHHHHHHHH
Confidence 445556662 4789999999988 6555555 5788998888777
No 29
>PF09053 CagZ: CagZ; InterPro: IPR015139 Helicobacter pylori (Campylobacter pylori) clinical isolates can be classified into two types according to their degree of pathogenicity. Type I strains are associated with a severe disease pathology, express functional VacA (vacuolating cytotoxin A) and contain an insertion of 40 kb of foreign DNA: the cag (cytotoxin-associated gene) pathogenicity island (cagPAI). Type II strains lack the 40 kb insert, cagPAI. The cagPAI may be divided into two regions, cag I and cag II and contain approximately 16 and 15 genes, respectively. The cagPAI encodes a type IV secretion system (T4SS), which delivers CagA into the cytosol of gastric epithelial cells through a rigid needle structure covered by Cag7 or CagY, a VirB10-homologous protein, and CagT, a VirB7-homologous protein, at the base []. The CagA protein is the virulence factor that induces morphological changes in host cells, which may be associated with the development of peptic ulcer and gastric carcinoma []. CagZ is a 23 kDa protein consisting of a single compact L-shaped domain, composed of seven alpha-helices that run antiparallel to each other. 70% of the residues are in alpha-helix conformation and no beta-sheet is present. CagZ is essential for the translocation of the pathogenic protein CagA into host cells []. ; PDB: 1S2X_A.
Probab=29.87 E-value=72 Score=22.87 Aligned_cols=31 Identities=19% Similarity=0.347 Sum_probs=24.0
Q ss_pred CCCCccHHHHHHHHHHHHHHhccCCCChhhh
Q psy4124 3 SQLNPAYEAIGKGFVQQYYALFDDPAQRPNL 33 (99)
Q Consensus 3 ~~~~p~~~~ig~~FV~~YY~~~d~~~~r~~L 33 (99)
|++...+.+|-..|+|.|=+-+.+.++|...
T Consensus 18 sslm~nanevrdkfiqnyatslkdsndpqdf 48 (199)
T PF09053_consen 18 SSLMRNANEVRDKFIQNYATSLKDSNDPQDF 48 (199)
T ss_dssp TTTTTTHHHHHHHHHHHHTGGGGG--SHHHH
T ss_pred hHHhhchHHHHHHHHHHHHhhcccCCCHHHH
Confidence 5677789999999999999998876676543
No 30
>PF12636 DUF3781: Protein of unknown function (DUF3781); InterPro: IPR024229 This family of functionally uncharacterised proteins is found in bacteria and archaea. These proteins are typically between 82 and 98 amino acids in length and have two conserved sequence motifs: GKNWY and ITA.
Probab=27.41 E-value=10 Score=24.03 Aligned_cols=44 Identities=20% Similarity=0.372 Sum_probs=29.9
Q ss_pred ccHHHHHhhhhcCCCCCeeEEEEEEEEee------CCEEEEEcceEeeec
Q psy4124 52 QGAVKIMEKFNCDDDPPHAYSQIFVLKPL------GASFYCQHDIFRLGI 95 (99)
Q Consensus 52 ~G~~~I~~kl~~d~~~~~~F~QtF~L~~~------~~~y~v~NDifR~~~ 95 (99)
-|..-|.+.|.++.+.+..|+-...|.|. |+.|||..|-.++-.
T Consensus 13 lG~~RIkrNL~l~~~dvVe~ck~~I~~~~a~I~rkGKN~Yv~~~~~~iTv 62 (73)
T PF12636_consen 13 LGVVRIKRNLGLDTSDVVEWCKNKILDPNAKITRKGKNWYVTIDDIIITV 62 (73)
T ss_pred HHHHHHHhcCCCCcccHHHHHHHHHcCchhhhhcCCceEEEecCCEEEEE
Confidence 46677777776665555666655555544 588999999877643
No 31
>PF12642 TpcC: Conjugative transposon protein TcpC; InterPro: IPR024735 This family of bacterial proteins are annotated as conjugative transposon protein TcpC. The transfer clostridial plasmid (tcp) locus is part of some conjugative antibiotic resistance and virulence plasmids. TcpC was one of five genes whose products had low-level sequence identity to Tn916 proteins, having similarity to ORF13 homologues from Tn916, Tn5397, and CW459tet [].; PDB: 3UB1_A.
Probab=27.14 E-value=26 Score=25.37 Aligned_cols=25 Identities=16% Similarity=0.373 Sum_probs=18.5
Q ss_pred HHHHHHHHHHH-----hccCCCChhhhhhhcc
Q psy4124 12 IGKGFVQQYYA-----LFDDPAQRPNLINMYN 38 (99)
Q Consensus 12 ig~~FV~~YY~-----~~d~~~~r~~L~~~Y~ 38 (99)
.|..||..|++ --+ ++.+.|.+||.
T Consensus 2 fa~~Fv~~Y~t~~~~~~~~--~r~~~L~~y~~ 31 (232)
T PF12642_consen 2 FAQDFVKEYLTKSDDEAPE--EREARLAPYLT 31 (232)
T ss_dssp HHHHHHHHHT--B-TTGHH--HHHHHHTTTS-
T ss_pred HHHHHHHHHcCCCCccChH--HHHHHHHHHhc
Confidence 57899999999 444 56688999994
No 32
>PF06851 DUF1247: Protein of unknown function (DUF1247); InterPro: IPR009657 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf2; it is a family of uncharacterised viral proteins.
Probab=21.69 E-value=53 Score=23.41 Aligned_cols=13 Identities=31% Similarity=0.667 Sum_probs=11.4
Q ss_pred HHHHHHHHhccCC
Q psy4124 15 GFVQQYYALFDDP 27 (99)
Q Consensus 15 ~FV~~YY~~~d~~ 27 (99)
+||+.||+.+..+
T Consensus 93 S~VElYY~yLs~~ 105 (148)
T PF06851_consen 93 SFVELYYTYLSVD 105 (148)
T ss_pred hhHHHHHHHHccc
Confidence 7999999999943
No 33
>PF08804 gp32: gp32 DNA binding protein like; InterPro: IPR012339 This entry is represented by the Bacteriophage T4, Gp32, single-stranded DNA-binding protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Gp32 is essential for T4 DNA replication, recombination and repair, acting to stimulate replisome processing and accuracy through its binding to ssDNA as the replication fork advances. The crystal structure of Gp32 shows an ssDNA binding cleft comprised of regions from three structural subdomains, through which ssDNA can slide freely []. The structure of Gp32 is similar to other phage ssDNA-binding proteins such as Gp2.5 from bacteriophage T4, and gene V protein, both of which have a nucleic acid-binding OB-type fold. However, Gp32 contains a zinc-finger subdomain at residues 63-111 that is not found in the other two phage proteins.; GO: 0003697 single-stranded DNA binding; PDB: 1GPC_A 2A1K_B 2ATQ_B.
Probab=20.69 E-value=47 Score=22.03 Aligned_cols=33 Identities=6% Similarity=0.215 Sum_probs=18.8
Q ss_pred HHHhhhhcCCCCCeeEEEEEEEEee-CCEEEEEc
Q psy4124 56 KIMEKFNCDDDPPHAYSQIFVLKPL-GASFYCQH 88 (99)
Q Consensus 56 ~I~~kl~~d~~~~~~F~QtF~L~~~-~~~y~v~N 88 (99)
|++++|...++.-..|+.++--.-+ +|+|||.|
T Consensus 17 AvIRFLPa~~~e~~Pf~kl~~H~Fk~~g~WyiEN 50 (94)
T PF08804_consen 17 AVIRFLPAKDEEELPFVKLVNHGFKGNGGWYIEN 50 (94)
T ss_dssp EEEEE---SSTTS-SCEEEEEEEEEETTEEEEEE
T ss_pred EEEEecCCCCCCCCchhhhhhhhccCCCcEEEec
Confidence 4455553333334667777766655 48999988
Done!