Query 034588
Match_columns 90
No_of_seqs 108 out of 1029
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 04:25:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034588.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034588hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11628 transcriptional regul 100.0 1.4E-34 3E-39 192.3 9.4 84 2-86 1-91 (105)
2 KOG3348 BolA (bacterial stress 100.0 2E-33 4.3E-38 179.9 7.5 83 1-84 1-83 (85)
3 COG0271 BolA Stress-induced mo 100.0 1E-32 2.2E-37 179.3 7.9 81 1-82 1-89 (90)
4 PF01722 BolA: BolA-like prote 100.0 5.6E-32 1.2E-36 170.6 6.6 69 11-80 1-76 (76)
5 COG5007 Predicted transcriptio 100.0 1.4E-30 3.1E-35 165.0 7.7 77 3-84 1-79 (80)
6 KOG2313 Stress-induced protein 99.9 1.4E-26 3.1E-31 152.0 6.5 78 2-80 9-100 (100)
7 PF06858 NOG1: Nucleolar GTP-b 62.5 25 0.00053 21.1 4.3 36 14-64 11-46 (58)
8 PF10330 Stb3: Putative Sin3 b 62.4 9.5 0.00021 25.0 2.7 41 39-82 33-74 (92)
9 PF06183 DinI: DinI-like famil 52.5 26 0.00056 21.2 3.3 49 4-63 9-57 (65)
10 TIGR02174 CXXU_selWTH selT/sel 51.9 51 0.0011 19.8 4.7 35 3-38 13-47 (72)
11 PF12685 SpoIIIAH: SpoIIIAH-li 51.2 24 0.00052 25.1 3.5 50 4-59 136-186 (196)
12 PF01877 RNA_binding: RNA bind 49.5 69 0.0015 21.2 5.3 39 4-46 14-55 (120)
13 PRK00447 hypothetical protein; 44.0 55 0.0012 22.7 4.3 33 4-41 16-48 (144)
14 PF05265 DUF723: Protein of un 39.8 63 0.0014 19.5 3.6 37 1-42 1-37 (60)
15 TIGR03435 Soli_TIGR03435 Solib 39.2 1.1E+02 0.0023 23.1 5.5 59 7-67 36-95 (237)
16 PF06006 DUF905: Bacterial pro 37.6 33 0.00071 21.4 2.1 17 20-39 22-38 (70)
17 PRK10597 DNA damage-inducible 36.6 54 0.0012 20.8 3.1 50 4-64 21-72 (81)
18 PF13739 DUF4163: Domain of un 35.3 78 0.0017 18.8 3.6 34 31-64 11-44 (101)
19 PF12170 DNA_pol3_tau_5: DNA p 34.5 1E+02 0.0023 21.1 4.5 53 31-85 51-109 (142)
20 COG1854 LuxS LuxS protein invo 33.8 1.1E+02 0.0024 21.9 4.6 33 7-40 59-92 (161)
21 PRK14635 hypothetical protein; 32.8 1.7E+02 0.0037 20.3 5.5 83 1-86 1-100 (162)
22 PF12543 DUF3738: Protein of u 31.6 1.1E+02 0.0024 21.9 4.4 58 9-68 2-61 (189)
23 cd02164 PPAT_CoAS phosphopante 31.5 1.2E+02 0.0026 20.6 4.4 49 6-54 57-111 (143)
24 COG3325 ChiA Chitinase [Carboh 30.0 60 0.0013 26.8 3.0 48 8-62 199-246 (441)
25 smart00542 FYRC "FY-rich" doma 29.4 1.1E+02 0.0024 19.0 3.6 32 33-64 1-35 (86)
26 KOG3246 Sentrin-specific cyste 27.8 97 0.0021 23.3 3.6 60 5-64 73-148 (223)
27 PF03493 BK_channel_a: Calcium 26.7 82 0.0018 20.1 2.8 28 32-60 67-94 (101)
28 PF04774 HABP4_PAI-RBP1: Hyalu 26.5 41 0.00089 21.3 1.3 15 73-87 78-92 (106)
29 PRK14634 hypothetical protein; 26.4 1.8E+02 0.0039 20.2 4.6 83 3-86 4-101 (155)
30 PF08671 SinI: Anti-repressor 25.8 63 0.0014 16.8 1.7 14 1-14 15-28 (30)
31 PRK13551 agmatine deiminase; P 25.6 2.8E+02 0.0061 22.0 6.1 61 2-62 179-252 (362)
32 PF05392 COX7B: Cytochrome C o 25.1 24 0.00052 22.5 0.0 11 73-83 70-80 (80)
33 PF12224 Amidoligase_2: Putati 25.1 53 0.0011 23.5 1.8 46 22-70 107-152 (252)
34 PF02742 Fe_dep_repr_C: Iron d 25.1 36 0.00079 20.2 0.8 19 46-64 9-27 (71)
35 PF01352 KRAB: KRAB box; Inte 24.9 40 0.00086 18.5 0.9 13 75-87 10-22 (41)
36 KOG3120 Predicted haloacid deh 24.0 20 0.00044 27.3 -0.6 58 2-63 70-132 (256)
37 PF05381 Peptidase_C21: Tymovi 21.8 81 0.0018 21.0 2.0 41 2-42 15-66 (104)
38 PF03413 PepSY: Peptidase prop 21.5 1.5E+02 0.0034 16.0 4.9 38 3-40 2-40 (64)
39 COG1019 Predicted nucleotidylt 21.1 2.7E+02 0.0059 19.9 4.7 47 7-53 62-113 (158)
40 PF12845 TBD: TBD domain; Int 20.9 32 0.0007 20.5 0.0 18 53-70 10-27 (57)
41 PRK00777 phosphopantetheine ad 20.9 2.4E+02 0.0053 19.2 4.4 47 8-54 59-110 (153)
42 PLN02388 phosphopantetheine ad 20.6 2.4E+02 0.0051 20.2 4.4 53 5-57 76-134 (177)
43 PF04444 Dioxygenase_N: Catech 20.0 1.3E+02 0.0028 18.6 2.6 19 63-82 12-31 (74)
No 1
>PRK11628 transcriptional regulator BolA; Provisional
Probab=100.00 E-value=1.4e-34 Score=192.35 Aligned_cols=84 Identities=35% Similarity=0.698 Sum_probs=78.5
Q ss_pred cccHHHHHHHHhhcCCCCeEEEEeCC------CCCcceEEEEEEccccCCCCHHHHHHHHHHHHHHhcc-cccccccCcc
Q 034588 2 GVTKEKVESTLTSKLNPSHLEVIDTS------GGCGAKFEIEIVSEQFEGKRLLARHRLVNAALEEEMK-QIHALSIKKA 74 (90)
Q Consensus 2 ~~~~~~I~~~l~~~l~~~~v~V~d~S------~~~gshf~i~VvS~~F~g~s~v~RHr~Vy~~L~~~~~-~IHAls~i~t 74 (90)
.|+.++|+++|+.+|+|.+|+|+|+| +|+|+||+|+|||+.|+|||+|+|||+||++|+++|+ +||||+ |+|
T Consensus 1 mm~~~~I~~~L~~~l~~~~l~V~d~S~~H~~~~g~~~Hf~v~IVS~~F~G~s~v~RHRlVy~~L~~~i~~~IHALs-i~t 79 (105)
T PRK11628 1 MMIREQIEEKLRAAFQPVFLEVVDESYRHNVPAGSESHFKVVLVSDRFTGERFLNRHRMIYSTLAEELSTTVHALA-LHT 79 (105)
T ss_pred CCcHHHHHHHHHhhCCCcEEEEEECcccccCCCCCCceEEEEEEChHhCCCCHHHHHHHHHHHHHHHHhCCcccee-eec
Confidence 37789999999999999999999999 3688999999999999999999999999999999999 699999 999
Q ss_pred CCHHHHHHchhh
Q 034588 75 MTPEQWKQQQES 86 (90)
Q Consensus 75 ~tp~Ew~~~~~~ 86 (90)
|||+||++++.+
T Consensus 80 ~tp~Ew~~~~~~ 91 (105)
T PRK11628 80 YTIKEWEGLQDT 91 (105)
T ss_pred CCHHHHHHhhCC
Confidence 999999976543
No 2
>KOG3348 consensus BolA (bacterial stress-induced morphogen)-related protein [Signal transduction mechanisms]
Probab=100.00 E-value=2e-33 Score=179.91 Aligned_cols=83 Identities=58% Similarity=0.954 Sum_probs=80.4
Q ss_pred CcccHHHHHHHHhhcCCCCeEEEEeCCCCCcceEEEEEEccccCCCCHHHHHHHHHHHHHHhcccccccccCccCCHHHH
Q 034588 1 MGVTKEKVESTLTSKLNPSHLEVIDTSGGCGAKFEIEIVSEQFEGKRLLARHRLVNAALEEEMKQIHALSIKKAMTPEQW 80 (90)
Q Consensus 1 m~~~~~~I~~~l~~~l~~~~v~V~d~S~~~gshf~i~VvS~~F~g~s~v~RHr~Vy~~L~~~~~~IHAls~i~t~tp~Ew 80 (90)
|...++.|+++|++.|.|.+|+|.|.|+|||+.|.|.|||+.|+|+|+|+|||+||.+|+++|+.||||+ ++|+||++|
T Consensus 1 m~~~e~~l~~~L~~~l~p~~v~V~D~SgGCG~~F~v~IvS~~FeGKs~L~rHRlVN~~L~Eeik~iHalt-~kt~t~~~w 79 (85)
T KOG3348|consen 1 MTVTEERLEELLTEALEPEHVEVQDVSGGCGSMFDVVIVSAAFEGKSLLARHRLVNSILAEEIKEIHALT-IKTYTPEEW 79 (85)
T ss_pred CcchHHHHHHHHHhhcCceEEEEEEcCCCccceEEEEEEccccCChHHHHHHHHHHHHHHHHHHHHhhhe-eeecChhhh
Confidence 7889999999999999999999999999999999999999999999999999999999999999999999 999999999
Q ss_pred HHch
Q 034588 81 KQQQ 84 (90)
Q Consensus 81 ~~~~ 84 (90)
.+-.
T Consensus 80 ~~~~ 83 (85)
T KOG3348|consen 80 SKAS 83 (85)
T ss_pred cccc
Confidence 8643
No 3
>COG0271 BolA Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]
Probab=99.98 E-value=1e-32 Score=179.26 Aligned_cols=81 Identities=49% Similarity=0.853 Sum_probs=76.5
Q ss_pred CcccHHHHHHHHhhcCCCCeEEEEeCCC-------CCcceEEEEEEccccCCCCHHHHHHHHHHHHHHhccc-ccccccC
Q 034588 1 MGVTKEKVESTLTSKLNPSHLEVIDTSG-------GCGAKFEIEIVSEQFEGKRLLARHRLVNAALEEEMKQ-IHALSIK 72 (90)
Q Consensus 1 m~~~~~~I~~~l~~~l~~~~v~V~d~S~-------~~gshf~i~VvS~~F~g~s~v~RHr~Vy~~L~~~~~~-IHAls~i 72 (90)
|.+..++|+++|+++|+|..++|.|+|+ |||+||+|+|||+.|+|+|+|+|||+||++|+|+|++ ||||+ |
T Consensus 1 m~i~~~~Ie~~l~~~f~p~~l~i~deS~~h~~~~~g~~~Hf~i~IVS~~F~G~s~v~rHr~V~~~L~del~~~iHALa-l 79 (90)
T COG0271 1 MSIQRERIEKKLRAAFPPSFLEIIDESHRHHGHAGGGGSHFKVVIVSEAFQGKSLVARHRLVYSALKDELSGGIHALA-L 79 (90)
T ss_pred CCccHHHHHHHHHhcCCCceEEEEecccccccCCCCCCCeEEEEEEchhhCCccHHHHHHHHHHHHHHHHhccceeeE-e
Confidence 6677789999999999999999999996 6999999999999999999999999999999999995 99999 9
Q ss_pred ccCCHHHHHH
Q 034588 73 KAMTPEQWKQ 82 (90)
Q Consensus 73 ~t~tp~Ew~~ 82 (90)
+|+||+||+.
T Consensus 80 ~t~t~~e~~~ 89 (90)
T COG0271 80 HTYTPEEWKG 89 (90)
T ss_pred Eeeccchhcc
Confidence 9999999864
No 4
>PF01722 BolA: BolA-like protein; InterPro: IPR002634 This family consist of the morpho-protein BolA from Escherichia coli and its various homologs. In E. coli, over-expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division []. The expression of BolA is growth rate regulated and is induced during the transition into the the stationary phase []. BolA is also induced by stress during early stages of growth [] and may have a general role in stress response. It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5 [, ].; PDB: 1XS3_A 1V60_A 3O2E_A 1NY8_A 3TR3_A 2KZ0_A 2DHM_A 2KDN_A 1V9J_A.
Probab=99.97 E-value=5.6e-32 Score=170.64 Aligned_cols=69 Identities=57% Similarity=0.883 Sum_probs=62.3
Q ss_pred HHhhcCCCCeEEEEeCCC------CCcceEEEEEEccccCCCCHHHHHHHHHHHHHHhcc-cccccccCccCCHHHH
Q 034588 11 TLTSKLNPSHLEVIDTSG------GCGAKFEIEIVSEQFEGKRLLARHRLVNAALEEEMK-QIHALSIKKAMTPEQW 80 (90)
Q Consensus 11 ~l~~~l~~~~v~V~d~S~------~~gshf~i~VvS~~F~g~s~v~RHr~Vy~~L~~~~~-~IHAls~i~t~tp~Ew 80 (90)
||++.|+|+.++|.|+|. ++|+||+|.|||+.|+|||+|+|||+||++|+++|+ +||||+ |+|+||+||
T Consensus 1 Kl~~~l~~~~l~V~d~S~~H~~h~~g~sHf~i~IvS~~F~g~s~i~rhr~V~~~L~~~i~~~iHAls-i~t~tp~Ew 76 (76)
T PF01722_consen 1 KLKAALPPTHLEVEDESHKHAGHAGGGSHFKIIIVSDEFEGKSRIKRHRLVYKALKDEIKDGIHALS-IKTYTPEEW 76 (76)
T ss_dssp HHHHHHTTSEEEEEE-SSSSSS-CCSSSEEEEEEECGGGTTS-HHHHHHHHHHHTHHHHGCTCSEEE-EEEE-HHHH
T ss_pred ChhHhCCCcEEEEEECcccccCCCCCCceEEEEEEcHHhCCCCHHHHHHHHHHHHHHHhcCCceEEE-EEcCCcccC
Confidence 688999999999999992 249999999999999999999999999999999999 599999 999999999
No 5
>COG5007 Predicted transcriptional regulator, BolA superfamily [Transcription]
Probab=99.97 E-value=1.4e-30 Score=165.01 Aligned_cols=77 Identities=38% Similarity=0.606 Sum_probs=73.8
Q ss_pred ccHHHHHHHHhhcCCCCeEEEEeCCCCCcceEEEEEEccccCCCCHHHHHHHHHHHHHHhcc--cccccccCccCCHHHH
Q 034588 3 VTKEKVESTLTSKLNPSHLEVIDTSGGCGAKFEIEIVSEQFEGKRLLARHRLVNAALEEEMK--QIHALSIKKAMTPEQW 80 (90)
Q Consensus 3 ~~~~~I~~~l~~~l~~~~v~V~d~S~~~gshf~i~VvS~~F~g~s~v~RHr~Vy~~L~~~~~--~IHAls~i~t~tp~Ew 80 (90)
|+.++|++.|++.||.++++|+ |+|+||.+++||+.|+|||+|+|||+||+.|.++|. .||||| |+||||+||
T Consensus 1 M~~e~Ik~ll~~~L~~e~v~V~----Gdg~Hf~vi~Vs~~F~g~srvkrqq~vYApL~~~i~~~~IHAls-ikt~Tp~eW 75 (80)
T COG5007 1 MDNEEIKSLLENALPLEEVEVE----GDGSHFQVIAVSEEFAGKSRVKRQQLVYAPLMAYIADNEIHALS-IKTYTPAEW 75 (80)
T ss_pred CCHHHHHHHHHhcCCccEEEEe----cCCceEEEEEehHhhcCccHHHHHHHHHHHHHHHhhcCceEEEE-eeecCHHHh
Confidence 6789999999999999999998 899999999999999999999999999999999998 599999 999999999
Q ss_pred HHch
Q 034588 81 KQQQ 84 (90)
Q Consensus 81 ~~~~ 84 (90)
++..
T Consensus 76 ~~~~ 79 (80)
T COG5007 76 ARDR 79 (80)
T ss_pred hhcc
Confidence 9764
No 6
>KOG2313 consensus Stress-induced protein UVI31+ [Signal transduction mechanisms]
Probab=99.93 E-value=1.4e-26 Score=151.95 Aligned_cols=78 Identities=41% Similarity=0.640 Sum_probs=73.5
Q ss_pred cccHHHHHHHHhhcCCCCeEEEEeCCC---------C---CcceEEEEEEccccCCCCHHHHHHHHHHHHHHhccc--cc
Q 034588 2 GVTKEKVESTLTSKLNPSHLEVIDTSG---------G---CGAKFEIEIVSEQFEGKRLLARHRLVNAALEEEMKQ--IH 67 (90)
Q Consensus 2 ~~~~~~I~~~l~~~l~~~~v~V~d~S~---------~---~gshf~i~VvS~~F~g~s~v~RHr~Vy~~L~~~~~~--IH 67 (90)
|.+...|+++|...|.|..+++.|+|+ | .++||.|.|||+.|+|+|+|+||||||++|+|++++ +|
T Consensus 9 g~~~~ri~~~l~~~lkp~~le~~n~S~~hagH~~~kg~~~~EtHFrv~vVS~~FeG~s~v~RHRlVy~~L~eEl~~~gvH 88 (100)
T KOG2313|consen 9 GPRESRIREKLFEALKPLNLELYNESHQHAGHAVPKGMDGAETHFRVEVVSSAFEGLSLVKRHRLVYKALKEELAGTGVH 88 (100)
T ss_pred CcHHHHHHHHhHhhcCcceEEEeeccccccccccccCCCCCccEEEEEEechhhCCccHHHHHHHHHHHHHHHhhcccee
Confidence 567899999999999999999999995 2 689999999999999999999999999999999983 99
Q ss_pred ccccCccCCHHHH
Q 034588 68 ALSIKKAMTPEQW 80 (90)
Q Consensus 68 Als~i~t~tp~Ew 80 (90)
||+ |.+.||+||
T Consensus 89 AL~-i~aKTP~e~ 100 (100)
T KOG2313|consen 89 ALS-IMAKTPSEV 100 (100)
T ss_pred EEE-eeccCCCCC
Confidence 999 999999998
No 7
>PF06858 NOG1: Nucleolar GTP-binding protein 1 (NOG1); InterPro: IPR010674 This domain represents a conserved region of approximately 60 residues in length within nucleolar GTP-binding protein 1 (NOG1). The NOG1 family includes eukaryotic, bacterial and archaeal proteins. In Saccharomyces cerevisiae, the NOG1 gene has been shown to be essential for cell viability, suggesting that NOG1 may play an important role in nucleolar functions. In particular, NOG1 is believed to be functionally linked to ribosome biogenesis, which occurs in the nucleolus. In eukaryotes, NOG1 mutants were found to disrupt the biogenesis of the 60S ribosomal subunit []. The DRG and OBG proteins as well as the prokaryotic NOG-like proteins are homologous throughout their length to the amino half of eukaryotic NOG1, which contains the GTP binding motifs (IPR006073 from INTERPRO); the N-terminal GTP-binding motif is required for function.; GO: 0005525 GTP binding; PDB: 2E87_A.
Probab=62.48 E-value=25 Score=21.09 Aligned_cols=36 Identities=19% Similarity=0.278 Sum_probs=28.0
Q ss_pred hcCCCCeEEEEeCCCCCcceEEEEEEccccCCCCHHHHHHHHHHHHHHhcc
Q 034588 14 SKLNPSHLEVIDTSGGCGAKFEIEIVSEQFEGKRLLARHRLVNAALEEEMK 64 (90)
Q Consensus 14 ~~l~~~~v~V~d~S~~~gshf~i~VvS~~F~g~s~v~RHr~Vy~~L~~~~~ 64 (90)
+.++...+-+.|.|+.||. .++.|-.+++-+++.|+
T Consensus 11 ~hL~~~ilfi~D~Se~CGy---------------sie~Q~~L~~~ik~~F~ 46 (58)
T PF06858_consen 11 AHLADAILFIIDPSEQCGY---------------SIEEQLSLFKEIKPLFP 46 (58)
T ss_dssp GGT-SEEEEEE-TT-TTSS----------------HHHHHHHHHHHHHHTT
T ss_pred HhhcceEEEEEcCCCCCCC---------------CHHHHHHHHHHHHHHcC
Confidence 5788999999999988875 68889999999999984
No 8
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=62.39 E-value=9.5 Score=24.99 Aligned_cols=41 Identities=20% Similarity=0.170 Sum_probs=27.8
Q ss_pred EccccCCCCHHHHHHHHHHHHHHhccc-ccccccCccCCHHHHHH
Q 034588 39 VSEQFEGKRLLARHRLVNAALEEEMKQ-IHALSIKKAMTPEQWKQ 82 (90)
Q Consensus 39 vS~~F~g~s~v~RHr~Vy~~L~~~~~~-IHAls~i~t~tp~Ew~~ 82 (90)
.-|.|.++|.=++-|+|..+|+ -.+ =+.+- +.-.--.+|..
T Consensus 33 ~vPgF~~ls~sKqRRLi~~ALE--~gd~~~~Vv-FEKvGWGrW~a 74 (92)
T PF10330_consen 33 SVPGFSDLSPSKQRRLIMAALE--GGDKDGDVV-FEKVGWGRWDA 74 (92)
T ss_pred cCCCcccCCHHHHHHHHHHHHh--cCCCCCCEE-EEEeccceeee
Confidence 3489999999999999999998 222 33333 44444455543
No 9
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=52.48 E-value=26 Score=21.18 Aligned_cols=49 Identities=10% Similarity=0.138 Sum_probs=29.5
Q ss_pred cHHHHHHHHhhcCCCCeEEEEeCCCCCcceEEEEEEccccCCCCHHHHHHHHHHHHHHhc
Q 034588 4 TKEKVESTLTSKLNPSHLEVIDTSGGCGAKFEIEIVSEQFEGKRLLARHRLVNAALEEEM 63 (90)
Q Consensus 4 ~~~~I~~~l~~~l~~~~v~V~d~S~~~gshf~i~VvS~~F~g~s~v~RHr~Vy~~L~~~~ 63 (90)
-..+|.++|...||+..|.|..-|. ..+.|. . -..=+ +..|..+|.+.+
T Consensus 9 L~~EL~kRl~~~yPd~~v~Vr~~s~---~~l~v~--g-----~~~~~-k~~i~~iLqe~w 57 (65)
T PF06183_consen 9 LESELTKRLHRQYPDAEVRVRPGSA---NGLSVS--G-----GKKDD-KERIEEILQEMW 57 (65)
T ss_dssp HHHHHHHHHHHH-SS-EEEEEEESS----EEEEE--S-------HHH-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCceEeeeeccc---CccccC--C-----cCchH-HHHHHHHHHHHH
Confidence 3578999999999999999985553 233332 1 11112 666777777654
No 10
>TIGR02174 CXXU_selWTH selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam.
Probab=51.86 E-value=51 Score=19.80 Aligned_cols=35 Identities=14% Similarity=0.184 Sum_probs=26.8
Q ss_pred ccHHHHHHHHhhcCCCCeEEEEeCCCCCcceEEEEE
Q 034588 3 VTKEKVESTLTSKLNPSHLEVIDTSGGCGAKFEIEI 38 (90)
Q Consensus 3 ~~~~~I~~~l~~~l~~~~v~V~d~S~~~gshf~i~V 38 (90)
.....+.+.|.+.||...+.+.... +.+.-|.|.+
T Consensus 13 ~Ra~~l~q~L~~~Fp~~~v~~~~~~-~~~G~Fev~~ 47 (72)
T TIGR02174 13 PRAAWLKQELLEEFPDLEIEGENTP-PTTGAFEVTV 47 (72)
T ss_pred HHHHHHHHHHHHHCCCCeeEEeeec-CCCcEEEEEE
Confidence 3567899999999999888777654 3455899976
No 11
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=51.21 E-value=24 Score=25.13 Aligned_cols=50 Identities=8% Similarity=0.151 Sum_probs=31.6
Q ss_pred cHHHHHHHHhhc-CCCCeEEEEeCCCCCcceEEEEEEccccCCCCHHHHHHHHHHHH
Q 034588 4 TKEKVESTLTSK-LNPSHLEVIDTSGGCGAKFEIEIVSEQFEGKRLLARHRLVNAAL 59 (90)
Q Consensus 4 ~~~~I~~~l~~~-l~~~~v~V~d~S~~~gshf~i~VvS~~F~g~s~v~RHr~Vy~~L 59 (90)
.+..|+.+|++. |+++.|.+. +..+.|+|-++.+...-..+-..+|.+-+
T Consensus 136 kE~~iE~llkakGf~davv~~~------~~~v~VvV~~~~L~~~~~~~I~diV~~~~ 186 (196)
T PF12685_consen 136 KEMEIENLLKAKGFEDAVVFIE------DDSVDVVVKADKLSDAEAAQIIDIVMRET 186 (196)
T ss_dssp HHHHHHHHHHTTS-SEEEEE-S------SSEEEEEEE-S---HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCCCceEEEee------CCEEEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence 357899999988 999999884 44899999999855554555555554443
No 12
>PF01877 RNA_binding: RNA binding; InterPro: IPR002739 The proteins in this entry are functionally uncharacterised.; PDB: 2WNY_B 2NWU_A 2NRQ_A 2OGK_A 3D7A_B 3C9G_B 2PZZ_D.
Probab=49.53 E-value=69 Score=21.19 Aligned_cols=39 Identities=28% Similarity=0.552 Sum_probs=27.2
Q ss_pred cHHHHHHHHhhcC-CCCeEEEEeCCCCCcceEE--EEEEccccCCC
Q 034588 4 TKEKVESTLTSKL-NPSHLEVIDTSGGCGAKFE--IEIVSEQFEGK 46 (90)
Q Consensus 4 ~~~~I~~~l~~~l-~~~~v~V~d~S~~~gshf~--i~VvS~~F~g~ 46 (90)
+.+++.+.|.+-| |+..+.++...| ||. |.+.+-...|.
T Consensus 14 D~eKV~~Al~nlf~~~~~~~~~~~~G----~ygn~I~~l~~~i~~~ 55 (120)
T PF01877_consen 14 DEEKVKKALSNLFPPDAEIEIEEEEG----HYGNPITILEVRIEGK 55 (120)
T ss_dssp -HHHHHHHHHHHSCTTSEEEEEEEEC----CEEEEEEEEEEEEEEC
T ss_pred CHHHHHHHHHHHhCCCCceEEEEecc----ccCCceEEEEEEEecc
Confidence 5688999999999 778888875553 554 55555555544
No 13
>PRK00447 hypothetical protein; Provisional
Probab=43.96 E-value=55 Score=22.67 Aligned_cols=33 Identities=18% Similarity=0.302 Sum_probs=24.3
Q ss_pred cHHHHHHHHhhcCCCCeEEEEeCCCCCcceEEEEEEcc
Q 034588 4 TKEKVESTLTSKLNPSHLEVIDTSGGCGAKFEIEIVSE 41 (90)
Q Consensus 4 ~~~~I~~~l~~~l~~~~v~V~d~S~~~gshf~i~VvS~ 41 (90)
+.+++.+.|.+-||+..+++.+ +.||.|.+.+-
T Consensus 16 D~eKV~~Ai~Nifp~~~ie~~~-----~G~~~I~v~~~ 48 (144)
T PRK00447 16 DEEKVKKAILNFFDFEKFEAED-----EGEYKILVGEA 48 (144)
T ss_pred CHHHHHHHHHhhCCcceEEEEe-----cCeeEEEEEEE
Confidence 4578899999999999988763 23777666544
No 14
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=39.81 E-value=63 Score=19.51 Aligned_cols=37 Identities=22% Similarity=0.310 Sum_probs=26.2
Q ss_pred CcccHHHHHHHHhhcCCCCeEEEEeCCCCCcceEEEEEEccc
Q 034588 1 MGVTKEKVESTLTSKLNPSHLEVIDTSGGCGAKFEIEIVSEQ 42 (90)
Q Consensus 1 m~~~~~~I~~~l~~~l~~~~v~V~d~S~~~gshf~i~VvS~~ 42 (90)
|.++-++...+.++.||. +++.+.+ |.-.-++|+.|.
T Consensus 1 ~~~t~~~~~~r~~e~Fp~--~slvef~---g~~~PvtI~CP~ 37 (60)
T PF05265_consen 1 MAMTFESAASRFEEKFPH--YSLVEFS---GVATPVTIRCPK 37 (60)
T ss_pred CceeHHHHHHHHHHHCCC--ceEEEEe---CCCCceEEECCC
Confidence 778899999999999998 5555444 334556665554
No 15
>TIGR03435 Soli_TIGR03435 Solibacter paralogous family TIGR03435. This model describes a paralogous family of about 40 proteins found in Solibacter usitatus Ellin6076, one of the first three members of the Acidobacteria to be sequenced, and nowhere else. The family is well-diversified, with few pairs showing greater than 50 % pairwise identity. Two members of the family are longer, multidomain proteins with (two different) fused peptidase domains.
Probab=39.19 E-value=1.1e+02 Score=23.06 Aligned_cols=59 Identities=14% Similarity=0.180 Sum_probs=43.3
Q ss_pred HHHHHHhhcCCCCeEEEEeCCCCCcceEEEEEEccccCCCCHHHHHHHHHHHHHHhcc-ccc
Q 034588 7 KVESTLTSKLNPSHLEVIDTSGGCGAKFEIEIVSEQFEGKRLLARHRLVNAALEEEMK-QIH 67 (90)
Q Consensus 7 ~I~~~l~~~l~~~~v~V~d~S~~~gshf~i~VvS~~F~g~s~v~RHr~Vy~~L~~~~~-~IH 67 (90)
.++++|..++.....+|.--+--...+|.|...-| .|-++=+.-.|+-++|.+-|+ .+|
T Consensus 36 tL~~lI~~AY~v~~~qv~GP~Wl~serfDi~Ak~p--~g~~~~q~~~MLQ~LLaeRF~L~~H 95 (237)
T TIGR03435 36 TLRDLIQAAYGVKPYQVSGPDWLDSERFDIVAKAP--AGATREQVRLMLQTLLAERFKLAVH 95 (237)
T ss_pred CHHHHHHHHhCCCHHheeCCCcCCccceeEEEeCC--CCCCHHHHHHHHHHHHHHhhCeEEe
Confidence 46777777776665556521111357899999888 788888888999999999998 666
No 16
>PF06006 DUF905: Bacterial protein of unknown function (DUF905); InterPro: IPR009253 This family consists of several short hypothetical proteobacterial proteins of unknown function.; PDB: 2HJJ_A.
Probab=37.57 E-value=33 Score=21.40 Aligned_cols=17 Identities=18% Similarity=0.376 Sum_probs=10.8
Q ss_pred eEEEEeCCCCCcceEEEEEE
Q 034588 20 HLEVIDTSGGCGAKFEIEIV 39 (90)
Q Consensus 20 ~v~V~d~S~~~gshf~i~Vv 39 (90)
.|-|+| +.|+||+++|-
T Consensus 22 NV~IeD---dqg~HfRlvvR 38 (70)
T PF06006_consen 22 NVFIED---DQGTHFRLVVR 38 (70)
T ss_dssp TEEEES----SSS--EEEEE
T ss_pred ceeecc---CCCCeEEEEEE
Confidence 467776 35789999998
No 17
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=36.63 E-value=54 Score=20.79 Aligned_cols=50 Identities=6% Similarity=0.125 Sum_probs=31.4
Q ss_pred cHHHHHHHHhhcCCCCe--EEEEeCCCCCcceEEEEEEccccCCCCHHHHHHHHHHHHHHhcc
Q 034588 4 TKEKVESTLTSKLNPSH--LEVIDTSGGCGAKFEIEIVSEQFEGKRLLARHRLVNAALEEEMK 64 (90)
Q Consensus 4 ~~~~I~~~l~~~l~~~~--v~V~d~S~~~gshf~i~VvS~~F~g~s~v~RHr~Vy~~L~~~~~ 64 (90)
-..+|.++|...||+.. |.|.--|. .+..|.=.+.. + +..|..+|.+.+.
T Consensus 21 L~~EL~kRl~~~fPd~~~~v~Vr~~s~---n~lsv~g~~k~-------d-K~~i~eiLqE~we 72 (81)
T PRK10597 21 LAGELSRRIQYAFPDNEGHVSVRYAAA---NNLSVIGATKE-------D-KDRISEILQETWE 72 (81)
T ss_pred HHHHHHHHHHhhCCCCCccEEEeecCC---CceEecCCCcc-------h-HHHHHHHHHHHHh
Confidence 35789999999999987 99973332 34443211111 2 4447777777653
No 18
>PF13739 DUF4163: Domain of unknown function (DUF4163); PDB: 3CYG_B.
Probab=35.26 E-value=78 Score=18.80 Aligned_cols=34 Identities=21% Similarity=0.332 Sum_probs=26.4
Q ss_pred cceEEEEEEccccCCCCHHHHHHHHHHHHHHhcc
Q 034588 31 GAKFEIEIVSEQFEGKRLLARHRLVNAALEEEMK 64 (90)
Q Consensus 31 gshf~i~VvS~~F~g~s~v~RHr~Vy~~L~~~~~ 64 (90)
...+.+.|.-|.|.|+.--+-.+.||+.|...+.
T Consensus 11 ~~~~~~~i~yP~~~~~~~~~~~~~IN~~i~~~i~ 44 (101)
T PF13739_consen 11 NDCYEIDIKYPVIEGLKNKELQKKINDFIENQID 44 (101)
T ss_dssp -SSEEEEEEEEEE-S-S-HHHHHHHHHHHHHHHH
T ss_pred CCeEEEEEEEEEEcCCCCHHHHHHHHHHHHHHHH
Confidence 4578999999999997777778899999988876
No 19
>PF12170 DNA_pol3_tau_5: DNA polymerase III tau subunit V interacting with alpha; InterPro: IPR021029 This domain family is found in bacteria, and is approximately 140 amino acids in length. The family is found in association with PF00004 from PFAM. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. The extreme C-terminal region of this domain 5 is the part which interacts with the alpha subunit of the DNA polymerase III holoenzyme [, ]. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 2AYA_A.
Probab=34.45 E-value=1e+02 Score=21.12 Aligned_cols=53 Identities=19% Similarity=0.107 Sum_probs=33.9
Q ss_pred cceEEEEEEccccCCCCHHHHHHHHHHHHHHhcc-ccccccc---C--ccCCHHHHHHchh
Q 034588 31 GAKFEIEIVSEQFEGKRLLARHRLVNAALEEEMK-QIHALSI---K--KAMTPEQWKQQQE 85 (90)
Q Consensus 31 gshf~i~VvS~~F~g~s~v~RHr~Vy~~L~~~~~-~IHAls~---i--~t~tp~Ew~~~~~ 85 (90)
|.+.. ..+.+.+.-+..=..+..+..+|.+.++ .|. |+| - ...||-||..+-.
T Consensus 51 ~~~v~-L~L~~~q~HL~~~~a~~~L~~ALs~~~g~~i~-L~I~~~~~~~~~TP~e~r~~i~ 109 (142)
T PF12170_consen 51 DDQVC-LHLRPSQKHLNNDSAQEQLQQALSEYLGEPIK-LSIEEGDNPARETPLEIRQRIY 109 (142)
T ss_dssp SSEEE-EEE-GGGTTT--HHHHHHHHHHHHHHHSS--E-EEEEE---TTS--HHHHHHHHH
T ss_pred CCEEE-EEEChhhHhhCCHHHHHHHHHHHHHHhCCCEE-EEEEECCCCCCCCHHHHHHHHH
Confidence 44664 4478889999999999999999999998 444 331 1 2479999986543
No 20
>COG1854 LuxS LuxS protein involved in autoinducer AI2 synthesis [Signal transduction mechanisms]
Probab=33.78 E-value=1.1e+02 Score=21.91 Aligned_cols=33 Identities=27% Similarity=0.539 Sum_probs=25.9
Q ss_pred HHHHHHhhcCCCCeEEEEeCCC-CCcceEEEEEEc
Q 034588 7 KVESTLTSKLNPSHLEVIDTSG-GCGAKFEIEIVS 40 (90)
Q Consensus 7 ~I~~~l~~~l~~~~v~V~d~S~-~~gshf~i~VvS 40 (90)
-+...|++.++.. ++|+|.|. ||.+=|.+.++-
T Consensus 59 L~A~~iRnh~~g~-~~iID~SPMGCrTGFYm~l~G 92 (161)
T COG1854 59 LLAGFIRNHLNGN-VEIIDISPMGCRTGFYMILIG 92 (161)
T ss_pred HHHHHHHhcccCc-eeEEEecCcccccceEEEEEC
Confidence 3456677888877 99999996 788888887764
No 21
>PRK14635 hypothetical protein; Provisional
Probab=32.75 E-value=1.7e+02 Score=20.35 Aligned_cols=83 Identities=19% Similarity=0.189 Sum_probs=52.5
Q ss_pred CcccHHHHHHHHhhcCCCCeEEEEeCCC-CCcceEEEEEEcccc----CCCCHHHHHHHHHHHHHHhcc---cccccccC
Q 034588 1 MGVTKEKVESTLTSKLNPSHLEVIDTSG-GCGAKFEIEIVSEQF----EGKRLLARHRLVNAALEEEMK---QIHALSIK 72 (90)
Q Consensus 1 m~~~~~~I~~~l~~~l~~~~v~V~d~S~-~~gshf~i~VvS~~F----~g~s~v~RHr~Vy~~L~~~~~---~IHAls~i 72 (90)
|.++.++|++.++..+.. -+++.|... +.|.+..++|.=+.. .| -.+..--.|-..+.+.+. .+++.. +
T Consensus 1 ~~~~~~~i~~l~~~~~~~-g~el~dve~~~~~~~~~lrV~ID~~~~~~~g-v~lddC~~vSr~is~~LD~~d~~~~Y~-L 77 (162)
T PRK14635 1 MTVSEEEISEILDRVLAL-PVKLYSLKVNQRPNHSLIEVVLDNLEHPYGS-VSLLECEQVSRKLKEELERISPDLDFT-L 77 (162)
T ss_pred CCCcHHHHHHHHHHHHCC-CCEEEEEEEEecCCCcEEEEEEecCCCCCCC-cCHHHHHHHHHHHHHHhCCCCCCCCeE-E
Confidence 788899999999888864 666666542 334454444444443 34 457777777777777775 244444 3
Q ss_pred ---------ccCCHHHHHHchhh
Q 034588 73 ---------KAMTPEQWKQQQES 86 (90)
Q Consensus 73 ---------~t~tp~Ew~~~~~~ 86 (90)
...+|.+|.+..++
T Consensus 78 EVSSPGldRpL~~~~~~~r~~G~ 100 (162)
T PRK14635 78 KVSSAGAERKLRLPEDLDRFRGI 100 (162)
T ss_pred EEcCCCCCCcCCCHHHHHHhCCC
Confidence 34667788766554
No 22
>PF12543 DUF3738: Protein of unknown function (DUF3738); InterPro: IPR017801 This entry describes a paralogous family of about 40 proteins first found in Solibacter usitatus (strain Ellin6076), one of the first three members of the Acidobacteria to be sequenced. The family is well-diversified, with few protein pairs showing greater than 50 % pairwise identity. A few members of the family are longer, multidomain proteins.
Probab=31.64 E-value=1.1e+02 Score=21.87 Aligned_cols=58 Identities=12% Similarity=0.185 Sum_probs=39.1
Q ss_pred HHHHhhcCCCCeEEEEeCCC-CCcceEEEEEEccccCCCCHHHHHHHHHHHHHHhcc-cccc
Q 034588 9 ESTLTSKLNPSHLEVIDTSG-GCGAKFEIEIVSEQFEGKRLLARHRLVNAALEEEMK-QIHA 68 (90)
Q Consensus 9 ~~~l~~~l~~~~v~V~d~S~-~~gshf~i~VvS~~F~g~s~v~RHr~Vy~~L~~~~~-~IHA 68 (90)
+.+|..++....-.|..-.. -...+|.|....|. +-+.=+...|+-+.|.+.|+ .+|-
T Consensus 2 ~~lI~~Ay~v~~~qiv~~P~W~~~~ryDI~Ak~p~--~~~~~q~~~MLq~lLaeRF~L~~H~ 61 (189)
T PF12543_consen 2 KDLIQFAYGVQPYQIVGGPDWLDSERYDIVAKVPP--GSTRDQLRLMLQALLAERFKLKVHR 61 (189)
T ss_pred HHHHHHHHCCChhhcccCCCCCccCceeEEEECCC--CCCHHHHHHHHHHHHHHHhCcEEEe
Confidence 45666666655444431111 03478999987754 66677799999999999998 6663
No 23
>cd02164 PPAT_CoAS phosphopantetheine adenylyltransferase domain of eukaryotic and archaeal bifunctional enzymes. The PPAT domain of the bifunctional enzyme with PPAT and DPCK functions. The final two steps of the CoA biosynthesis pathway are catalyzed by phosphopantetheine adenylyltransferase (PPAT) and dephospho-CoA (dPCoA) kinase (DPCK). The PPAT reaction involves the reversible adenylation of 4'-phosphopantetheine to form 3'-dPCoA and PPi, and DPCK catalyses phosphorylation of the 3'-hydroxy group of the ribose moiety of dPCoA. In eukaryotes the two enzymes are part of a large multienzyme complex . Studies in Corynebacterium ammoniagenes suggested that separate enzymes were present, and this was confirmed through identification of the bacterial PPAT/CoAD.
Probab=31.47 E-value=1.2e+02 Score=20.62 Aligned_cols=49 Identities=18% Similarity=0.235 Sum_probs=27.5
Q ss_pred HHHHHHHhhcCCCCeEEEEeCC---CCC--cceEEEEEEcccc-CCCCHHHHHHH
Q 034588 6 EKVESTLTSKLNPSHLEVIDTS---GGC--GAKFEIEIVSEQF-EGKRLLARHRL 54 (90)
Q Consensus 6 ~~I~~~l~~~l~~~~v~V~d~S---~~~--gshf~i~VvS~~F-~g~s~v~RHr~ 54 (90)
+.+++.|...-|+..++|...+ |.. .-.|++.|||+.. .|--.|+..|.
T Consensus 57 ~~l~~~l~~~~~~~~~~i~~i~d~~Gpt~~~~~~d~lVVS~ET~~~~~~iN~~R~ 111 (143)
T cd02164 57 ANLHEFLVDLKPTLKYEIVPIDDPYGPTGTDPDLEAIVVSPETYPGALKINRKRE 111 (143)
T ss_pred HHHHHHHHhcCCCceEEEEEccCCCCCcccCCCCCEEEEcHHHhhhHHHHHHHHH
Confidence 3455555433333344444333 222 3579999999987 55555666665
No 24
>COG3325 ChiA Chitinase [Carbohydrate transport and metabolism]
Probab=29.96 E-value=60 Score=26.76 Aligned_cols=48 Identities=17% Similarity=0.195 Sum_probs=35.9
Q ss_pred HHHHHhhcCCCCeEEEEeCCCCCcceEEEEEEccccCCCCHHHHHHHHHHHHHHh
Q 034588 8 VESTLTSKLNPSHLEVIDTSGGCGAKFEIEIVSEQFEGKRLLARHRLVNAALEEE 62 (90)
Q Consensus 8 I~~~l~~~l~~~~v~V~d~S~~~gshf~i~VvS~~F~g~s~v~RHr~Vy~~L~~~ 62 (90)
+-+-|++.|..+.++ .|.||.++|-++.+.++-.-..|..|-+.|...
T Consensus 199 Ll~eLR~~LD~a~~e-------dgr~Y~LTiA~~as~~~l~~~~~~~~~~~vDyi 246 (441)
T COG3325 199 LLQELRKKLDKAGVE-------DGRHYQLTIAAPASKDKLEGLNHAEIAQYVDYI 246 (441)
T ss_pred HHHHHHHHHhhcccc-------cCceEEEEEecCCchhhhhcccHHHHHHHHhhh
Confidence 344455555555442 478999999999999999888888888887654
No 25
>smart00542 FYRC "FY-rich" domain, C-terminal region. is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.
Probab=29.35 E-value=1.1e+02 Score=19.04 Aligned_cols=32 Identities=28% Similarity=0.335 Sum_probs=26.6
Q ss_pred eEEEEEEc---cccCCCCHHHHHHHHHHHHHHhcc
Q 034588 33 KFEIEIVS---EQFEGKRLLARHRLVNAALEEEMK 64 (90)
Q Consensus 33 hf~i~VvS---~~F~g~s~v~RHr~Vy~~L~~~~~ 64 (90)
+|.|++.+ ..|.|.|.=.=|++|++.+.+...
T Consensus 1 lF~v~~~~~~~~~~~~~S~~~~W~~vl~~v~~~r~ 35 (86)
T smart00542 1 LFRVEIESDPDEVFKGESPEKCWEMVLERVQEARI 35 (86)
T ss_pred CeEEEEecCCCCeEEeCCHHHHHHHHHHHHHHHHH
Confidence 46677776 358999999999999999999875
No 26
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=27.81 E-value=97 Score=23.33 Aligned_cols=60 Identities=18% Similarity=0.294 Sum_probs=32.7
Q ss_pred HHHHHHHHhh-cCCCC---eEEEEeCCC----CCcceEEEEEEccc------cCCCCH--HHHHHHHHHHHHHhcc
Q 034588 5 KEKVESTLTS-KLNPS---HLEVIDTSG----GCGAKFEIEIVSEQ------FEGKRL--LARHRLVNAALEEEMK 64 (90)
Q Consensus 5 ~~~I~~~l~~-~l~~~---~v~V~d~S~----~~gshf~i~VvS~~------F~g~s~--v~RHr~Vy~~L~~~~~ 64 (90)
.++++..+.. .++.. .+-|.|.+. .+|+|+.+.|+|-. |..++. -.--+.+.+.|++.++
T Consensus 73 ~~e~~~~~~pl~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~~f~hyDS~~n~nt~~a~~l~~kl~~ll~ 148 (223)
T KOG3246|consen 73 PEEIAMVLDPLDLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDGKFYHYDSLSNGNTKDAKSLMKKLRALLK 148 (223)
T ss_pred cHHHHHhcChhhcCCCceEEEEecCCCcccccCCCcceEEEEEEeeCCcEEEeecccCCCcHHHHHHHHHHHHHHh
Confidence 3455555554 55543 445566552 35799999999842 222222 1223445555666554
No 27
>PF03493 BK_channel_a: Calcium-activated BK potassium channel alpha subunit; InterPro: IPR003929 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. Ca2+-activated K+ channels are a diverse group of channels that are activated by an increase in intracellular Ca2+ concentration. They are found in the majority of nerve cells, where they modulate cell excitability and action potential. Three types of Ca2+-activated K+ channel have been characterised, termed small-conductance (SK), intermediate conductance (IK) and large conductance (BK) respectively []. BK channels (also referred to as maxi-K channels) are widely expressed in the body, being found in glandular tissue, smooth and skeletal muscle, as well as in neural tissues. They have been demonstrated to regulate arteriolar and airway diameter, and also neurotransmitter release. Each channel complex is thought to be composed of 2 types of subunit; the pore-forming (alpha) subunits and smaller accessory (beta) subunits. The alpha subunit of the BK channel was initially thought to share the characteristic 6TM organisation of the voltage-gated K+ channels. However, the molecule is now thought to possess an additional TM domain, with an extracellular N terminus and intracellular C terminus. This C-terminal region contains 4 predominantly hydrophobic domains, which are also thought to lie intracellularly. The extracellular N terminus and the first TM region are required for modulation by the beta subunit. The precise location of the Ca2+-binding site that modulates channel activation remains unknown, but it is thought to lie within the C-terminal hydrophobic domains.; GO: 0015269 calcium-activated potassium channel activity, 0006813 potassium ion transport, 0016020 membrane; PDB: 3NAF_A 3MT5_A 3U6N_E.
Probab=26.73 E-value=82 Score=20.15 Aligned_cols=28 Identities=18% Similarity=0.376 Sum_probs=19.7
Q ss_pred ceEEEEEEccccCCCCHHHHHHHHHHHHH
Q 034588 32 AKFEIEIVSEQFEGKRLLARHRLVNAALE 60 (90)
Q Consensus 32 shf~i~VvS~~F~g~s~v~RHr~Vy~~L~ 60 (90)
.=|.+.+ |+.|.|++.-+-=+.+|+-++
T Consensus 67 eIy~~~l-~~~f~G~~F~~~~~~~~~~~~ 94 (101)
T PF03493_consen 67 EIYTVKL-SSAFVGMTFTEAARLLYEKFG 94 (101)
T ss_dssp EEEEEE---GGGTTSBHHHHHHHHHHHS-
T ss_pred EEEEEeC-ChhhCCCcHHHHHHHHHHHcC
Confidence 3466666 999999999888888877543
No 28
>PF04774 HABP4_PAI-RBP1: Hyaluronan / mRNA binding family; InterPro: IPR006861 This entry includes the HABP4 protein family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan []. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability []. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function. Hyaluronan/mRNA-binding protein may be involved in nuclear functions such as the remodeling of chromatin and the regulation of transcription [, ].
Probab=26.51 E-value=41 Score=21.28 Aligned_cols=15 Identities=40% Similarity=0.541 Sum_probs=11.2
Q ss_pred ccCCHHHHHHchhhh
Q 034588 73 KAMTPEQWKQQQESN 87 (90)
Q Consensus 73 ~t~tp~Ew~~~~~~~ 87 (90)
+.+|.+||+.++.+.
T Consensus 78 k~mTLdE~k~~q~k~ 92 (106)
T PF04774_consen 78 KEMTLDEYKALQEKR 92 (106)
T ss_pred cccCHHHHHHHHHhh
Confidence 678999997666553
No 29
>PRK14634 hypothetical protein; Provisional
Probab=26.38 E-value=1.8e+02 Score=20.16 Aligned_cols=83 Identities=8% Similarity=0.068 Sum_probs=50.4
Q ss_pred ccHHHHHHHHhhcCCCCeEEEEeCCC-CCcceEEEEEEccccCCC-CHHHHHHHHHHHHHHhcc--c-c-cccccC----
Q 034588 3 VTKEKVESTLTSKLNPSHLEVIDTSG-GCGAKFEIEIVSEQFEGK-RLLARHRLVNAALEEEMK--Q-I-HALSIK---- 72 (90)
Q Consensus 3 ~~~~~I~~~l~~~l~~~~v~V~d~S~-~~gshf~i~VvS~~F~g~-s~v~RHr~Vy~~L~~~~~--~-I-HAls~i---- 72 (90)
...++|+++++..+...-+++.|... +.|.+.-++|.=+.=.|. -.+..--.|...|.+.+. . | .+.. +
T Consensus 4 ~~~~~i~~l~~~~~~~~G~elvdve~~~~~~~~~lrV~ID~~~g~~v~lddC~~vSr~is~~LD~~d~i~~~Y~-LEVSS 82 (155)
T PRK14634 4 PLLPDLETLASATAADKGFELCGIQVLTHLQPMTLQVQIRRSSGSDVSLDDCAGFSGPMGEALEASQLLTEAYV-LEISS 82 (155)
T ss_pred hhHHHHHHHHHHHHHHcCCEEEEEEEEeCCCCcEEEEEEECCCCCcccHHHHHHHHHHHHHHhcccccCCCCeE-EEEeC
Confidence 55788999998877766666665442 233444444444444662 558888888888877775 1 2 2222 2
Q ss_pred -----ccCCHHHHHHchhh
Q 034588 73 -----KAMTPEQWKQQQES 86 (90)
Q Consensus 73 -----~t~tp~Ew~~~~~~ 86 (90)
-..+|.+|.+..++
T Consensus 83 PGldRpL~~~~~f~r~~G~ 101 (155)
T PRK14634 83 PGIGDQLSSDRDFQTFRGF 101 (155)
T ss_pred CCCCCcCCCHHHHHHhCCC
Confidence 23667888766554
No 30
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=25.85 E-value=63 Score=16.78 Aligned_cols=14 Identities=29% Similarity=0.456 Sum_probs=9.6
Q ss_pred CcccHHHHHHHHhh
Q 034588 1 MGVTKEKVESTLTS 14 (90)
Q Consensus 1 m~~~~~~I~~~l~~ 14 (90)
||++.+++++.|+.
T Consensus 15 ~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 15 SGLSKEEIREFLEF 28 (30)
T ss_dssp TT--HHHHHHHHHH
T ss_pred cCCCHHHHHHHHHh
Confidence 68899999988863
No 31
>PRK13551 agmatine deiminase; Provisional
Probab=25.61 E-value=2.8e+02 Score=21.96 Aligned_cols=61 Identities=18% Similarity=0.223 Sum_probs=37.5
Q ss_pred cccHHHHHHHHhhcCCCCeEEEEeCC--CC-CcceEE----------EEEEccccCCCCHHHHHHHHHHHHHHh
Q 034588 2 GVTKEKVESTLTSKLNPSHLEVIDTS--GG-CGAKFE----------IEIVSEQFEGKRLLARHRLVNAALEEE 62 (90)
Q Consensus 2 ~~~~~~I~~~l~~~l~~~~v~V~d~S--~~-~gshf~----------i~VvS~~F~g~s~v~RHr~Vy~~L~~~ 62 (90)
+++.++|++.|++.|....+...+.- ++ ...|.. |.+....-..=+.-++-+..++.|+..
T Consensus 179 ~ls~~~ie~~Lk~~LGv~kvIWL~~g~~~DdTdGHiD~~arFv~~~~vl~~~~~d~~d~~~~~~~~~~~~L~~~ 252 (362)
T PRK13551 179 HLTKEQIEQLLRDYLGVEKVIWLPDGIYNDETDGHVDNVCCFVRPGEVALAWTDDENDPQYARSKAALEVLENT 252 (362)
T ss_pred CCCHHHHHHHHHHHHCCCEEEEECCCCCCCCCCcchhheEEeeCCCEEEEEecCCCCCccHHHHHHHHHHHHhh
Confidence 46889999999999999988876422 10 113542 444433333334446666666677664
No 32
>PF05392 COX7B: Cytochrome C oxidase chain VIIB; InterPro: IPR008433 Cytochrome oxidase subunit VIIB is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. The X-ray structure of azide-bound fully oxidized cytochrome c oxidase from bovine heart at 2.9 A resolution has been determined [].; GO: 0004129 cytochrome-c oxidase activity, 0005746 mitochondrial respiratory chain; PDB: 3AG2_X 3ASO_K 3ABL_X 1V55_K 1OCR_K 2DYS_X 1OCO_X 2EIK_X 3AG1_K 2Y69_X ....
Probab=25.13 E-value=24 Score=22.53 Aligned_cols=11 Identities=36% Similarity=1.036 Sum_probs=1.5
Q ss_pred ccCCHHHHHHc
Q 034588 73 KAMTPEQWKQQ 83 (90)
Q Consensus 73 ~t~tp~Ew~~~ 83 (90)
--.||.||+++
T Consensus 70 GRVtPKeWr~q 80 (80)
T PF05392_consen 70 GRVTPKEWREQ 80 (80)
T ss_dssp TTS--------
T ss_pred cccCchhhccC
Confidence 34688888764
No 33
>PF12224 Amidoligase_2: Putative amidoligase enzyme; InterPro: IPR022025 This family of proteins are likely to act as amidoligase enzymes [] Protein in this family are found in conserved gene neighbourhoods encoding a glutamine amidotransferase-like thiol peptidase (in proteobacteria) or an Aig2 family cyclotransferase protein (in firmicutes) [].
Probab=25.12 E-value=53 Score=23.51 Aligned_cols=46 Identities=15% Similarity=0.146 Sum_probs=32.0
Q ss_pred EEEeCCCCCcceEEEEEEccccCCCCHHHHHHHHHHHHHHhcccccccc
Q 034588 22 EVIDTSGGCGAKFEIEIVSEQFEGKRLLARHRLVNAALEEEMKQIHALS 70 (90)
Q Consensus 22 ~V~d~S~~~gshf~i~VvS~~F~g~s~v~RHr~Vy~~L~~~~~~IHAls 70 (90)
.+.|.| ||.|.+|-.-...|. ...+++.=.++-.+.+.|..+|...
T Consensus 107 ~~~~~s--cg~HVHv~~~~~~~~-~~~l~~l~~~~~~~E~~l~~~~~~~ 152 (252)
T PF12224_consen 107 IGTNDS--CGFHVHVGPEPPSFS-LETLKRLAKAFWLFEPWLRRLLPPD 152 (252)
T ss_pred ccccCC--eeEEEEECCCCCCcc-HHHHHHHHHHHHHHHHHHHHHcCCc
Confidence 334555 888998877655554 6667777777778888887666555
No 34
>PF02742 Fe_dep_repr_C: Iron dependent repressor, metal binding and dimerisation domain; InterPro: IPR001367 The diphtheria toxin repressor protein (DTXR) is a member of this group []. In Corynebacterium diphtheriae where it has been studied in some detail this protein acts as an iron-binding repressor of dipheteria toxin gene expression and may serve as a global regulator of gene expression. The N terminus may be involved in iron binding and may associate with the Tox operator. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005506 iron ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2X4H_D 2H09_A 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A 2F5D_A 3R61_A ....
Probab=25.11 E-value=36 Score=20.19 Aligned_cols=19 Identities=37% Similarity=0.635 Sum_probs=15.8
Q ss_pred CCHHHHHHHHHHHHHHhcc
Q 034588 46 KRLLARHRLVNAALEEEMK 64 (90)
Q Consensus 46 ~s~v~RHr~Vy~~L~~~~~ 64 (90)
...+.|||++...|.+.++
T Consensus 9 ~~i~~rH~~le~fl~~~lg 27 (71)
T PF02742_consen 9 ERILRRHRILEEFLVEVLG 27 (71)
T ss_dssp HHHHHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHHHHHHhC
Confidence 4568999999999988765
No 35
>PF01352 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) []. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box []. The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II, and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [, ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [, ]. KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome []. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1V65_A.
Probab=24.89 E-value=40 Score=18.49 Aligned_cols=13 Identities=15% Similarity=0.580 Sum_probs=7.5
Q ss_pred CCHHHHHHchhhh
Q 034588 75 MTPEQWKQQQESN 87 (90)
Q Consensus 75 ~tp~Ew~~~~~~~ 87 (90)
+|++||....+.+
T Consensus 10 fs~eEW~~L~~~Q 22 (41)
T PF01352_consen 10 FSQEEWELLDPAQ 22 (41)
T ss_dssp --HHHHHTS-HHH
T ss_pred cChhhccccccee
Confidence 8999998665544
No 36
>KOG3120 consensus Predicted haloacid dehalogenase-like hydrolase [General function prediction only]
Probab=23.98 E-value=20 Score=27.34 Aligned_cols=58 Identities=22% Similarity=0.380 Sum_probs=32.8
Q ss_pred cccHHHHHHHHhhcCC--CCeEEEEeCCCCCcceEEEEEEccc---cCCCCHHHHHHHHHHHHHHhc
Q 034588 2 GVTKEKVESTLTSKLN--PSHLEVIDTSGGCGAKFEIEIVSEQ---FEGKRLLARHRLVNAALEEEM 63 (90)
Q Consensus 2 ~~~~~~I~~~l~~~l~--~~~v~V~d~S~~~gshf~i~VvS~~---F~g~s~v~RHr~Vy~~L~~~~ 63 (90)
|.++++|++.++ .+| |-.+.+..--...| +|.+.||||+ |-+ .+=||--+.+++.+.+
T Consensus 70 gv~~~~ik~~~r-~iP~~Pgmv~lik~~ak~g-~~eliIVSDaNsfFIe--~~Lea~~~~d~F~~If 132 (256)
T KOG3120|consen 70 GVRIAEIKQVLR-SIPIVPGMVRLIKSAAKLG-CFELIIVSDANSFFIE--EILEAAGIHDLFSEIF 132 (256)
T ss_pred CCCHHHHHHHHh-cCCCCccHHHHHHHHHhCC-CceEEEEecCchhHHH--HHHHHccHHHHHHHHh
Confidence 567889999886 555 33444432222233 4999999986 222 2334444445554443
No 37
>PF05381 Peptidase_C21: Tymovirus endopeptidase; InterPro: IPR008043 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This entry is found in cysteine peptidases belong to the MEROPS peptidase family C21 (tymovirus endopeptidase family, clan CA). The type example is tymovirus endopeptidase (turnip yellow mosaic virus). The noncapsid protein expressed from ORF-206 of turnip yellow mosaic virus (TYMV) is autocatalytically processed by a papain-like protease, producing N-terminal 150kDa and C-terminal 70kDa proteins.; GO: 0003968 RNA-directed RNA polymerase activity, 0016032 viral reproduction
Probab=21.77 E-value=81 Score=21.02 Aligned_cols=41 Identities=22% Similarity=0.264 Sum_probs=29.1
Q ss_pred cccHHHHHHHHhhcCCCCeEEEEeCCC-C----------CcceEEEEEEccc
Q 034588 2 GVTKEKVESTLTSKLNPSHLEVIDTSG-G----------CGAKFEIEIVSEQ 42 (90)
Q Consensus 2 ~~~~~~I~~~l~~~l~~~~v~V~d~S~-~----------~gshf~i~VvS~~ 42 (90)
+..++++.+-|.+.||+..+.-...+. | .--||++++.|+.
T Consensus 15 ~~~~~~LW~~L~~~lPDSlL~n~ei~~~GLSTDhltaLa~~~~~~~~~hs~~ 66 (104)
T PF05381_consen 15 SISPETLWATLCEILPDSLLDNPEIRTLGLSTDHLTALAYRYHFQCTFHSDH 66 (104)
T ss_pred CCCHHHHHHHHHHhCchhhcCchhhhhcCCcHHHHHHHHHHHheEEEEEcCC
Confidence 578899999999999999885333331 1 1256888887764
No 38
>PF03413 PepSY: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification. ; InterPro: IPR005075 This signature, PepSY, is found in the propeptide of members of the MEROPS peptidase family M4 (clan MA(E)), which contains the thermostable thermolysins (3.4.24.27 from EC), and related thermolabile neutral proteases (bacillolysins) (3.4.24.28 from EC) from various species of Bacillus. It is also in many non-peptidase proteins, including Bacillus subtilis YpeB protein - a regulator of SleB spore cortex lytic enzyme - and a large number of eubacterial and archaeal cell wall-associated and secreted proteins which are mostly annotated as 'hypothetical protein'. Many extracellular bacterial proteases are produced as proenzymes. The propeptides usually have a dual function, i.e. they function as an intramolecular chaperone required for the folding of the polypeptide and as an inhibitor preventing premature activation of the enzyme. Analysis of the propeptide region of the M4 family of peptidases reveals two regions of conservation, the PepSY domain and a second domain, proximate to the N terminus, the FTP domain (IPR011096 from INTERPRO), which is also found in isolation in the propeptide of eukaryotic peptidases belong to MEROPS peptidase family M36. Propeptide domain swapping experiments, for example swapping the propeptide domain of PA protease with that of vibrolysin, both propeptides contain the FTP and PepSY domains, allows the PA protease domain to fold correctly and inhibits the C-terminal autoprocessing activity. However, swapping the propeptide of PA protease for the thermolysin propeptide, does not facilitate the correct folding nor the processing of the chimaeric protein into an active peptidase []. Mutational analysis of the Pseudomonas aeruginosa elastase gene revealed two mutations in the propeptide which resulted in the loss of inhibitory activity but not chaperone activity: A-15V and T-153I (where +1 is defined as the first residue of the mature peptidase). Both mutations resulted in peptidase activity, the T-153V mutation being much less effective than the A-15I mutation [] in activating peptidase activity. The T-153V mutation lies N-terminal to the FTP domain while the A-15I mutation is C-terminal to the PepSY domain. Given the diverse range of other proteins, both domains occur in in isolation, the exact function of each is still unclear; though it has been proposed that the PepSY domain primarily has inhibitory activity and in conjunction with the FTP domain in chaperone activity. ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0005576 extracellular region; PDB: 2GU3_A 3NQZ_A 3NQY_A 2KGY_A.
Probab=21.48 E-value=1.5e+02 Score=16.04 Aligned_cols=38 Identities=16% Similarity=0.194 Sum_probs=27.6
Q ss_pred ccHHHHHHHHhhcCCCCeEEEEeCCC-CCcceEEEEEEc
Q 034588 3 VTKEKVESTLTSKLNPSHLEVIDTSG-GCGAKFEIEIVS 40 (90)
Q Consensus 3 ~~~~~I~~~l~~~l~~~~v~V~d~S~-~~gshf~i~VvS 40 (90)
++.++..+...+.+|...+.+..... ....-|.|.+.+
T Consensus 2 is~~~A~~~A~~~~~~~~~~~~~~~~~~~~~~Y~v~~~~ 40 (64)
T PF03413_consen 2 ISEEQAVEIALKQYPGKVISVELEEDENGRLVYEVEVVS 40 (64)
T ss_dssp --HHHHHHHHHCCCCCEEEEEEEECC-TCEEEEEEEEEB
T ss_pred cCHHHHHHHHHHHCCCCEEEEEEccccCCcEEEEEEEEE
Confidence 57788889999999988777766554 444678888876
No 39
>COG1019 Predicted nucleotidyltransferase [General function prediction only]
Probab=21.09 E-value=2.7e+02 Score=19.90 Aligned_cols=47 Identities=21% Similarity=0.174 Sum_probs=24.6
Q ss_pred HHHHHHhhcCCCC--eEEEEeCCCC--CcceEEEEEEccccC-CCCHHHHHH
Q 034588 7 KVESTLTSKLNPS--HLEVIDTSGG--CGAKFEIEIVSEQFE-GKRLLARHR 53 (90)
Q Consensus 7 ~I~~~l~~~l~~~--~v~V~d~S~~--~gshf~i~VvS~~F~-g~s~v~RHr 53 (90)
.+.+.|...-++. .+.+.|.-|. ...+|.+.||||.=. |--.|++-|
T Consensus 62 ~l~~fl~~~~~~~~~iv~i~Dp~G~t~~~~~~e~iVVS~ET~~~Al~IN~~R 113 (158)
T COG1019 62 NLRNFLESIKADYEEIVPIDDPYGPTVEDPDFEAIVVSPETYPGALKINEIR 113 (158)
T ss_pred HHHHHHHHhcCCcceEEEecCCCCCCCCcCceeEEEEccccchhHHHHHHHH
Confidence 3444444333332 4444444332 346999999999753 333344443
No 40
>PF12845 TBD: TBD domain; InterPro: IPR024581 The Tbk1/Ikki binding domain (TBD) is a 40 amino acid domain able to bind kinases which is essential for poly(I:C)-induced IRF activation []. The domain is found in the SINTBAD, TANK and NAP1 proteins. This domain is predicted to form an alpha-helix with residues essential for kinase binding clustering on one side [].; PDB: 1KZZ_B 1L0A_B.
Probab=20.93 E-value=32 Score=20.50 Aligned_cols=18 Identities=39% Similarity=0.593 Sum_probs=0.0
Q ss_pred HHHHHHHHHhcccccccc
Q 034588 53 RLVNAALEEEMKQIHALS 70 (90)
Q Consensus 53 r~Vy~~L~~~~~~IHAls 70 (90)
+..|--|+++|..||.|+
T Consensus 10 ~~ay~ELkeE~~rl~~lt 27 (57)
T PF12845_consen 10 QLAYWELKEEMSRLHLLT 27 (57)
T ss_dssp ------------------
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 357888999999999998
No 41
>PRK00777 phosphopantetheine adenylyltransferase; Provisional
Probab=20.91 E-value=2.4e+02 Score=19.24 Aligned_cols=47 Identities=17% Similarity=0.287 Sum_probs=27.2
Q ss_pred HHHHHhhcCCCCeEEEEeCCC--C--CcceEEEEEEccc-cCCCCHHHHHHH
Q 034588 8 VESTLTSKLNPSHLEVIDTSG--G--CGAKFEIEIVSEQ-FEGKRLLARHRL 54 (90)
Q Consensus 8 I~~~l~~~l~~~~v~V~d~S~--~--~gshf~i~VvS~~-F~g~s~v~RHr~ 54 (90)
++..+....+...+.+...+. | ....|.+.|+|++ ..|-..|++.|.
T Consensus 59 v~~~~~~~~~~~~~~i~~i~d~~gp~~~~~~d~ivvs~et~~~~~~in~~r~ 110 (153)
T PRK00777 59 LKKFLKAVEYDREYEIVKIDDPYGPALEDDFDAIVVSPETYPGALKINEIRR 110 (153)
T ss_pred HHHHHHhcCCCCcEEEEeccccCCCccccCCCEEEEChhhhhhHHHHHHHHH
Confidence 344444434455555543221 1 1235999999998 777777766655
No 42
>PLN02388 phosphopantetheine adenylyltransferase
Probab=20.63 E-value=2.4e+02 Score=20.20 Aligned_cols=53 Identities=21% Similarity=0.249 Sum_probs=31.2
Q ss_pred HHHHHHHHhhcCCCCeEE---EEeCCCCC--cceEEEEEEcccc-CCCCHHHHHHHHHH
Q 034588 5 KEKVESTLTSKLNPSHLE---VIDTSGGC--GAKFEIEIVSEQF-EGKRLLARHRLVNA 57 (90)
Q Consensus 5 ~~~I~~~l~~~l~~~~v~---V~d~S~~~--gshf~i~VvS~~F-~g~s~v~RHr~Vy~ 57 (90)
.+.+++.|...-|...++ |.|.-|.. .-.|+..|||+.. .|--.|+..|.=+.
T Consensus 76 ~~~l~~fl~~~~p~~~~~i~~i~D~~Gpt~~~~~~d~LVVS~ET~~g~~~IN~~R~e~G 134 (177)
T PLN02388 76 MHNVEEYIKSIKPELVVQAEPIIDPYGPSIVDENLEAIVVSKETLPGGLSVNKKRAERG 134 (177)
T ss_pred HHHHHHHHHHcCCCceEEEEEecCCCCCcccCCCCCEEEEcHhHhhhHHHHHHHHHHCC
Confidence 345566665433433334 33333322 3589999999987 56666777775543
No 43
>PF04444 Dioxygenase_N: Catechol dioxygenase N terminus; InterPro: IPR007535 This domain is the N-terminal region of catechol, chlorocatechol or hydroxyquinol 1,2-dioxygenase proteins. This region is always found adjacent to the dioxygenase domain (IPR000627 from INTERPRO). Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes (IPR000486 from INTERPRO) use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) []. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Enzymes that belong to the intradiol family include catechol 1,2-dioxygenase (1,2-CTD) (1.13.11.1 from EC); protocatechuate 3,4-dioxygenase (3,4-PCD) (1.13.11.3 from EC); and chlorocatechol 1,2-dioxygenase (1.13.11.1 from EC) [].; GO: 0005506 iron ion binding, 0018576 catechol 1,2-dioxygenase activity, 0009712 catechol-containing compound metabolic process, 0055114 oxidation-reduction process; PDB: 3O6R_B 1S9A_A 3O6J_A 3O5U_B 3O32_B 3HHY_A 3HHX_A 3HJS_A 3HJQ_A 3HKP_A ....
Probab=20.00 E-value=1.3e+02 Score=18.58 Aligned_cols=19 Identities=16% Similarity=0.665 Sum_probs=9.7
Q ss_pred cccccccccCcc-CCHHHHHH
Q 034588 63 MKQIHALSIKKA-MTPEQWKQ 82 (90)
Q Consensus 63 ~~~IHAls~i~t-~tp~Ew~~ 82 (90)
+..+|++- -+. .|++||..
T Consensus 12 v~~lh~~i-~e~~lT~~E~~~ 31 (74)
T PF04444_consen 12 VRHLHDFI-REVDLTEDEWWA 31 (74)
T ss_dssp HHHHHHHH-HHCT--HHHHHH
T ss_pred HHHHHHHH-HHhCCCHHHHHH
Confidence 33455554 222 78999975
Done!