Query 031255
Match_columns 163
No_of_seqs 26 out of 28
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 11:30:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031255.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031255hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05697 Trigger_N: Bacterial 98.1 5.5E-06 1.2E-10 61.9 5.5 48 97-148 2-49 (145)
2 PRK01490 tig trigger factor; P 96.9 0.0018 3.8E-08 56.0 5.4 45 97-142 2-46 (435)
3 COG0544 Tig FKBP-type peptidyl 95.7 0.018 3.9E-07 52.1 5.2 45 97-142 2-46 (441)
4 TIGR00115 tig trigger factor. 93.5 0.082 1.8E-06 45.4 3.6 35 109-144 2-36 (408)
5 PRK02103 malonate decarboxylas 80.7 9.1 0.0002 29.6 6.8 56 95-151 30-88 (105)
6 TIGR03130 malonate_delta malon 79.7 11 0.00023 29.0 6.8 56 95-151 28-86 (98)
7 PRK01220 malonate decarboxylas 76.3 15 0.00032 28.3 6.8 55 95-150 27-83 (99)
8 PF13103 TonB_2: TonB C termin 67.5 8.9 0.00019 25.6 3.4 50 96-147 28-77 (85)
9 PF06857 ACP: Malonate decarbo 60.7 21 0.00046 26.3 4.6 37 95-131 15-56 (87)
10 PF03160 Calx-beta: Calx-beta 48.5 45 0.00097 22.9 4.4 33 83-116 4-37 (100)
11 PF02566 OsmC: OsmC-like prote 48.3 61 0.0013 21.8 5.0 40 90-129 32-80 (100)
12 cd04920 ACT_AKiii-DAPDC_2 ACT 45.7 18 0.00038 23.7 2.0 55 73-127 3-58 (63)
13 PF08175 SspO: Small acid-solu 34.2 17 0.00038 25.3 0.6 13 133-145 5-17 (51)
14 PF13656 RNA_pol_L_2: RNA poly 33.3 99 0.0022 21.8 4.3 31 102-132 37-68 (77)
15 cd04905 ACT_CM-PDT C-terminal 30.6 1.5E+02 0.0032 19.7 4.6 30 103-132 39-68 (80)
16 TIGR01920 Shik_kin_archae shik 29.2 1.5E+02 0.0031 24.7 5.3 62 72-143 7-68 (261)
17 PF05292 MCD: Malonyl-CoA deca 28.9 15 0.00032 33.6 -0.6 8 135-142 225-232 (354)
18 PF12549 TOH_N: Tyrosine hydro 28.2 27 0.00057 21.3 0.6 12 132-143 5-16 (25)
19 cd04917 ACT_AKiii-LysC-EC_2 AC 28.1 58 0.0013 20.7 2.2 56 73-128 4-60 (64)
20 PF12727 PBP_like: PBP superfa 25.0 52 0.0011 26.2 1.9 29 115-143 101-129 (193)
21 PRK13253 citrate lyase subunit 23.4 2.2E+02 0.0047 21.4 4.8 36 95-130 16-56 (92)
22 KOG3018 Malonyl-CoA decarboxyl 22.5 44 0.00095 30.7 1.2 22 121-142 182-212 (362)
23 TIGR01352 tonB_Cterm TonB fami 22.4 2.1E+02 0.0046 18.0 4.8 40 99-140 15-55 (74)
24 cd04915 ACT_AK-Ectoine_2 ACT d 21.7 64 0.0014 21.3 1.6 57 72-129 4-63 (66)
25 cd07620 BAR_SH3BP1 The Bin/Amp 20.9 26 0.00057 30.7 -0.6 44 117-162 25-69 (257)
26 cd06469 p23_DYX1C1_like p23_li 20.6 75 0.0016 20.7 1.7 16 103-118 3-18 (78)
27 cd07615 BAR_Endophilin_A3 The 20.4 42 0.0009 28.5 0.5 47 117-163 17-77 (223)
28 cd00298 ACD_sHsps_p23-like Thi 20.4 93 0.002 18.7 2.0 15 104-118 4-18 (80)
No 1
>PF05697 Trigger_N: Bacterial trigger factor protein (TF); InterPro: IPR008881 In the Escherichia coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains []. This group of sequences contain the ribosomal subunit association domain.; GO: 0006457 protein folding, 0015031 protein transport; PDB: 2D3O_1 1W26_A 1P9Y_A 1OMS_C 1T11_A 3GU0_A 2NSB_A 2NSC_A 3GTY_X.
Probab=98.12 E-value=5.5e-06 Score=61.90 Aligned_cols=48 Identities=33% Similarity=0.766 Sum_probs=42.4
Q ss_pred EEEEEcCCCCeEEEEEEecChhhHHHHHHHHHHhhhcCCCCCCceeccCCcc
Q 031255 97 KIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGNA 148 (163)
Q Consensus 97 kV~v~s~dd~~IqiRVdlsG~~Tq~VFd~Vf~klvraAqPIPGFRR~KGGKT 148 (163)
+|.++..++.++++.|++++...+..+++++.++++.+. |||||. ||.
T Consensus 2 ~v~~~~~~~~~~~~~v~v~~~~~~~~~~~~l~~~~k~~~-ipGFRk---GK~ 49 (145)
T PF05697_consen 2 KVTVEKIEDSKVKLEVEVPAEEVEKAYEKALKELAKKVK-IPGFRK---GKA 49 (145)
T ss_dssp EEEEEEESTTEEEEEEEE-HHHHHHHHHHHHHHHHTTTT-BTTS-T---TSS
T ss_pred ccEEEECCCcEEEEEEEECHHHHHHHHHHHHHHHHhhCC-CCCCCC---CCC
Confidence 577888999999999999999999999999999999996 999998 563
No 2
>PRK01490 tig trigger factor; Provisional
Probab=96.89 E-value=0.0018 Score=56.03 Aligned_cols=45 Identities=27% Similarity=0.574 Sum_probs=41.9
Q ss_pred EEEEEcCCCCeEEEEEEecChhhHHHHHHHHHHhhhcCCCCCCcee
Q 031255 97 KIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRR 142 (163)
Q Consensus 97 kV~v~s~dd~~IqiRVdlsG~~Tq~VFd~Vf~klvraAqPIPGFRR 142 (163)
+|.++..++.+.++.|+|+....+..+|+++.++++.+ -|||||+
T Consensus 2 ~v~~~~~~~~~~~l~v~v~~~~~~~~~~~~~~~~~k~~-~ipGFRk 46 (435)
T PRK01490 2 QVTVEKLEGLERRLTITVPAEEIEKAVDKALKKLAKTV-RIPGFRK 46 (435)
T ss_pred cceEEEcCCcEEEEEEEEcHHHHHHHHHHHHHHHHhhC-cCCCccC
Confidence 46788889999999999999999999999999999998 5999997
No 3
>COG0544 Tig FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones]
Probab=95.71 E-value=0.018 Score=52.07 Aligned_cols=45 Identities=31% Similarity=0.654 Sum_probs=42.2
Q ss_pred EEEEEcCCCCeEEEEEEecChhhHHHHHHHHHHhhhcCCCCCCcee
Q 031255 97 KIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRR 142 (163)
Q Consensus 97 kV~v~s~dd~~IqiRVdlsG~~Tq~VFd~Vf~klvraAqPIPGFRR 142 (163)
+|+++..++..+.|.|.|+....+.-+|++|.++++.+. |||||+
T Consensus 2 ~v~~e~~~~~~~~l~v~vp~~~~~~~~~~~~~~~~k~v~-IpGFRk 46 (441)
T COG0544 2 KVTVEKLEGLEVRLTVEVPAEEIKKALDKALKKLAKKVK-IPGFRK 46 (441)
T ss_pred CeeeeecCCcEEEEEEEECHHHHHHHHHHHHHHHHhhCc-CCCCCC
Confidence 367888999999999999999999999999999999987 999996
No 4
>TIGR00115 tig trigger factor. Trigger factor is a ribosome-associated molecular chaperone and is the first chaperone to interact with nascent polypeptide. Trigger factor can bind at the same time as the signal recognition particle (SRP), but is excluded by the SRP receptor (FtsY). The central domain of trigger factor has peptidyl-prolyl cis/trans isomerase activity. This protein is found in a single copy in virtually every bacterial genome.
Probab=93.53 E-value=0.082 Score=45.38 Aligned_cols=35 Identities=34% Similarity=0.679 Sum_probs=32.1
Q ss_pred EEEEEecChhhHHHHHHHHHHhhhcCCCCCCceecc
Q 031255 109 QVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREK 144 (163)
Q Consensus 109 qiRVdlsG~~Tq~VFd~Vf~klvraAqPIPGFRR~K 144 (163)
++.|+|+....+..||+++.++++.+ -|||||+=|
T Consensus 2 ~l~v~v~~~~~~~~~~k~~~~~~k~~-~ipGFRkGK 36 (408)
T TIGR00115 2 KLTVEVPAEEVEEEVDKALKELAKKV-KIPGFRKGK 36 (408)
T ss_pred eEEEEECHHHHHHHHHHHHHHHHhhC-CCCCccCCC
Confidence 58899999999999999999999999 599999854
No 5
>PRK02103 malonate decarboxylase subunit delta; Provisional
Probab=80.73 E-value=9.1 Score=29.63 Aligned_cols=56 Identities=16% Similarity=0.243 Sum_probs=44.9
Q ss_pred eeEEEEEcCC-CCeEEEEEEecChhhHHHHHHHHHHhhhcCCCCCCceec--cCCccCCc
Q 031255 95 DAKIVVESQD-EDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRRE--KGGNALYL 151 (163)
Q Consensus 95 dfkV~v~s~d-d~~IqiRVdlsG~~Tq~VFd~Vf~klvraAqPIPGFRR~--KGGKT~~I 151 (163)
|..|-++..+ +++++|+|+-|=+--+.+++.||+..+... |.||-|-. -+|-||.+
T Consensus 30 dLEVL~ep~~~~~~~~v~I~Tsv~Gf~~~WqaVl~~f~~r~-~~~~~~i~InD~GATP~V 88 (105)
T PRK02103 30 NLEVLVERVLPGGECEVEIRTAAVGFGAVWQAVVADFVERR-SPGGLRISINDGGARPDT 88 (105)
T ss_pred ceEEEEeccCCCCeEEEEEEecccCcHHHHHHHHHHHHhhC-CCCccEEEEeCCCCCchh
Confidence 7788888886 899999999998889999999999999888 77776643 35555543
No 6
>TIGR03130 malonate_delta malonate decarboxylase acyl carrier protein. Members of this protein family are the acyl carrier protein, also called the delta subunit, of malonate decarboxylase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl groups are transferred to the prosthetic group for catalysis.
Probab=79.65 E-value=11 Score=28.96 Aligned_cols=56 Identities=23% Similarity=0.382 Sum_probs=43.9
Q ss_pred eeEEEEEcC-CCCeEEEEEEecChhhHHHHHHHHHHhhhcCCCCCCceec--cCCccCCc
Q 031255 95 DAKIVVESQ-DEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRRE--KGGNALYL 151 (163)
Q Consensus 95 dfkV~v~s~-dd~~IqiRVdlsG~~Tq~VFd~Vf~klvraAqPIPGFRR~--KGGKT~~I 151 (163)
|..|-++.. ..++++|+|+-|=+--+.+++.||...+... |+||-|-. -.|-||.+
T Consensus 28 dLEVL~ep~~~~~~~~v~I~Tsv~Gf~~~Wqavl~rf~~~~-~~~~~~i~InD~GATP~V 86 (98)
T TIGR03130 28 DLEVLVEPGAEGGKTEVRITTSVDGFGAVWQAVIERFFARY-PLAGLQIEINDFGATPAV 86 (98)
T ss_pred ceEEEEEcCCCCCeEEEEEEecccCcHHHHHHHHHHHHhhC-CCCccEEEEecCCCCchh
Confidence 777888885 4899999999998888999999999998887 77875543 45555543
No 7
>PRK01220 malonate decarboxylase subunit delta; Provisional
Probab=76.29 E-value=15 Score=28.26 Aligned_cols=55 Identities=13% Similarity=0.224 Sum_probs=42.6
Q ss_pred eeEEEEEcCCCCeEEEEEEecChhhHHHHHHHHHHhhhcCCCCCCceec--cCCccCC
Q 031255 95 DAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRRE--KGGNALY 150 (163)
Q Consensus 95 dfkV~v~s~dd~~IqiRVdlsG~~Tq~VFd~Vf~klvraAqPIPGFRR~--KGGKT~~ 150 (163)
|..|-++...+++++|+|+-|=+--+.+++.||+..+... |+||-|-. -.|-||.
T Consensus 27 dLEVL~ep~~~~~~~v~I~Tsv~Gf~~~Wqavl~rf~~~~-~~~~~~i~InD~GATP~ 83 (99)
T PRK01220 27 DLEVLLEPGDAGKLSIQVVTSVNGSAARWKALFERFFTAQ-TPPAANIDIHDFGATPG 83 (99)
T ss_pred ceEEEEEcCCCCcEEEEEEecccCcHHHHHHHHHHHHhhC-CCCccEEEEeCCCCCcH
Confidence 7778888888999999999998888999999999998877 56665432 3444443
No 8
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=67.48 E-value=8.9 Score=25.64 Aligned_cols=50 Identities=18% Similarity=0.339 Sum_probs=29.6
Q ss_pred eEEEEEcCCCCeEEEEEEecChhhHHHHHHHHHHhhhcCCCCCCceeccCCc
Q 031255 96 AKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGN 147 (163)
Q Consensus 96 fkV~v~s~dd~~IqiRVdlsG~~Tq~VFd~Vf~klvraAqPIPGFRR~KGGK 147 (163)
+.|.+.=..||.|. ++.+-...-..-||+...+.++.+.|+|=+- ..|+.
T Consensus 28 ~~V~i~i~~dG~v~-~~~i~~sSG~~~~D~av~~ai~~~~p~p~pP-~~~~~ 77 (85)
T PF13103_consen 28 VTVRITIDPDGRVI-SVRIVKSSGNPAFDAAVRRAIRRASPFPPPP-EYGKQ 77 (85)
T ss_dssp EEEEEEE-TTSBEE-EEEEEE--S-HHHHHHHHHHHHHH-B-GGGG------
T ss_pred EEEEEEECCCCCEE-EEEEecCCCCHHHHHHHHHHHHHcCCCCcCC-ccccc
Confidence 44556667788873 5555555667789999999999999988776 44443
No 9
>PF06857 ACP: Malonate decarboxylase delta subunit (MdcD); InterPro: IPR023439 This family consists of the acyl carrier protein found in malonate decarboxylase and citrate lyase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl groups are transferred to the prosthetic group for catalysis.
Probab=60.70 E-value=21 Score=26.29 Aligned_cols=37 Identities=24% Similarity=0.505 Sum_probs=31.7
Q ss_pred eeEEEEEcCCCCeEEEEEEec-----ChhhHHHHHHHHHHhh
Q 031255 95 DAKIVVESQDEDKIQVRVDLT-----GDATQRVFDKVLTNLA 131 (163)
Q Consensus 95 dfkV~v~s~dd~~IqiRVdls-----G~~Tq~VFd~Vf~klv 131 (163)
|..|.++..+++.|+|.++=+ |+..+++.++++..+.
T Consensus 15 D~~V~v~p~~~~gi~i~l~S~v~~~fg~~i~~vi~~~l~~~~ 56 (87)
T PF06857_consen 15 DLEVTVEPAESGGIEIELESSVVKQFGDQIRAVIRETLEELG 56 (87)
T ss_pred cEEEEEEeCCCCcEEEEEEchHHhhhHHHHHHHHHHHHHhcC
Confidence 888999999889999888877 7888889999888774
No 10
>PF03160 Calx-beta: Calx-beta domain; InterPro: IPR003644 The calx-beta motif is present as a tandem repeat in the cytoplasmic domains of Calx Na-Ca exchangers, which are used to expel calcium from cells. This motif overlaps domains used for calcium binding and regulation. The calx-beta motif is also present in the cytoplasmic tail of mammalian integrin-beta4, which mediates the bi-directional transfer of signals across the plasma membrane, as well as in some cyanobacterial proteins. This motif contains a series of beta-strands and turns that form a self-contained beta-sheet [, ].; GO: 0007154 cell communication, 0016021 integral to membrane; PDB: 3H6A_B 3FSO_A 3FQ4_B 2DPK_A 2QVM_A 3GIN_B 2QVK_A 2FWU_A 2FWS_A 3E9U_A ....
Probab=48.50 E-value=45 Score=22.88 Aligned_cols=33 Identities=21% Similarity=0.437 Sum_probs=22.8
Q ss_pred eecCCCc-eeeeeeeEEEEEcCCCCeEEEEEEecC
Q 031255 83 SITEPED-LITVKDAKIVVESQDEDKIQVRVDLTG 116 (163)
Q Consensus 83 S~Td~~~-sis~~dfkV~v~s~dd~~IqiRVdlsG 116 (163)
.|.|++. .+.|.+-.+.+ .|+++.+++.|.++|
T Consensus 4 tI~d~d~~~v~f~~~~~~v-~E~~~~~~v~V~~~~ 37 (100)
T PF03160_consen 4 TILDDDDPTVSFSSPSYTV-SEGDGTVTVTVTRSG 37 (100)
T ss_dssp EEE-TTSEEEEESSSEEEE-ETTSSEEEEEEEEES
T ss_pred EEECCCCCEEEEeCCEEEE-EeCCCEEEEEEEEcc
Confidence 4566665 78888877665 556666888888875
No 11
>PF02566 OsmC: OsmC-like protein; InterPro: IPR003718 Osmotically inducible protein C (OsmC) is a stress-induced protein found in Escherichia coli. The transcription of the osmC gene of E. coli is regulated as a function of the phase of growth and is induced during the late exponential phase when the growth rate slows before entry into stationary phase. The transcription is initiated by two overlapping promoters, osmCp1 and osmCp2 []. An organic hydroperoxide detoxification protein (OHR) from Xanthomonas campestris pv. phaseoli is highly induced by organic hydroperoxides, weakly induced by H2O2, and not induced at all by a superoxide generator. Ohr may be a new type of organic hydroperoxide detoxification protein [, ].; GO: 0006950 response to stress; PDB: 2D7V_A 2BJO_A 1USP_A 2PN2_A 2QL8_A 1N2F_A 1UKK_A 1VLA_D 3CJE_A 2ONF_B ....
Probab=48.25 E-value=61 Score=21.82 Aligned_cols=40 Identities=25% Similarity=0.504 Sum_probs=22.7
Q ss_pred eeeeeeeEEEEEcC--CCC-----eEEEEEEe--cChhhHHHHHHHHHH
Q 031255 90 LITVKDAKIVVESQ--DED-----KIQVRVDL--TGDATQRVFDKVLTN 129 (163)
Q Consensus 90 sis~~dfkV~v~s~--dd~-----~IqiRVdl--sG~~Tq~VFd~Vf~k 129 (163)
.+.++++.|.++.+ +++ .|.+++.| ++..++.-.+++...
T Consensus 32 gi~~~~~~v~v~~~~~~~~~~~~~~i~~~~~v~~~~~~~~~~~~~~~~~ 80 (100)
T PF02566_consen 32 GIDLEDLEVEVEGELDPEGPRRFESIHLRITVKSDGDDDEEELEELLER 80 (100)
T ss_dssp T-EEEEEEEEEEEEEETTTCECEEEEEEEEEEEETTSHHHHHHHHHHHH
T ss_pred CCCcceEEEEEEEEEeecCCccceEEEEEEEEEcCCCCcHHHHHHHHHH
Confidence 46678888888863 222 24444444 665555666666554
No 12
>cd04920 ACT_AKiii-DAPDC_2 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC). This CD includes the second of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=45.71 E-value=18 Score=23.73 Aligned_cols=55 Identities=15% Similarity=0.210 Sum_probs=36.1
Q ss_pred eeeecCCCeeeecCCCc-eeeeeeeEEEEEcCCCCeEEEEEEecChhhHHHHHHHH
Q 031255 73 VSAVDSGVEVSITEPED-LITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVL 127 (163)
Q Consensus 73 VsAV~SG~~~S~Td~~~-sis~~dfkV~v~s~dd~~IqiRVdlsG~~Tq~VFd~Vf 127 (163)
||.||.|+....--..+ .-.|.+..|.+.+....+++|.+=+..+..++.-..+-
T Consensus 3 VsvVG~g~~~~~gv~~~~~~~L~~~~i~~i~~~~s~~~is~vv~~~d~~~av~~LH 58 (63)
T cd04920 3 VSLVGRGIRSLLHKLGPALEVFGKKPVHLVSQAANDLNLTFVVDEDQADGLCARLH 58 (63)
T ss_pred EEEECCCcccCccHHHHHHHHHhcCCceEEEEeCCCCeEEEEEeHHHHHHHHHHHH
Confidence 78999998632110111 22256667778888888899999888888776554443
No 13
>PF08175 SspO: Small acid-soluble spore protein O family; InterPro: IPR012613 This family consists of the small acid-soluble spore proteins (SASP) O type (sspO). SspO (originally cotK) are unique to the spores of Bacillus subtilis and are expressed only in the forespore compartment of sporulating cells of this organism. The sspO is the first gene in a likely operon with sspP and transcription of this gene is primarily by RNA polymerase with the forespore-specific sigma factor, sigma-G. Mutation deleting sspO causes the loss of the SspO from the forespore but had no discernible effect on sporulation, spore properties or spore germination [].; GO: 0030436 asexual sporulation, 0042601 endospore-forming forespore
Probab=34.24 E-value=17 Score=25.30 Aligned_cols=13 Identities=46% Similarity=0.915 Sum_probs=10.8
Q ss_pred cCCCCCCceeccC
Q 031255 133 SAPPIPGFRREKG 145 (163)
Q Consensus 133 aAqPIPGFRR~KG 145 (163)
+--|||||++.|+
T Consensus 5 ~nH~~pGmn~ak~ 17 (51)
T PF08175_consen 5 ANHPIPGMNRAKS 17 (51)
T ss_pred ccCcCcCcccccc
Confidence 4568999999986
No 14
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=33.31 E-value=99 Score=21.77 Aligned_cols=31 Identities=26% Similarity=0.457 Sum_probs=24.8
Q ss_pred cCCCCeEEEEEEecCh-hhHHHHHHHHHHhhh
Q 031255 102 SQDEDKIQVRVDLTGD-ATQRVFDKVLTNLAR 132 (163)
Q Consensus 102 s~dd~~IqiRVdlsG~-~Tq~VFd~Vf~klvr 132 (163)
---+++|.|||+..|. .-..++.+++.++..
T Consensus 37 HPl~~~i~l~Iqt~~~~~p~~~l~~a~~~l~~ 68 (77)
T PF13656_consen 37 HPLENKINLRIQTKGGITPIEALKKALEDLIK 68 (77)
T ss_dssp ETTSSEEEEEEEESTTS-HHHHHHHHHHHHHH
T ss_pred CCCCCceEEEEEECCCCCHHHHHHHHHHHHHH
Confidence 3457889999999998 788899999888754
No 15
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=30.64 E-value=1.5e+02 Score=19.74 Aligned_cols=30 Identities=17% Similarity=0.167 Sum_probs=23.3
Q ss_pred CCCCeEEEEEEecChhhHHHHHHHHHHhhh
Q 031255 103 QDEDKIQVRVDLTGDATQRVFDKVLTNLAR 132 (163)
Q Consensus 103 ~dd~~IqiRVdlsG~~Tq~VFd~Vf~klvr 132 (163)
++..++.++||..|...+.-+++++..|-.
T Consensus 39 ~~~~~~~f~vd~~~~~~~~~~~~~l~~l~~ 68 (80)
T cd04905 39 GGLWEYVFFIDFEGHIEDPNVAEALEELKR 68 (80)
T ss_pred CCCceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 356678899999997667788888877764
No 16
>TIGR01920 Shik_kin_archae shikimate kinase. This model represents the shikimate kinase (SK) gene found in archaea which is only distantly related to homoserine kinase (thrB) and not atr all to the bacterial SK enzyme. The SK from M. janaschii has been overexpressed in E. coli and characterized. SK catalyzes the fifth step of the biosynthesis of chorismate from D-erythrose-4-phosphate and phosphoenolpyruvate.
Probab=29.24 E-value=1.5e+02 Score=24.66 Aligned_cols=62 Identities=15% Similarity=0.159 Sum_probs=31.6
Q ss_pred eeeeecCCCeeeecCCCceeeeeeeEEEEEcCCCCeEEEEEEecChhhHHHHHHHHHHhhhcCCCCCCceec
Q 031255 72 TVSAVDSGVEVSITEPEDLITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRRE 143 (163)
Q Consensus 72 pVsAV~SG~~~S~Td~~~sis~~dfkV~v~s~dd~~IqiRVdlsG~~Tq~VFd~Vf~klvraAqPIPGFRR~ 143 (163)
-|.|..+|.++-++-+. -.+|.|+..++.++.+.+.-..+..+++++.++.. ...-|||+-.
T Consensus 7 ~~~a~~~~~g~a~aI~~------~~~v~v~~~~~~~~~~~~~~~~n~i~~~~~~~~~~----~~~~~g~~i~ 68 (261)
T TIGR01920 7 ILNAIATGLGGAFGIDL------WVEAKVREGDEAGVSTYVRGNPRLIERILTAIRSK----FGIVDGLEVE 68 (261)
T ss_pred hHhhhhcCcceEEEccC------ceEEEEEECCCCceeeeecCChHHHHHHHHHHHHh----cCCCCCEEEE
Confidence 35677778777666432 34555655555555443322223444444444443 3323787643
No 17
>PF05292 MCD: Malonyl-CoA decarboxylase (MCD); InterPro: IPR007956 This family consists of several eukaryotic malonyl-CoA decarboxylase (MLYCD) proteins. Malonyl-CoA, in addition to being an intermediate in the de novo synthesis of fatty acids, is an inhibitor of carnitine palmitoyltransferase I, the enzyme that regulates the transfer of long-chain fatty acyl-CoA into mitochondria, where they are oxidised. After exercise, malonyl-CoA decarboxylase participates with acetyl-CoA carboxylase in regulating the concentration of malonyl-CoA in liver and adipose tissue, as well as in muscle. Malonyl-CoA decarboxylase is regulated by AMP-activated protein kinase (AMPK) [].; GO: 0050080 malonyl-CoA decarboxylase activity, 0006633 fatty acid biosynthetic process; PDB: 2YGW_B.
Probab=28.85 E-value=15 Score=33.63 Aligned_cols=8 Identities=88% Similarity=1.771 Sum_probs=3.1
Q ss_pred CCCCCcee
Q 031255 135 PPIPGFRR 142 (163)
Q Consensus 135 qPIPGFRR 142 (163)
-||||||+
T Consensus 225 SPiPgF~~ 232 (354)
T PF05292_consen 225 SPIPGFRR 232 (354)
T ss_dssp B----HHH
T ss_pred CCCccHHH
Confidence 49999997
No 18
>PF12549 TOH_N: Tyrosine hydroxylase N terminal ; InterPro: IPR021164 This domain family is found in eukaryotes, and is approximately 30 amino acids in length. There is a single completely conserved residue G that may be functionally important. Tyrosine hydroxylase converts L-tyrosine to L-DOPA in the catecholamine synthesis pathway. ; GO: 0004511 tyrosine 3-monooxygenase activity, 0055114 oxidation-reduction process
Probab=28.21 E-value=27 Score=21.28 Aligned_cols=12 Identities=42% Similarity=0.811 Sum_probs=9.7
Q ss_pred hcCCCCCCceec
Q 031255 132 RSAPPIPGFRRE 143 (163)
Q Consensus 132 raAqPIPGFRR~ 143 (163)
.++|+-+||||.
T Consensus 5 ~ts~~~~G~r~a 16 (25)
T PF12549_consen 5 ITSPQAKGFRRA 16 (25)
T ss_pred ccCCCCccchhh
Confidence 357899999985
No 19
>cd04917 ACT_AKiii-LysC-EC_2 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The E. coli AKIII (LysC) binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. The second ACT domain (ACT2), this CD, is not involved in the binding of heterotrophic effectors. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=28.10 E-value=58 Score=20.75 Aligned_cols=56 Identities=5% Similarity=0.127 Sum_probs=35.3
Q ss_pred eeeecCCCeeeecCCCc-eeeeeeeEEEEEcCCCCeEEEEEEecChhhHHHHHHHHH
Q 031255 73 VSAVDSGVEVSITEPED-LITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLT 128 (163)
Q Consensus 73 VsAV~SG~~~S~Td~~~-sis~~dfkV~v~s~dd~~IqiRVdlsG~~Tq~VFd~Vf~ 128 (163)
||.||.|....---..+ .-.|.+..|.+.++...++.|.+=+..+..+++-..+-.
T Consensus 4 IsvvG~~~~~~~~v~~~i~~~L~~i~i~~i~~~~s~~~is~~V~~~~~~~a~~~Lh~ 60 (64)
T cd04917 4 VALIGNDISETAGVEKRIFDALEDINVRMICYGASNHNLCFLVKEEDKDEVVQRLHS 60 (64)
T ss_pred EEEECCCccCCcCHHHHHHHHHHhCCeEEEEEecCccEEEEEEeHHHHHHHHHHHHH
Confidence 78888887521000011 222466778888888888888888888777766554433
No 20
>PF12727 PBP_like: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []. It is often associated with a helix-turn-helix domain.
Probab=25.03 E-value=52 Score=26.22 Aligned_cols=29 Identities=31% Similarity=0.625 Sum_probs=24.9
Q ss_pred cChhhHHHHHHHHHHhhhcCCCCCCceec
Q 031255 115 TGDATQRVFDKVLTNLARSAPPIPGFRRE 143 (163)
Q Consensus 115 sG~~Tq~VFd~Vf~klvraAqPIPGFRR~ 143 (163)
.|.-|+.+||..+....-+..-|+||.+.
T Consensus 101 ~GSGtR~l~d~~l~~~gi~~~~i~gy~~~ 129 (193)
T PF12727_consen 101 PGSGTRILFDQLLAEEGIDPEDIPGYAQE 129 (193)
T ss_pred CCCHHHHHHHHHHHHcCCChhhCCCcccc
Confidence 57789999999999998888889999543
No 21
>PRK13253 citrate lyase subunit gamma; Provisional
Probab=23.43 E-value=2.2e+02 Score=21.38 Aligned_cols=36 Identities=25% Similarity=0.454 Sum_probs=27.0
Q ss_pred eeEEEEEcCCCCeEEEEEEec-----ChhhHHHHHHHHHHh
Q 031255 95 DAKIVVESQDEDKIQVRVDLT-----GDATQRVFDKVLTNL 130 (163)
Q Consensus 95 dfkV~v~s~dd~~IqiRVdls-----G~~Tq~VFd~Vf~kl 130 (163)
|..|.|+..+++.+.|.++=+ |..-+++++++|..+
T Consensus 16 Dl~V~veP~~~~~i~i~i~SsV~~~Fg~~i~~vv~~~l~~~ 56 (92)
T PRK13253 16 DVMIRIAPADTQGIDIQLESSVEKQFGDQIRAVILETLAKL 56 (92)
T ss_pred CEEEEEEeCCCCcEEEEEEeeHHhhhHHHHHHHHHHHHHhc
Confidence 888889998667777776644 556778888888777
No 22
>KOG3018 consensus Malonyl-CoA decarboxylase [Carbohydrate transport and metabolism]
Probab=22.53 E-value=44 Score=30.71 Aligned_cols=22 Identities=41% Similarity=0.833 Sum_probs=16.4
Q ss_pred HHHHHHHHHhhhcCC---------CCCCcee
Q 031255 121 RVFDKVLTNLARSAP---------PIPGFRR 142 (163)
Q Consensus 121 ~VFd~Vf~klvraAq---------PIPGFRR 142 (163)
-.-.+|.+++-++-| ||||||.
T Consensus 182 fLIKrV~t~lqkd~Phv~tfstLSPIPGF~~ 212 (362)
T KOG3018|consen 182 FLIKRVITLLQKDMPHVSTFSTLSPIPGFMQ 212 (362)
T ss_pred HHHHHHHHHHHhcCCccccccccCCCccHHH
Confidence 345677777777665 9999985
No 23
>TIGR01352 tonB_Cterm TonB family C-terminal domain. This model represents the C-terminal of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to help span the periplasm.
Probab=22.38 E-value=2.1e+02 Score=18.01 Aligned_cols=40 Identities=15% Similarity=0.149 Sum_probs=25.8
Q ss_pred EEEcCCCCeE-EEEEEecChhhHHHHHHHHHHhhhcCCCCCCc
Q 031255 99 VVESQDEDKI-QVRVDLTGDATQRVFDKVLTNLARSAPPIPGF 140 (163)
Q Consensus 99 ~v~s~dd~~I-qiRVdlsG~~Tq~VFd~Vf~klvraAqPIPGF 140 (163)
.+.=..+|.+ .++|.= ......||+.-.+.++.+.+.|..
T Consensus 15 ~~~i~~~G~v~~~~i~~--ssg~~~ld~~a~~av~~~~~~p~~ 55 (74)
T TIGR01352 15 RFTVDADGRVTSVSVLK--SSGDEALDRAALEAVRKARFEPPP 55 (74)
T ss_pred EEEECCCCCEEEEEEEE--cCCChhHHHHHHHHHHhCCCCCCC
Confidence 3444445544 355531 113578999999999999888875
No 24
>cd04915 ACT_AK-Ectoine_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinas
Probab=21.69 E-value=64 Score=21.32 Aligned_cols=57 Identities=11% Similarity=0.154 Sum_probs=34.9
Q ss_pred eeeeecCCCeeeecCCCc-eeeeee--eEEEEEcCCCCeEEEEEEecChhhHHHHHHHHHH
Q 031255 72 TVSAVDSGVEVSITEPED-LITVKD--AKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTN 129 (163)
Q Consensus 72 pVsAV~SG~~~S~Td~~~-sis~~d--fkV~v~s~dd~~IqiRVdlsG~~Tq~VFd~Vf~k 129 (163)
-||.||.|.. ..--..+ .-.|.+ +.+...++..++++|.+=+..+.++++-..+...
T Consensus 4 ~VsvVG~gm~-~~gv~~ki~~~L~~~~I~v~~i~~~~s~~~is~~V~~~~~~~av~~Lh~~ 63 (66)
T cd04915 4 IVSVIGRDLS-TPGVLARGLAALAEAGIEPIAAHQSMRNVDVQFVVDRDDYDNAIKALHAA 63 (66)
T ss_pred EEEEECCCCC-cchHHHHHHHHHHHCCCCEEEEEecCCeeEEEEEEEHHHHHHHHHHHHHH
Confidence 4889999994 2110111 212334 4444477777889999988888777665554443
No 25
>cd07620 BAR_SH3BP1 The Bin/Amphiphysin/Rvs (BAR) domain of SH3-domain Binding Protein 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. SH3-domain binding protein 1 (SH3BP1 or 3BP-1) is a Rac GTPase activating protein that inhibits Rac-mediated platelet-derived growth factor (PDGF)-induced membrane ruffling. SH3BP1 contains an N-terminal BAR domain followed by a GAP domain for Rho and Rac GTPases and a C-terminal proline-rich domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=20.86 E-value=26 Score=30.74 Aligned_cols=44 Identities=18% Similarity=0.219 Sum_probs=34.9
Q ss_pred hhhHHHHHHHHHHhhhcCCCCCCceeccCCccCCccc-ceeeeeccc
Q 031255 117 DATQRVFDKVLTNLARSAPPIPGFRREKGGNALYLGI-FSYKSLVKS 162 (163)
Q Consensus 117 ~~Tq~VFd~Vf~klvraAqPIPGFRR~KGGKT~~IP~-f~y~~l~~~ 162 (163)
+.|.++..++..++.+--||-||.|..|. ..++|- .|-.|++++
T Consensus 25 D~~k~~~~~i~kkl~~~LQpn~~~~aekr--~kKlpe~~Ls~~M~es 69 (257)
T cd07620 25 EPAKKAAQLIHKKLQGCLQSQPGLEAEKR--MKKLPLMALSISMAES 69 (257)
T ss_pred HHHHHHHHHHHHHHHHHcCCChHHHHHHH--hhhccHhHHHHHHHHH
Confidence 35778899999999999999999999987 777776 444555544
No 26
>cd06469 p23_DYX1C1_like p23_like domain found in proteins similar to dyslexia susceptibility 1 (DYX1) candidate 1 (C1) protein, DYX1C1. The human gene encoding this protein is a positional candidate gene for developmental dyslexia (DD), it is located on 15q21.3 by the DYX1 DD susceptibility locus (15q15-21). Independent association studies have reported conflicting results. However, association of short-term memory, which plays a role in DD, with a variant within the DYX1C1 gene has been reported. Most proteins belonging to this group contain a C-terminal tetratricopeptide repeat (TPR) protein binding region.
Probab=20.58 E-value=75 Score=20.69 Aligned_cols=16 Identities=25% Similarity=0.547 Sum_probs=9.2
Q ss_pred CCCCeEEEEEEecChh
Q 031255 103 QDEDKIQVRVDLTGDA 118 (163)
Q Consensus 103 ~dd~~IqiRVdlsG~~ 118 (163)
|+++.+.|+|+++|..
T Consensus 3 Qt~~~v~i~i~~p~v~ 18 (78)
T cd06469 3 QTDEDVKISVPLKGVK 18 (78)
T ss_pred ccCCEEEEEEEeCCCc
Confidence 4455566666666543
No 27
>cd07615 BAR_Endophilin_A3 The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-A3. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins are accessory proteins localized at synapses that interacts with the endocytic proteins, dynamin and synaptojanin. They are essential for synaptic vesicle formation from the plasma membrane. They interact with voltage-gated calcium channels, thus linking vesicle endocytosis to calcium regulation. They also play roles in virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. They are classified into two types, A and B. Endophilin-A proteins are enriched in the brain and play multiple roles in receptor-mediated e
Probab=20.45 E-value=42 Score=28.51 Aligned_cols=47 Identities=19% Similarity=0.368 Sum_probs=34.5
Q ss_pred hhhHHHHHHHHHHhhhcCCCCCCce----------eccCC-ccCCccc---ceeeeecccC
Q 031255 117 DATQRVFDKVLTNLARSAPPIPGFR----------REKGG-NALYLGI---FSYKSLVKSG 163 (163)
Q Consensus 117 ~~Tq~VFd~Vf~klvraAqPIPGFR----------R~KGG-KT~~IP~---f~y~~l~~~~ 163 (163)
+.|....++++.++..--||=||-| +.+|- |.+..|. .|=.|+++.|
T Consensus 17 d~t~~~~~~l~~~t~~~LqpNP~~r~~~~~~~~~~k~~g~~k~~~~p~~~~~Lg~~M~~~G 77 (223)
T cd07615 17 DVTNKVVAELLSKTTEYLQPNPAYRAKLGMLNTVSKIRGQVKTTGYPQTEGLLGDCMLRYG 77 (223)
T ss_pred HHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHhcccccCCCCCchhHHHHHHHHHH
Confidence 3467778899999999999999999 77753 3666665 5555555443
No 28
>cd00298 ACD_sHsps_p23-like This domain family includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this family is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind
Probab=20.40 E-value=93 Score=18.70 Aligned_cols=15 Identities=40% Similarity=0.643 Sum_probs=8.1
Q ss_pred CCCeEEEEEEecChh
Q 031255 104 DEDKIQVRVDLTGDA 118 (163)
Q Consensus 104 dd~~IqiRVdlsG~~ 118 (163)
.++.+.|+|+++|..
T Consensus 4 ~~~~v~i~i~~~~~~ 18 (80)
T cd00298 4 TDDEVVVTVDLPGVK 18 (80)
T ss_pred cCCEEEEEEECCCCC
Confidence 344555666665543
Done!