Query 029914
Match_columns 185
No_of_seqs 168 out of 1041
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 05:38:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029914.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029914hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05697 Trigger_N: Bacterial 99.9 9.3E-21 2E-25 148.7 12.1 81 96-184 1-81 (145)
2 COG0544 Tig FKBP-type peptidyl 99.8 5.1E-18 1.1E-22 156.7 11.4 81 96-184 1-81 (441)
3 PRK01490 tig trigger factor; P 99.7 7E-18 1.5E-22 152.3 11.5 81 96-184 1-81 (435)
4 TIGR00115 tig trigger factor. 99.6 2.8E-15 6E-20 134.3 9.4 69 108-184 1-69 (408)
5 cd04920 ACT_AKiii-DAPDC_2 ACT 79.8 3.2 6.9E-05 28.3 3.7 58 73-130 3-61 (63)
6 cd04917 ACT_AKiii-LysC-EC_2 AC 69.7 11 0.00023 25.2 4.2 58 73-130 4-62 (64)
7 PHA00440 host protein H-NS-int 69.2 53 0.0011 25.7 8.5 60 117-184 19-80 (98)
8 PF11247 DUF2675: Protein of u 65.7 62 0.0014 25.2 8.6 67 109-184 12-80 (98)
9 cd04937 ACT_AKi-DapG-BS_2 ACT 65.2 7.6 0.00017 26.1 2.8 59 72-130 3-62 (64)
10 cd04915 ACT_AK-Ectoine_2 ACT d 64.1 18 0.0004 24.7 4.6 58 72-130 4-64 (66)
11 PRK13848 conjugal transfer pro 53.0 15 0.00032 28.7 2.8 27 111-147 41-67 (98)
12 PF06857 ACP: Malonate decarbo 52.1 60 0.0013 24.4 5.9 46 95-141 15-61 (87)
13 cd04922 ACT_AKi-HSDH-ThrA_2 AC 51.6 46 0.001 21.4 4.8 59 72-130 3-64 (66)
14 cd04919 ACT_AK-Hom3_2 ACT doma 50.1 51 0.0011 21.4 4.8 58 73-130 4-64 (66)
15 cd04918 ACT_AK1-AT_2 ACT domai 48.5 43 0.00092 22.6 4.3 57 73-130 4-63 (65)
16 cd04924 ACT_AK-Arch_2 ACT doma 46.4 64 0.0014 20.7 4.8 58 73-130 4-64 (66)
17 KOG3018 Malonyl-CoA decarboxyl 45.4 16 0.00034 33.7 2.3 21 122-142 183-212 (362)
18 PRK02103 malonate decarboxylas 43.3 68 0.0015 25.2 5.2 47 95-142 30-77 (105)
19 TIGR03130 malonate_delta malon 40.7 82 0.0018 24.5 5.2 46 95-141 28-74 (98)
20 cd04911 ACT_AKiii-YclM-BS_1 AC 40.5 21 0.00046 26.2 1.9 43 93-135 25-68 (76)
21 PRK13253 citrate lyase subunit 40.1 1.3E+02 0.0027 23.0 6.1 46 95-141 16-62 (92)
22 PRK01220 malonate decarboxylas 39.4 82 0.0018 24.6 5.0 46 95-141 27-72 (99)
23 cd04916 ACT_AKiii-YclM-BS_2 AC 34.9 1.2E+02 0.0027 19.4 4.8 58 73-130 4-64 (66)
24 COG2036 HHT1 Histones H3 and H 33.4 77 0.0017 24.1 4.0 33 150-183 22-54 (91)
25 COG0199 RpsN Ribosomal protein 30.1 32 0.0007 24.5 1.4 18 125-143 42-59 (61)
26 cd04936 ACT_AKii-LysC-BS-like_ 29.6 66 0.0014 20.3 2.7 25 106-130 37-61 (63)
27 cd04890 ACT_AK-like_1 ACT doma 27.1 85 0.0018 20.4 3.0 38 93-130 24-61 (62)
28 PHA02938 hypothetical protein; 26.8 88 0.0019 29.1 3.9 63 120-182 32-99 (361)
29 cd04912 ACT_AKiii-LysC-EC-like 26.1 70 0.0015 22.1 2.6 40 93-132 25-67 (75)
30 PF00344 SecY: SecY translocas 25.8 1.1E+02 0.0025 27.4 4.5 36 125-167 269-305 (346)
31 PRK07431 aspartate kinase; Pro 25.5 89 0.0019 30.0 3.9 65 66-130 515-580 (587)
32 KOG3939 Selenophosphate synthe 25.2 1.6E+02 0.0034 27.1 5.1 63 69-132 98-180 (312)
33 PRK08961 bifunctional aspartat 24.6 1.5E+02 0.0032 30.2 5.5 68 66-133 394-462 (861)
34 PF02120 Flg_hook: Flagellar h 24.2 1.3E+02 0.0028 20.8 3.7 48 93-142 24-71 (85)
35 PF02800 Gp_dh_C: Glyceraldehy 24.1 1E+02 0.0022 25.0 3.4 40 93-132 71-110 (157)
36 KOG0884 Similar to cyclophilin 22.3 2.8E+02 0.0061 23.0 5.7 53 96-148 1-65 (161)
37 COG0201 SecY Preprotein transl 22.0 1.8E+02 0.004 27.8 5.2 28 127-161 341-369 (436)
38 PF01077 NIR_SIR: Nitrite and 21.9 1.7E+02 0.0036 22.8 4.3 47 112-171 103-151 (157)
39 PF05698 Trigger_C: Bacterial 21.9 3.6E+02 0.0078 20.4 6.1 33 110-143 37-69 (162)
40 PRK12907 secY preprotein trans 21.7 93 0.002 29.5 3.2 37 112-161 330-366 (434)
41 PF10923 DUF2791: P-loop Domai 21.4 1.9E+02 0.0042 27.4 5.2 56 107-171 78-137 (416)
42 PRK09466 metL bifunctional asp 21.1 89 0.0019 31.9 3.1 68 67-134 388-456 (810)
43 PRK09084 aspartate kinase III; 20.0 1.6E+02 0.0034 27.7 4.3 65 66-130 380-445 (448)
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=99.85 E-value=9.3e-21 Score=148.67 Aligned_cols=81 Identities=26% Similarity=0.607 Sum_probs=75.6
Q ss_pred cEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHHhhcCCCCCCcccCCCCCCCCCcHHHHHHHhCHHHHHHHHHHHHHH
Q 029914 96 AKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILGEERVTKFVVQEIVR 175 (185)
Q Consensus 96 MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkklaK~akpIPGFRKGKGgk~~KVP~~Vl~k~yG~e~V~~eai~elI~ 175 (185)
|+++++..+++.+.++|+|++++|++++++++++++++++ ||||||| |||.++++++||.+ |++++++++++
T Consensus 1 M~v~~~~~~~~~~~~~v~v~~~~~~~~~~~~l~~~~k~~~-ipGFRkG------K~P~~vi~~~~g~~-i~~~~~~~~~~ 72 (145)
T PF05697_consen 1 MKVTVEKIEDSKVKLEVEVPAEEVEKAYEKALKELAKKVK-IPGFRKG------KAPRNVIEKRYGKE-IREEAIEELLQ 72 (145)
T ss_dssp -EEEEEEESTTEEEEEEEE-HHHHHHHHHHHHHHHHTTTT-BTTS-TT------SS-HHHHHHHHCHH-HHHHHHHHHHH
T ss_pred CccEEEECCCcEEEEEEEECHHHHHHHHHHHHHHHHhhCC-CCCCCCC------CCCHHHHHHHHHHH-HHHHHHHHHHH
Confidence 8999999999999999999999999999999999999999 9999999 89999999999996 99999999999
Q ss_pred HHHHHHHhh
Q 029914 176 STLTDYTKK 184 (185)
Q Consensus 176 ~a~~eAvee 184 (185)
.+|.+|+++
T Consensus 73 ~~~~~~~~~ 81 (145)
T PF05697_consen 73 EAYEEAIKE 81 (145)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 999999986
No 2
>COG0544 Tig FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones]
Probab=99.75 E-value=5.1e-18 Score=156.72 Aligned_cols=81 Identities=31% Similarity=0.563 Sum_probs=79.1
Q ss_pred cEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHHhhcCCCCCCcccCCCCCCCCCcHHHHHHHhCHHHHHHHHHHHHHH
Q 029914 96 AKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILGEERVTKFVVQEIVR 175 (185)
Q Consensus 96 MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkklaK~akpIPGFRKGKGgk~~KVP~~Vl~k~yG~e~V~~eai~elI~ 175 (185)
|++++++++++.+.|+|+||+++|++.++++|++++++++ ||||||| |||+++++++|| +.|++++++++|+
T Consensus 1 M~v~~e~~~~~~~~l~v~vp~~~~~~~~~~~~~~~~k~v~-IpGFRkG------KvP~~ii~~ryg-~~v~~d~~~~ll~ 72 (441)
T COG0544 1 MKVTVEKLEGLEVRLTVEVPAEEIKKALDKALKKLAKKVK-IPGFRKG------KVPRKVIEQRYG-EAVRQDVLNELLP 72 (441)
T ss_pred CCeeeeecCCcEEEEEEEECHHHHHHHHHHHHHHHHhhCc-CCCCCCC------CCCHHHHHHHHh-HHHHHHHHHHHHH
Confidence 8899999999999999999999999999999999999999 9999999 999999999999 5799999999999
Q ss_pred HHHHHHHhh
Q 029914 176 STLTDYTKK 184 (185)
Q Consensus 176 ~a~~eAvee 184 (185)
++|.+|+++
T Consensus 73 ~~~~~a~~e 81 (441)
T COG0544 73 EAFEEAIKE 81 (441)
T ss_pred HHHHHHHHH
Confidence 999999986
No 3
>PRK01490 tig trigger factor; Provisional
Probab=99.75 E-value=7e-18 Score=152.32 Aligned_cols=81 Identities=26% Similarity=0.498 Sum_probs=79.0
Q ss_pred cEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHHhhcCCCCCCcccCCCCCCCCCcHHHHHHHhCHHHHHHHHHHHHHH
Q 029914 96 AKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILGEERVTKFVVQEIVR 175 (185)
Q Consensus 96 MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkklaK~akpIPGFRKGKGgk~~KVP~~Vl~k~yG~e~V~~eai~elI~ 175 (185)
|++++++.+++++.++|+||+++|++.+++++++++++++ ||||||| |||+++|+++||++ |++++++++|+
T Consensus 1 M~v~~~~~~~~~~~l~v~v~~~~~~~~~~~~~~~~~k~~~-ipGFRkG------kvP~~ii~k~~g~~-i~~e~~~~li~ 72 (435)
T PRK01490 1 MQVTVEKLEGLERRLTITVPAEEIEKAVDKALKKLAKTVR-IPGFRKG------KVPRKIVEQRYGES-VRQEALNDLLP 72 (435)
T ss_pred CcceEEEcCCcEEEEEEEEcHHHHHHHHHHHHHHHHhhCc-CCCccCC------CCCHHHHHHHHhHH-HHHHHHHHHHH
Confidence 8899999999999999999999999999999999999999 9999999 99999999999985 99999999999
Q ss_pred HHHHHHHhh
Q 029914 176 STLTDYTKK 184 (185)
Q Consensus 176 ~a~~eAvee 184 (185)
++|.+|+++
T Consensus 73 ~~~~~~i~~ 81 (435)
T PRK01490 73 EAYEEAIKE 81 (435)
T ss_pred HHHHHHHHH
Confidence 999999976
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=99.60 E-value=2.8e-15 Score=134.28 Aligned_cols=69 Identities=28% Similarity=0.551 Sum_probs=66.1
Q ss_pred EEEEEEeCHHHHHHHHHHHHHHHhhcCCCCCCcccCCCCCCCCCcHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhh
Q 029914 108 IQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILGEERVTKFVVQEIVRSTLTDYTKK 184 (185)
Q Consensus 108 ikL~VtVp~eeveka~dkalkklaK~akpIPGFRKGKGgk~~KVP~~Vl~k~yG~e~V~~eai~elI~~a~~eAvee 184 (185)
+.|+|+||++++++.+++++++++++++ ||||||| |||+++|+++||+ .|+.++++++++++|.+|+++
T Consensus 1 ~~l~v~v~~~~~~~~~~k~~~~~~k~~~-ipGFRkG------KvP~~~i~k~~g~-~i~~e~~~~li~~~~~~~~~~ 69 (408)
T TIGR00115 1 RKLTVEVPAEEVEEEVDKALKELAKKVK-IPGFRKG------KVPRSVVEKRYGK-EVRQEALNELLQEAFSEAVKE 69 (408)
T ss_pred CeEEEEECHHHHHHHHHHHHHHHHhhCC-CCCccCC------CCCHHHHHHHHhH-HHHHHHHHHHHHHHHHHHHHh
Confidence 3689999999999999999999999999 9999999 9999999999998 499999999999999999975
No 5
>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=79.80 E-value=3.2 Score=28.26 Aligned_cols=58 Identities=14% Similarity=0.184 Sum_probs=42.5
Q ss_pred ceeccCCcccccCCcccc-ccccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029914 73 VSAVDSGVEVSITEPEDL-ITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 130 (185)
Q Consensus 73 vsav~sg~~~s~~~~~~~-~s~~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkkl 130 (185)
||.||.|+....-=..+. -++.+.++.+.....+.+.+.+-|+.++.++++...-.++
T Consensus 3 VsvVG~g~~~~~gv~~~~~~~L~~~~i~~i~~~~s~~~is~vv~~~d~~~av~~LH~~f 61 (63)
T cd04920 3 VSLVGRGIRSLLHKLGPALEVFGKKPVHLVSQAANDLNLTFVVDEDQADGLCARLHFQL 61 (63)
T ss_pred EEEECCCcccCccHHHHHHHHHhcCCceEEEEeCCCCeEEEEEeHHHHHHHHHHHHHHH
Confidence 789999986542112222 2355667778888899999999999999999888776554
No 6
>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=69.71 E-value=11 Score=25.19 Aligned_cols=58 Identities=7% Similarity=0.152 Sum_probs=41.7
Q ss_pred ceeccCCcccccCCcccc-ccccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029914 73 VSAVDSGVEVSITEPEDL-ITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 130 (185)
Q Consensus 73 vsav~sg~~~s~~~~~~~-~s~~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkkl 130 (185)
||.||.|+.....-..+. .++.+.++..-....+...+.+-|+.++.++++....+++
T Consensus 4 IsvvG~~~~~~~~v~~~i~~~L~~i~i~~i~~~~s~~~is~~V~~~~~~~a~~~Lh~~f 62 (64)
T cd04917 4 VALIGNDISETAGVEKRIFDALEDINVRMICYGASNHNLCFLVKEEDKDEVVQRLHSRL 62 (64)
T ss_pred EEEECCCccCCcCHHHHHHHHHHhCCeEEEEEecCccEEEEEEeHHHHHHHHHHHHHHH
Confidence 678888875432222232 3355667777778889999999999999999988877654
No 7
>PHA00440 host protein H-NS-interacting protein
Probab=69.24 E-value=53 Score=25.66 Aligned_cols=60 Identities=23% Similarity=0.472 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHHHhhcCCCCCCcccCCCCCCCCCcHHHHHHHh--CHHHHHHHHHHHHHHHHHHHHHhh
Q 029914 117 DATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQIL--GEERVTKFVVQEIVRSTLTDYTKK 184 (185)
Q Consensus 117 eeveka~dkalkklaK~akpIPGFRKGKGgk~~KVP~~Vl~k~y--G~e~V~~eai~elI~~a~~eAvee 184 (185)
.+.++.+.+.|.+|++.+. -|-+...--+.+|.+-+ |.+.+...+++.=|.+.+.+...|
T Consensus 19 se~e~~~~e~l~~Lak~v~--------~GE~~~~~~re~lvqaLT~G~egai~F~~k~giRe~IKe~~~E 80 (98)
T PHA00440 19 SETEAILEEDILDLAKQAG--------AGEEVNPKDKELLVQALTHGPEGAAAFAVRQGIREAIKDMHEE 80 (98)
T ss_pred hHHHHHHHHHHHHHHhhcC--------CcccCChHHHHHHHHHHhhChHHHHHHHHHHHHHHHHHHHhHh
Confidence 5788999999999999887 33454445567888765 777777777776666666665543
No 8
>PF11247 DUF2675: Protein of unknown function (DUF2675) ; InterPro: IPR022611 Members in this family of proteins include Bacteriophage T7 gene 5.5; they have no known function.
Probab=65.74 E-value=62 Score=25.21 Aligned_cols=67 Identities=25% Similarity=0.448 Sum_probs=41.8
Q ss_pred EEEEEeCHHHHHHHHHHHHHHHhhcCCCCCCcccCCCCCCCCCcHHHHHHHh--CHHHHHHHHHHHHHHHHHHHHHhh
Q 029914 109 QVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQIL--GEERVTKFVVQEIVRSTLTDYTKK 184 (185)
Q Consensus 109 kL~VtVp~eeveka~dkalkklaK~akpIPGFRKGKGgk~~KVP~~Vl~k~y--G~e~V~~eai~elI~~a~~eAvee 184 (185)
.++..++. +.++.+.+.+-.+++.+- .|-|.+.--+.+|.+-+ |.+.+...+++.=+.+.+.+...|
T Consensus 12 ~vtav~~s-e~e~~~~e~ll~Lak~v~--------~GE~~~~~~re~l~qaLT~G~egav~f~~k~g~R~~IKe~~~E 80 (98)
T PF11247_consen 12 DVTAVIDS-EQEEEFEEDLLELAKKVG--------AGEKVSGFQREMLVQALTHGPEGAVAFVVKQGIREAIKEMLSE 80 (98)
T ss_pred EEEEEeCH-HHHHHHHHHHHHHHhhcC--------CccccCHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455554 455667777788988886 23333334556777754 777777777777666666665544
No 9
>cd04937 ACT_AKi-DapG-BS_2 ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI. This CD includes the C-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) strain 168), Clostridia, and Actinobacteria bacterial species. In B. subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive AK isoenzymes. AKI activity is invariant during the exponential and stationary phases of growth and is not altered by addition of amino acids to the growth medium. The role of this isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulation. The BS AKI is tetrameric consisting of two alpha and two beta subunits; th
Probab=65.22 E-value=7.6 Score=26.10 Aligned_cols=59 Identities=7% Similarity=0.099 Sum_probs=38.9
Q ss_pred eceeccCCcccccCCcccc-ccccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029914 72 TVSAVDSGVEVSITEPEDL-ITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 130 (185)
Q Consensus 72 ~vsav~sg~~~s~~~~~~~-~s~~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkkl 130 (185)
-||.||.|+....-=..+. -++.+..+.+.....+++.+.+-|+.++.+++++...+.+
T Consensus 3 ~isvvG~~~~~~~gi~~~if~aL~~~~I~v~~~~~Se~~is~~v~~~~~~~av~~Lh~~f 62 (64)
T cd04937 3 KVTIIGSRIRGVPGVMAKIVGALSKEGIEILQTADSHTTISCLVSEDDVKEAVNALHEAF 62 (64)
T ss_pred EEEEECCCccCCcCHHHHHHHHHHHCCCCEEEEEcCccEEEEEEcHHHHHHHHHHHHHHh
Confidence 3788888886542112222 2344444444444558999999999999999888776654
No 10
>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=64.06 E-value=18 Score=24.74 Aligned_cols=58 Identities=10% Similarity=0.119 Sum_probs=40.7
Q ss_pred eceeccCCcccccCCcccc---ccccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029914 72 TVSAVDSGVEVSITEPEDL---ITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 130 (185)
Q Consensus 72 ~vsav~sg~~~s~~~~~~~---~s~~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkkl 130 (185)
-||.||.|+..+ -=..+. +...+.++.......+++.+.+-|+.++.+++++...+.+
T Consensus 4 ~VsvVG~gm~~~-gv~~ki~~~L~~~~I~v~~i~~~~s~~~is~~V~~~~~~~av~~Lh~~f 64 (66)
T cd04915 4 IVSVIGRDLSTP-GVLARGLAALAEAGIEPIAAHQSMRNVDVQFVVDRDDYDNAIKALHAAL 64 (66)
T ss_pred EEEEECCCCCcc-hHHHHHHHHHHHCCCCEEEEEecCCeeEEEEEEEHHHHHHHHHHHHHHH
Confidence 488999999522 111122 2234455555777788999999999999999999887765
No 11
>PRK13848 conjugal transfer protein TraC; Provisional
Probab=52.96 E-value=15 Score=28.66 Aligned_cols=27 Identities=22% Similarity=0.500 Sum_probs=19.2
Q ss_pred EEEeCHHHHHHHHHHHHHHHhhcCCCCCCcccCCCCC
Q 029914 111 RVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGK 147 (185)
Q Consensus 111 ~VtVp~eeveka~dkalkklaK~akpIPGFRKGKGgk 147 (185)
.++|+.++++.+|+++..+ ||.|||+-
T Consensus 41 eieI~d~eL~~aFeeiAaR----------FR~g~~~~ 67 (98)
T PRK13848 41 EIEIEEAELQAAFEELAKR----------FRGGKGAA 67 (98)
T ss_pred ccccCHHHHHHHHHHHHHH----------HhcCCCcc
Confidence 4678888888888877654 66676653
No 12
>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=52.08 E-value=60 Score=24.40 Aligned_cols=46 Identities=13% Similarity=0.208 Sum_probs=33.6
Q ss_pred CcEEEEEecCCceEEEEEEeC-HHHHHHHHHHHHHHHhhcCCCCCCcc
Q 029914 95 DAKIVVESQDEDKIQVRVDLT-GDATQRVFDKVLTNLARSAPPIPGFR 141 (185)
Q Consensus 95 ~MkV~Ve~le~~~ikL~VtVp-~eeveka~dkalkklaK~akpIPGFR 141 (185)
|+.|.++..++..+++.++=+ ...+.+.+++++.+..+... |++-+
T Consensus 15 D~~V~v~p~~~~gi~i~l~S~v~~~fg~~i~~vi~~~l~~~~-i~~~~ 61 (87)
T PF06857_consen 15 DLEVTVEPAESGGIEIELESSVVKQFGDQIRAVIRETLEELG-IEDAK 61 (87)
T ss_pred cEEEEEEeCCCCcEEEEEEchHHhhhHHHHHHHHHHHHHhcC-CCceE
Confidence 566788888778888888888 66666666677766666766 66543
No 13
>cd04922 ACT_AKi-HSDH-ThrA_2 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). This CD includes the second of two ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). The ACT domains are positioned between the N-terminal catalytic domain of AK and the C-terminal HSDH domain found in bacteria (Escherichia coli (EC) ThrA) and higher plants (Zea mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. HSDH is the first committed reaction in the branch of the pathway that leads to Thr and Met. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pathwa
Probab=51.63 E-value=46 Score=21.44 Aligned_cols=59 Identities=10% Similarity=0.177 Sum_probs=34.2
Q ss_pred eceeccCCcccccCCcccc---ccccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029914 72 TVSAVDSGVEVSITEPEDL---ITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 130 (185)
Q Consensus 72 ~vsav~sg~~~s~~~~~~~---~s~~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkkl 130 (185)
-||.|+.|.....--..+. ++-.+.++..-........+.+.|+.++.+++.++..+.+
T Consensus 3 ~isvvg~~~~~~~~~~~~i~~~l~~~~I~v~~i~~~~s~~~is~~v~~~~~~~~~~~lh~~~ 64 (66)
T cd04922 3 ILALVGDGMAGTPGVAATFFSALAKANVNIRAIAQGSSERNISAVIDEDDATKALRAVHERF 64 (66)
T ss_pred EEEEECCCCCCCccHHHHHHHHHHHCCCCEEEEEecCcccEEEEEEeHHHHHHHHHHHHHHH
Confidence 4788888886641111111 2222333332333335689999999999888876655543
No 14
>cd04919 ACT_AK-Hom3_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. AK is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and in fungi, is responsible for the production of threonine, isoleucine and methionine. S. cerevisiae has a single AK, which is regulated by feedback, allosteric inhibition by L-threonine. Recent studies shown that the allosteric transition triggered by binding of threonine to AK involves a large change in the conformation of the native hexameric enzyme that is converted to an inactive one of different shape and substantially smaller hydrodynamic size. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=50.13 E-value=51 Score=21.44 Aligned_cols=58 Identities=17% Similarity=0.216 Sum_probs=34.4
Q ss_pred ceeccCCcccccCCcccc---ccccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029914 73 VSAVDSGVEVSITEPEDL---ITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 130 (185)
Q Consensus 73 vsav~sg~~~s~~~~~~~---~s~~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkkl 130 (185)
||.||+|+....--..+. ++..+.++..-........+.+.|+.++.+++.+...+.+
T Consensus 4 isvvg~~~~~~~~~~~~if~~L~~~~I~v~~i~q~~s~~~isf~v~~~~~~~a~~~lh~~~ 64 (66)
T cd04919 4 LSLVGKHMKNMIGIAGRMFTTLADHRINIEMISQGASEINISCVIDEKDAVKALNIIHTNL 64 (66)
T ss_pred EEEECCCCCCCcCHHHHHHHHHHHCCCCEEEEEecCccceEEEEEeHHHHHHHHHHHHHHH
Confidence 678888886641111122 2233344433333335689999999999888876655543
No 15
>cd04918 ACT_AK1-AT_2 ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1). This CD includes the second of two ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1), which can be synergistically inhibited by S-adenosylmethionine (SAM). This isoenzyme is found in higher plants, Arabidopsis thaliana (AT) and Zea mays, and also in Chlorophyta. In its inactive state, Arabidopsis AK1 binds the effectors lysine and SAM (two molecules each) at the interface of two ACT1 domain subunits. The second ACT domain (ACT2), this CD, does not interact with an effector. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=48.48 E-value=43 Score=22.58 Aligned_cols=57 Identities=12% Similarity=0.179 Sum_probs=38.2
Q ss_pred ceeccCCcccccCCcccc-ccc--cCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029914 73 VSAVDSGVEVSITEPEDL-ITV--KDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 130 (185)
Q Consensus 73 vsav~sg~~~s~~~~~~~-~s~--~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkkl 130 (185)
||.||...+..- -..+. -++ .+.++..-....+++.+.+-|+.++.+++++...+.+
T Consensus 4 VsvVG~~~~~~~-~~~~i~~aL~~~~I~v~~i~~g~s~~sis~~v~~~~~~~av~~Lh~~f 63 (65)
T cd04918 4 ISLIGNVQRSSL-ILERAFHVLYTKGVNVQMISQGASKVNISLIVNDSEAEGCVQALHKSF 63 (65)
T ss_pred EEEECCCCCCcc-HHHHHHHHHHHCCCCEEEEEecCccceEEEEEeHHHHHHHHHHHHHHH
Confidence 677776333321 11122 223 4566666777789999999999999999988877665
No 16
>cd04924 ACT_AK-Arch_2 ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). Included in this CD is the second of two ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). The first or N-terminal ACT domain of these proteins cluster with the ThrA-like ACT 1 domains (ACT_AKi-HSDH-ThrA-like_1) which includes the threonine-sensitive archaeal Methanococcus jannaschii aspartokinase ACT 1 domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=46.42 E-value=64 Score=20.69 Aligned_cols=58 Identities=14% Similarity=0.178 Sum_probs=32.9
Q ss_pred ceeccCCcccccCCcccc---ccccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029914 73 VSAVDSGVEVSITEPEDL---ITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 130 (185)
Q Consensus 73 vsav~sg~~~s~~~~~~~---~s~~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkkl 130 (185)
||.|+.|.....-=..+. ++-.+.++-.-........+.+.++.++.+++.+...+.+
T Consensus 4 isivg~~~~~~~~~~~~i~~~L~~~~I~v~~i~q~~s~~~isf~i~~~~~~~~~~~Lh~~~ 64 (66)
T cd04924 4 VAVVGSGMRGTPGVAGRVFGALGKAGINVIMISQGSSEYNISFVVAEDDGWAAVKAVHDEF 64 (66)
T ss_pred EEEECCCCCCCccHHHHHHHHHHHCCCCEEEEEecCccceEEEEEeHHHHHHHHHHHHHHh
Confidence 677787775541111122 2222333332332224588999999999988877666554
No 17
>KOG3018 consensus Malonyl-CoA decarboxylase [Carbohydrate transport and metabolism]
Probab=45.43 E-value=16 Score=33.71 Aligned_cols=21 Identities=38% Similarity=0.801 Sum_probs=15.2
Q ss_pred HHHHHHHHHhhc---------CCCCCCccc
Q 029914 122 VFDKVLTNLARS---------APPIPGFRR 142 (185)
Q Consensus 122 a~dkalkklaK~---------akpIPGFRK 142 (185)
.+.++.+++.|. +.||||||+
T Consensus 183 LIKrV~t~lqkd~Phv~tfstLSPIPGF~~ 212 (362)
T KOG3018|consen 183 LIKRVITLLQKDMPHVSTFSTLSPIPGFMQ 212 (362)
T ss_pred HHHHHHHHHHhcCCccccccccCCCccHHH
Confidence 456666777665 459999997
No 18
>PRK02103 malonate decarboxylase subunit delta; Provisional
Probab=43.29 E-value=68 Score=25.20 Aligned_cols=47 Identities=15% Similarity=0.243 Sum_probs=39.5
Q ss_pred CcEEEEEecC-CceEEEEEEeCHHHHHHHHHHHHHHHhhcCCCCCCccc
Q 029914 95 DAKIVVESQD-EDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRR 142 (185)
Q Consensus 95 ~MkV~Ve~le-~~~ikL~VtVp~eeveka~dkalkklaK~akpIPGFRK 142 (185)
||.|-+|..+ +.+.++.|.-+..-+....+.++.++....+ .+|-|-
T Consensus 30 dLEVL~ep~~~~~~~~v~I~Tsv~Gf~~~WqaVl~~f~~r~~-~~~~~i 77 (105)
T PRK02103 30 NLEVLVERVLPGGECEVEIRTAAVGFGAVWQAVVADFVERRS-PGGLRI 77 (105)
T ss_pred ceEEEEeccCCCCeEEEEEEecccCcHHHHHHHHHHHHhhCC-CCccEE
Confidence 5677778887 7899999999999999999999999988886 787663
No 19
>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=40.69 E-value=82 Score=24.48 Aligned_cols=46 Identities=24% Similarity=0.437 Sum_probs=37.9
Q ss_pred CcEEEEEecC-CceEEEEEEeCHHHHHHHHHHHHHHHhhcCCCCCCcc
Q 029914 95 DAKIVVESQD-EDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFR 141 (185)
Q Consensus 95 ~MkV~Ve~le-~~~ikL~VtVp~eeveka~dkalkklaK~akpIPGFR 141 (185)
||.|-+|... +.+..+.|+-+.+-+....+.++.++..... .+|-|
T Consensus 28 dLEVL~ep~~~~~~~~v~I~Tsv~Gf~~~Wqavl~rf~~~~~-~~~~~ 74 (98)
T TIGR03130 28 DLEVLVEPGAEGGKTEVRITTSVDGFGAVWQAVIERFFARYP-LAGLQ 74 (98)
T ss_pred ceEEEEEcCCCCCeEEEEEEecccCcHHHHHHHHHHHHhhCC-CCccE
Confidence 5677778854 8888999999998888999999999888886 88765
No 20
>cd04911 ACT_AKiii-YclM-BS_1 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Bacillus subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from Bacillus subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=40.46 E-value=21 Score=26.17 Aligned_cols=43 Identities=12% Similarity=0.144 Sum_probs=37.9
Q ss_pred ccCcEEEEEecCCceEEEEEEeCHHHHHH-HHHHHHHHHhhcCC
Q 029914 93 VKDAKIVVESQDEDKIQVRVDLTGDATQR-VFDKVLTNLARSAP 135 (185)
Q Consensus 93 ~~~MkV~Ve~le~~~ikL~VtVp~eevek-a~dkalkklaK~ak 135 (185)
+++-.+++|..+...-.++|.+..++++. ..+++++++.+.++
T Consensus 25 ~E~~~is~Eh~PSGID~~Siii~~~~~~~~~~~~i~~~i~~~~~ 68 (76)
T cd04911 25 LEDNGISYEHMPSGIDDISIIIRDNQLTDEKEQKILAEIKEELH 68 (76)
T ss_pred HHHcCCCEeeecCCCccEEEEEEccccchhhHHHHHHHHHHhcC
Confidence 56667778888888889999999999999 99999999999877
No 21
>PRK13253 citrate lyase subunit gamma; Provisional
Probab=40.05 E-value=1.3e+02 Score=23.00 Aligned_cols=46 Identities=11% Similarity=0.170 Sum_probs=29.6
Q ss_pred CcEEEEEecCCceEEEEEEeCHH-HHHHHHHHHHHHHhhcCCCCCCcc
Q 029914 95 DAKIVVESQDEDKIQVRVDLTGD-ATQRVFDKVLTNLARSAPPIPGFR 141 (185)
Q Consensus 95 ~MkV~Ve~le~~~ikL~VtVp~e-eveka~dkalkklaK~akpIPGFR 141 (185)
|+.|.++..++..+++.++=+.+ .+.+.+++++.+...... +++-+
T Consensus 16 Dl~V~veP~~~~~i~i~i~SsV~~~Fg~~i~~vv~~~l~~~~-v~~~~ 62 (92)
T PRK13253 16 DVMIRIAPADTQGIDIQLESSVEKQFGDQIRAVILETLAKLG-VENAQ 62 (92)
T ss_pred CEEEEEEeCCCCcEEEEEEeeHHhhhHHHHHHHHHHHHHhcC-CCceE
Confidence 56677888755667777776666 666666666666666665 55544
No 22
>PRK01220 malonate decarboxylase subunit delta; Provisional
Probab=39.40 E-value=82 Score=24.55 Aligned_cols=46 Identities=13% Similarity=0.295 Sum_probs=38.4
Q ss_pred CcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHHhhcCCCCCCcc
Q 029914 95 DAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFR 141 (185)
Q Consensus 95 ~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkklaK~akpIPGFR 141 (185)
||.|-+|...+.+..+.|.-+.+-+....+.++.++..... .+|-|
T Consensus 27 dLEVL~ep~~~~~~~v~I~Tsv~Gf~~~Wqavl~rf~~~~~-~~~~~ 72 (99)
T PRK01220 27 DLEVLLEPGDAGKLSIQVVTSVNGSAARWKALFERFFTAQT-PPAAN 72 (99)
T ss_pred ceEEEEEcCCCCcEEEEEEecccCcHHHHHHHHHHHHhhCC-CCccE
Confidence 56677788888889999999998888899999999888886 77665
No 23
>cd04916 ACT_AKiii-YclM-BS_2 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. B. subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from B. subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=34.87 E-value=1.2e+02 Score=19.36 Aligned_cols=58 Identities=9% Similarity=0.258 Sum_probs=32.2
Q ss_pred ceeccCCcccccCCcccc---ccccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029914 73 VSAVDSGVEVSITEPEDL---ITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 130 (185)
Q Consensus 73 vsav~sg~~~s~~~~~~~---~s~~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkkl 130 (185)
||.++.|+.....=..+. ++..+.++-.-........+.+.|+.++.+++.+..-+++
T Consensus 4 isivg~~~~~~~~~~~~i~~~L~~~~i~v~~i~~~~s~~~isf~v~~~d~~~~~~~lh~~~ 64 (66)
T cd04916 4 IMVVGEGMKNTVGVSARATAALAKAGINIRMINQGSSEISIMIGVHNEDADKAVKAIYEEF 64 (66)
T ss_pred EEEEcCCCCCCccHHHHHHHHHHHCCCCEEEEEecCcccEEEEEEeHHHHHHHHHHHHHHH
Confidence 677887775531101111 2222334433333234588899999999888866655443
No 24
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=33.45 E-value=77 Score=24.13 Aligned_cols=33 Identities=27% Similarity=0.548 Sum_probs=23.2
Q ss_pred CCcHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHh
Q 029914 150 KVPRDFLIQILGEERVTKFVVQEIVRSTLTDYTK 183 (185)
Q Consensus 150 KVP~~Vl~k~yG~e~V~~eai~elI~~a~~eAve 183 (185)
++|..=|.+..|.++|..++++.+ ++.+.+++.
T Consensus 22 ~apv~Ri~r~~~~~Rvs~~A~~~l-~~~~e~~~~ 54 (91)
T COG2036 22 KAPVRRILRKAGAERVSSSAIEEL-QEALEEYLE 54 (91)
T ss_pred chHHHHHHHHHhHHHhhHHHHHHH-HHHHHHHHH
Confidence 778888888899888887776655 444444443
No 25
>COG0199 RpsN Ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=30.15 E-value=32 Score=24.54 Aligned_cols=18 Identities=28% Similarity=0.582 Sum_probs=15.3
Q ss_pred HHHHHHhhcCCCCCCcccC
Q 029914 125 KVLTNLARSAPPIPGFRRE 143 (185)
Q Consensus 125 kalkklaK~akpIPGFRKG 143 (185)
..+.++|-+=+ ||||+|.
T Consensus 42 ~cfRE~A~~g~-ipGv~K~ 59 (61)
T COG0199 42 ICFRELAHKGE-IPGVKKA 59 (61)
T ss_pred HHHHHHhhccC-CCCeEec
Confidence 46788999999 9999985
No 26
>cd04936 ACT_AKii-LysC-BS-like_2 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains. This CD includes the C-terminal of the two ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis strain 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive AK isoenzymes. The B. subtilis strain 168 AKII is induced by methionine and repressed and inhibited by lysine. Although C. glutamicum is known to contain a single AK, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In corynebacteria and other various Gram-positive bacteria, the DAP-lysine pathway is feedback regu
Probab=29.62 E-value=66 Score=20.28 Aligned_cols=25 Identities=8% Similarity=0.248 Sum_probs=18.1
Q ss_pred ceEEEEEEeCHHHHHHHHHHHHHHH
Q 029914 106 DKIQVRVDLTGDATQRVFDKVLTNL 130 (185)
Q Consensus 106 ~~ikL~VtVp~eeveka~dkalkkl 130 (185)
....+.+.|+.++.+++.+...+.+
T Consensus 37 s~~~is~~v~~~d~~~~~~~l~~~~ 61 (63)
T cd04936 37 SEIKISCLIDEDDAEKAVRALHEAF 61 (63)
T ss_pred cCceEEEEEeHHHHHHHHHHHHHHh
Confidence 3577889999999888865554443
No 27
>cd04890 ACT_AK-like_1 ACT domains found C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). This CD includes the first of two ACT domains found C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and is the first enzyme in the pathway of the biosynthesis of the aspartate family of amino acids, lysine, threonine, methionine, and isoleucine. This CD, includes the first ACT domain of the Escherichia coli (EC) isoenzyme, AKIII (LysC) and the Arabidopsis isoenzyme, asparate kinase 1, both enzymes monofunctional and involved in lysine synthesis, as well as the the first ACT domain of Bacillus subtilis (BS) isoenzyme, AKIII (YclM), and of the Saccharomyces cerevisiae AK (Hom3). Also included are the first ACT domains of the Methylomicrobium alcaliphilum AK, the first enzyme of the ectoine biosynthetic pathway. Members of this CD bel
Probab=27.13 E-value=85 Score=20.37 Aligned_cols=38 Identities=16% Similarity=0.235 Sum_probs=26.4
Q ss_pred ccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029914 93 VKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 130 (185)
Q Consensus 93 ~~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkkl 130 (185)
+++-.+.+.-.......+.+.|+.++.++.+++.++++
T Consensus 24 l~~~~i~v~~i~t~~~~is~~v~~~~~~~~~~~l~~~l 61 (62)
T cd04890 24 LEKHGISVDLIPTSENSVTLYLDDSLLPKKLKRLLAEL 61 (62)
T ss_pred HHHcCCeEEEEecCCCEEEEEEehhhhhHHHHHHHHhh
Confidence 44444444555445588999999988888888777665
No 28
>PHA02938 hypothetical protein; Provisional
Probab=26.76 E-value=88 Score=29.11 Aligned_cols=63 Identities=16% Similarity=0.325 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHhhcCCCCC----CcccC-CCCCCCCCcHHHHHHHhCHHHHHHHHHHHHHHHHHHHHH
Q 029914 120 QRVFDKVLTNLARSAPPIP----GFRRE-KGGKTTKVPRDFLIQILGEERVTKFVVQEIVRSTLTDYT 182 (185)
Q Consensus 120 eka~dkalkklaK~akpIP----GFRKG-KGgk~~KVP~~Vl~k~yG~e~V~~eai~elI~~a~~eAv 182 (185)
..++..-..+=-.+++|+| ||-+- --|-.--+|.+++++.|.-..-+.-.+..+...++.+.+
T Consensus 32 ~aai~af~enpp~ti~plp~~~~gf~~k~~~~v~l~lpkdiieki~sya~skgls~r~vae~~v~dfl 99 (361)
T PHA02938 32 KAAIIAFAENPPETIKPLPDLNYGFSKKDLIRVYLSLPKDIIEKIRSYASSKGLSIRRVAESAVDDFL 99 (361)
T ss_pred HHHHHHHHhCCHhhcCCCCcccCCcchhhhhheeeeCCHHHHHHHHHHHhhcCccHHHHHHHHHHHHh
Confidence 4445555555567888998 66221 011111469999999986554455556666666555543
No 29
>cd04912 ACT_AKiii-LysC-EC-like_1 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first 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) and plants, (Zea mays Ask1, Ask2, and Arabidopsis thaliana AK1). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Like the A. thaliana AK1 (AK1-AT), the E. coli AKIII (LysC) has two bound feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. The lysine-sensitive plant isoenzyme is synergistically inhibited by S-adenosylmethionine. A homolog of this group appears to be the Saccharomyces cerevisiae AK (Hom3) which clusters with this group as well. Members of this CD
Probab=26.13 E-value=70 Score=22.10 Aligned_cols=40 Identities=15% Similarity=0.303 Sum_probs=26.5
Q ss_pred ccCcEEEEEecCCceEEEEEEeCHHHH---HHHHHHHHHHHhh
Q 029914 93 VKDAKIVVESQDEDKIQVRVDLTGDAT---QRVFDKVLTNLAR 132 (185)
Q Consensus 93 ~~~MkV~Ve~le~~~ikL~VtVp~eev---eka~dkalkklaK 132 (185)
+.+-.+.+.-...+...+.+.|+.++. +...++.++++.+
T Consensus 25 L~~~~I~v~~i~~s~~~is~~v~~~~~~~~~~~~~~~~~~l~~ 67 (75)
T cd04912 25 FAKHGLSVDLISTSEVSVSLTLDPTKNLSDQLLLDALVKDLSQ 67 (75)
T ss_pred HHHcCCeEEEEEcCCcEEEEEEEchhhccchHHHHHHHHHHHh
Confidence 444444444444566888899998887 5577777777665
No 30
>PF00344 SecY: SecY translocase; InterPro: IPR002208 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion []. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains []. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. The eubacterial secY protein [] interacts with the signal sequences of secretory proteins as well as with two other components of the protein translocation system: secA and secE. SecY is an integral plasma membrane protein of 419 to 492 amino acid residues that apparently contains 10 transmembrane (TM), 6 cytoplasmic and 5 periplasmic regions. Cytoplasmic regions 2 and 3, and TM domains 1, 2, 4, 5, 7 and 10 are well conserved: the conserved cytoplasmic regions are believed to interact with cytoplasmic secretion factors, while the TM domains may participate in protein export []. Homologs of secY are found in archaebacteria []. SecY is also encoded in the chloroplast genome of some algae [] where it could be involved in a prokaryotic-like protein export system across the two membranes of the chloroplast endoplasmic reticulum (CER) which is present in chromophyte and cryptophyte algae.; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0015031 protein transport, 0016020 membrane; PDB: 3J01_A 2ZJS_Y 2ZQP_Y 2WWA_A 2WW9_A 2YXR_A 1RHZ_A 3KCR_A 3DKN_A 2YXQ_A ....
Probab=25.77 E-value=1.1e+02 Score=27.40 Aligned_cols=36 Identities=22% Similarity=0.383 Sum_probs=23.7
Q ss_pred HHHHHHhh-cCCCCCCcccCCCCCCCCCcHHHHHHHhCHHHHHH
Q 029914 125 KVLTNLAR-SAPPIPGFRREKGGKTTKVPRDFLIQILGEERVTK 167 (185)
Q Consensus 125 kalkklaK-~akpIPGFRKGKGgk~~KVP~~Vl~k~yG~e~V~~ 167 (185)
+.-+++.| ..- |||+||| |.-.+.+++..-.-.+..
T Consensus 269 ~iA~~lkk~g~~-I~GirpG------~~T~~yL~~~i~~~~~~G 305 (346)
T PF00344_consen 269 DIAENLKKSGDY-IPGIRPG------KPTEKYLNKVIPRLSFLG 305 (346)
T ss_dssp HHHHHCHCTTSS-SSTCTTS------CHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCE-eCCCCCC------hhHHHHHHHHHHHHhhhh
Confidence 33445555 455 9999999 777777777665443333
No 31
>PRK07431 aspartate kinase; Provisional
Probab=25.50 E-value=89 Score=30.02 Aligned_cols=65 Identities=17% Similarity=0.189 Sum_probs=48.9
Q ss_pred eeeceeeceeccCCcccccCCcccc-ccccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029914 66 VQHVLKTVSAVDSGVEVSITEPEDL-ITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 130 (185)
Q Consensus 66 ~~~~~~~vsav~sg~~~s~~~~~~~-~s~~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkkl 130 (185)
+.+-+.-||.||.|+....-=..+. -++.+..+.+.-...+++.+.+-|+.++.++++....+.+
T Consensus 515 ~~~~va~VSvVG~gm~~~~gv~~ri~~aL~~~~I~v~~i~~S~~~Is~vV~~~~~~~av~~Lh~~f 580 (587)
T PRK07431 515 DGPAIAKVSIVGAGMPGTPGVAARMFRALADAGINIEMIATSEIRTSCVVAEDDGVKALQAVHQAF 580 (587)
T ss_pred EeCCeEEEEEECCCccCCcCHHHHHHHHHHHCCCcEEEeeccceEEEEEEeHHHHHHHHHHHHHHh
Confidence 5567778999999997653222333 3355556666666789999999999999999999888776
No 32
>KOG3939 consensus Selenophosphate synthetase [Signal transduction mechanisms]
Probab=25.17 E-value=1.6e+02 Score=27.07 Aligned_cols=63 Identities=17% Similarity=0.521 Sum_probs=43.8
Q ss_pred ceeeceeccCCcccccCCccccccccCc--------------EEE------EEecCCceEEEEEEeCHHHHHHHHHHHHH
Q 029914 69 VLKTVSAVDSGVEVSITEPEDLITVKDA--------------KIV------VESQDEDKIQVRVDLTGDATQRVFDKVLT 128 (185)
Q Consensus 69 ~~~~vsav~sg~~~s~~~~~~~~s~~~M--------------kV~------Ve~le~~~ikL~VtVp~eeveka~dkalk 128 (185)
+.-|-+-.+ |+.+|+-|++++|.-++. ++. +....+.-.++.++|+.++++++|+.+..
T Consensus 98 v~npw~~ig-GVatsVcq~ne~i~pdnAvpGdvlvLTkplg~qvAv~~h~wi~~~~ek~~~~~l~vs~~die~ay~~a~~ 176 (312)
T KOG3939|consen 98 VINPWCIIG-GVATSVCQPNEIIMPDNAVPGDVLVLTKPLGGQVAVNAHQWIDNQPEKWNKLKLEVSDEDIEKAYEEAMK 176 (312)
T ss_pred ecCcceeec-cccccccCccceecccCCCCcceEEEeccCCceeehHHHHHHhcCcceeeeeeeeecHHHHHHHHHHHHh
Confidence 445666667 889999999887665441 111 11234445579999999999999999877
Q ss_pred HHhh
Q 029914 129 NLAR 132 (185)
Q Consensus 129 klaK 132 (185)
.+++
T Consensus 177 ~M~~ 180 (312)
T KOG3939|consen 177 SMAR 180 (312)
T ss_pred hhhh
Confidence 6653
No 33
>PRK08961 bifunctional aspartate kinase/diaminopimelate decarboxylase protein; Provisional
Probab=24.59 E-value=1.5e+02 Score=30.16 Aligned_cols=68 Identities=13% Similarity=0.182 Sum_probs=53.6
Q ss_pred eeeceeeceeccCCcccccCCcccc-ccccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHHhhc
Q 029914 66 VQHVLKTVSAVDSGVEVSITEPEDL-ITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARS 133 (185)
Q Consensus 66 ~~~~~~~vsav~sg~~~s~~~~~~~-~s~~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkklaK~ 133 (185)
+.+-+.-||.||.|+.....-..+. -++.+..|.+-....+++.|.+-|+.++.+++++...+++-..
T Consensus 394 ~~~~va~ISvVG~gm~~~~gv~arif~aL~~~~I~~i~~gsSe~~Is~vV~~~d~~~av~~LH~~f~~~ 462 (861)
T PRK08961 394 IIVPCAAVSLVGRGMRSLLHKLGPAWATFGAERVHLISQASNDLNLTFVIDESDADGLLPRLHAELIES 462 (861)
T ss_pred EeCCeEEEEEeCCCcccCcChHHHHHHHHhhcCeEEEECCCccccEEEEEeHHHHHHHHHHHHHHHhcC
Confidence 4456677999999997663333343 3366677888899999999999999999999999999988554
No 34
>PF02120 Flg_hook: Flagellar hook-length control protein FliK; InterPro: IPR021136 This entry represents the C-terminal domain of the flagellar hook-length control protein FliK. This entry also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. During flagellar morphogenesis in Salmonella typhimurium and Escherichia coli, flagellar hook-length control protein (FliK) controls the length of the hook by directly measuring the hook length [, ]. It is considered unlikely that FliK functions as a molecular ruler for determining hook length, but that it is more likely to be employing a novel mechanism. The deduced amino acid sequences of FliK proteins from S. typhimurium and E. coli have molecular masses of 41,748 and 39,246 Da, respectively, and are fairly hydrophilic []. Sequence comparison reveals around 50% identity, with greatest conservation in the C-terminal region, with 71% identity in the last 154 amino acids - mutagenesis of this conserved region completely abolishes motility. The central and C-terminal regions are rich in proline and glutamine respectively; it is thought that they may constitute distinct domains [].; PDB: 2RRL_A.
Probab=24.24 E-value=1.3e+02 Score=20.82 Aligned_cols=48 Identities=13% Similarity=0.236 Sum_probs=35.2
Q ss_pred ccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHHhhcCCCCCCccc
Q 029914 93 VKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRR 142 (185)
Q Consensus 93 ~~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkklaK~akpIPGFRK 142 (185)
+-.|.|.+...++ .+.+.+.++..++.+.++..+..|...+. =-||.-
T Consensus 24 LG~v~v~l~~~~~-~l~v~~~~~~~~~~~~L~~~~~~L~~~L~-~~G~~~ 71 (85)
T PF02120_consen 24 LGSVEVKLRLQGG-NLSVQFTAENPETKELLRQNLPELKERLQ-AQGLEV 71 (85)
T ss_dssp G--EEEEEEEETT-EEEEEEE--SSHHHHHHHHTHHHHHHHHH-TTT-EE
T ss_pred cCcEEEEEEEeCC-EEEEEEEECCHHHHHHHHHHHHHHHHHHH-HCCCCe
Confidence 3347788766555 99999999999999999999999988877 556543
No 35
>PF02800 Gp_dh_C: Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; InterPro: IPR020829 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and gluconeogenesis [] by reversibly catalysing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. The enzyme exists as a tetramer of identical subunits, each containing 2 conserved functional domains: an NAD-binding domain, and a highly conserved catalytic domain []. The enzyme has been found to bind to actin and tropomyosin, and may thus have a role in cytoskeleton assembly. Alternatively, the cytoskeleton may provide a framework for precise positioning of the glycolytic enzymes, thus permitting efficient passage of metabolites from enzyme to enzyme []. GAPDH displays diverse non-glycolytic functions as well, its role depending upon its subcellular location. For instance, the translocation of GAPDH to the nucleus acts as a signalling mechanism for programmed cell death, or apoptosis []. The accumulation of GAPDH within the nucleus is involved in the induction of apoptosis, where GAPDH functions in the activation of transcription. The presence of GAPDH is associated with the synthesis of pro-apoptotic proteins like BAX, c-JUN and GAPDH itself. GAPDH has been implicated in certain neurological diseases: GAPDH is able to bind to the gene products from neurodegenerative disorders such as Huntington's disease, Alzheimer's disease, Parkinson's disease and Machado-Joseph disease through stretches encoded by their CAG repeats. Abnormal neuronal apoptosis is associated with these diseases. Propargylamines such as deprenyl increase neuronal survival by interfering with apoptosis signalling pathways via their binding to GAPDH, which decreases the synthesis of pro-apoptotic proteins []. This entry represents the C-terminal domain which is a mixed alpha/antiparallel beta fold.; GO: 0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor, 0055114 oxidation-reduction process; PDB: 1DSS_R 1IHY_C 1CRW_R 1IHX_B 1SZJ_R 3HJA_D 2YYY_B 1OBF_O 3PYM_A 2VYN_D ....
Probab=24.06 E-value=1e+02 Score=24.95 Aligned_cols=40 Identities=18% Similarity=0.265 Sum_probs=34.6
Q ss_pred ccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHHhh
Q 029914 93 VKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLAR 132 (185)
Q Consensus 93 ~~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkklaK 132 (185)
++.|-+.|-....+-+.|++++......+.+++++++.++
T Consensus 71 i~g~a~rVPt~~~s~~dl~~~l~k~~t~eeV~~~~~~aa~ 110 (157)
T PF02800_consen 71 ITGMAVRVPTPNVSLHDLTVELEKPVTKEEVNEALKQAAR 110 (157)
T ss_dssp EEEEEEEESSSSEEEEEEEEEESSSS-HHHHHHHHHHHHH
T ss_pred ceeeEEeeeecccCceEEEEecccchhhhhhhhhhhhhhH
Confidence 4668899999999999999999999888999999988886
No 36
>KOG0884 consensus Similar to cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=22.34 E-value=2.8e+02 Score=22.97 Aligned_cols=53 Identities=17% Similarity=0.271 Sum_probs=31.3
Q ss_pred cEEEEE-ecCCceEEEEEEeCHHHHHHHHHHHHHHHh---hcCCCCCCc--------ccCCCCCC
Q 029914 96 AKIVVE-SQDEDKIQVRVDLTGDATQRVFDKVLTNLA---RSAPPIPGF--------RREKGGKT 148 (185)
Q Consensus 96 MkV~Ve-~le~~~ikL~VtVp~eeveka~dkalkkla---K~akpIPGF--------RKGKGgk~ 148 (185)
|.|+.. ...+.++++-++-.+...+.-+...-.++. ---+||||| |-||||.+
T Consensus 1 msvtlht~~gdikiev~~e~tpktce~~l~~~~~~~~n~~~~~~~~~~f~v~~~~~~~tgrgg~s 65 (161)
T KOG0884|consen 1 MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASDYYNGCIFHRNIKGFMVQTGDPTHTGRGGNS 65 (161)
T ss_pred CeEEEeeccCcEEEEEEecCChhHHHHHHHHhhhhhccceeecCCCCCcEEEeCCCCCCCCCCcc
Confidence 444433 345566777777777776665544433332 223569999 67888864
No 37
>COG0201 SecY Preprotein translocase subunit SecY [Intracellular trafficking and secretion]
Probab=21.98 E-value=1.8e+02 Score=27.77 Aligned_cols=28 Identities=32% Similarity=0.516 Sum_probs=16.9
Q ss_pred HHHHhhc-CCCCCCcccCCCCCCCCCcHHHHHHHhC
Q 029914 127 LTNLARS-APPIPGFRREKGGKTTKVPRDFLIQILG 161 (185)
Q Consensus 127 lkklaK~-akpIPGFRKGKGgk~~KVP~~Vl~k~yG 161 (185)
.+++.|. .. |||+||| |.=.+.+++...
T Consensus 341 A~~lkksG~~-IPGiRpg------~~te~yL~rvi~ 369 (436)
T COG0201 341 AENLKKSGGF-IPGIRPG------KDTEKYLNRVIP 369 (436)
T ss_pred HHHHHHcCCc-CCCcCCC------hhHHHHHHHHHH
Confidence 3334343 55 9999999 555555555443
No 38
>PF01077 NIR_SIR: Nitrite and sulphite reductase 4Fe-4S domain; InterPro: IPR006067 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP) (IPR005117 from INTERPRO), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a siroheme through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. In the E. coli SiR-HP enzyme (1.8.1.2 from EC), the iron is bound to cysteine residues at positions 433, 439, 478 and 482, the latter also forming the siroheme ligand.; GO: 0016491 oxidoreductase activity, 0020037 heme binding, 0051536 iron-sulfur cluster binding, 0055114 oxidation-reduction process; PDB: 1ZJ8_B 1ZJ9_A 2AKJ_A 3VKT_A 3VKR_A 3VKS_A 3B0M_A 3B0N_A 3VKP_A 3B0J_A ....
Probab=21.95 E-value=1.7e+02 Score=22.77 Aligned_cols=47 Identities=21% Similarity=0.186 Sum_probs=35.1
Q ss_pred EEeCHHHHHHHHHHHHHHHh--hcCCCCCCcccCCCCCCCCCcHHHHHHHhCHHHHHHHHHH
Q 029914 112 VDLTGDATQRVFDKVLTNLA--RSAPPIPGFRREKGGKTTKVPRDFLIQILGEERVTKFVVQ 171 (185)
Q Consensus 112 VtVp~eeveka~dkalkkla--K~akpIPGFRKGKGgk~~KVP~~Vl~k~yG~e~V~~eai~ 171 (185)
..++.+++-..+++++.-+. ++.+ . +....-+..++|.+.+++++.+
T Consensus 103 ~~~~~ee~~~~i~~il~~y~~~~~~~-------~------~er~~~~i~r~G~e~~~~~v~~ 151 (157)
T PF01077_consen 103 GFVPEEEVLEVIEAILEYYRGNREAR-------K------KERFKDFIERLGFEKFREEVEE 151 (157)
T ss_dssp EEEEGGGHHHHHHHHHHHHHS-HSSG-------T------T-SHHHHHHHHHHHHHHHHHHH
T ss_pred ccccHHHHHHHHHHHHHHHHHhccCC-------C------CCCHHHHHHHHCHHHHHHHHHH
Confidence 35788889999999999998 4444 2 5667777778999888877744
No 39
>PF05698 Trigger_C: Bacterial trigger factor protein (TF) C-terminus; InterPro: IPR008880 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 entry represents the C-terminal domain of bacterial trigger factor proteins, which has a multi-helical structure consisting of an irregular array of long and short helices. This domain is structurally similar to the peptide-binding domain of the bacterial porin chaperone SurA.; GO: 0006457 protein folding, 0015031 protein transport; PDB: 1T11_A 3GU0_A 3GTY_X 2NSA_A 1ZXJ_A 1W26_A.
Probab=21.89 E-value=3.6e+02 Score=20.41 Aligned_cols=33 Identities=12% Similarity=0.304 Sum_probs=25.0
Q ss_pred EEEEeCHHHHHHHHHHHHHHHhhcCCCCCCcccC
Q 029914 110 VRVDLTGDATQRVFDKVLTNLARSAPPIPGFRRE 143 (185)
Q Consensus 110 L~VtVp~eeveka~dkalkklaK~akpIPGFRKG 143 (185)
..|++|...++..++..+..+...++ -.|....
T Consensus 37 ~~~~lP~~lv~~~~~~~~~~~~~~~~-~~g~~~e 69 (162)
T PF05698_consen 37 SEVELPESLVEEEIERLIEQMEQQLK-QQGMSLE 69 (162)
T ss_dssp EEEEE-HHHHHHHHHHHHHHHHHTT----TSSCC
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhh-hhhhHHH
Confidence 56799999999999999999999997 5555544
No 40
>PRK12907 secY preprotein translocase subunit SecY; Reviewed
Probab=21.68 E-value=93 Score=29.47 Aligned_cols=37 Identities=19% Similarity=0.423 Sum_probs=23.2
Q ss_pred EEeCHHHHHHHHHHHHHHHhhcCCCCCCcccCCCCCCCCCcHHHHHHHhC
Q 029914 112 VDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILG 161 (185)
Q Consensus 112 VtVp~eeveka~dkalkklaK~akpIPGFRKGKGgk~~KVP~~Vl~k~yG 161 (185)
|.++++|+.+.++| .-.- |||+||| |.=.+.+++...
T Consensus 330 i~~nP~~iAenL~k------~G~~-IPGiRPG------k~T~~yL~~~i~ 366 (434)
T PRK12907 330 IQVNPEQMAENLKK------QNGY-VPGIRPG------KSTEQYVTKILY 366 (434)
T ss_pred HccCHHHHHHHHHH------CCCc-CCCcCCC------hhHHHHHHHHHH
Confidence 44566655544433 3456 9999999 666666666543
No 41
>PF10923 DUF2791: P-loop Domain of unknown function (DUF2791); InterPro: IPR021228 This is a family of proteins found in archaea and bacteria. Some of the proteins in this family are annotated as being methyl-accepting chemotaxis proteins and ATP/GTP binding proteins.
Probab=21.39 E-value=1.9e+02 Score=27.44 Aligned_cols=56 Identities=14% Similarity=0.128 Sum_probs=40.0
Q ss_pred eEEEEEEeCHHHH----HHHHHHHHHHHhhcCCCCCCcccCCCCCCCCCcHHHHHHHhCHHHHHHHHHH
Q 029914 107 KIQVRVDLTGDAT----QRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILGEERVTKFVVQ 171 (185)
Q Consensus 107 ~ikL~VtVp~eev----eka~dkalkklaK~akpIPGFRKGKGgk~~KVP~~Vl~k~yG~e~V~~eai~ 171 (185)
-+...|+++++.- +...+.+|.++.+++. .++...| .+-..+|++-+.. +.+++.+
T Consensus 78 fvvs~v~ls~e~~lh~~~g~~~~~Yr~l~~nL~-t~~~p~G------~al~~ild~wi~~--~~~~~~~ 137 (416)
T PF10923_consen 78 FVVSEVDLSPERPLHGTGGQLEALYRELMRNLS-TKTKPEG------GALRSILDRWIYN--LEEEVAA 137 (416)
T ss_pred CEEEEEecCCCcccccccccHHHHHHHHHHhcC-CCCCCCc------hHHHHHHHHHHHH--HHHHHHh
Confidence 3344455555332 2367889999999999 9999999 7999999987753 6665553
No 42
>PRK09466 metL bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional
Probab=21.07 E-value=89 Score=31.89 Aligned_cols=68 Identities=21% Similarity=0.217 Sum_probs=51.1
Q ss_pred eeceeeceeccCCcccccCCcccc-ccccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHHhhcC
Q 029914 67 QHVLKTVSAVDSGVEVSITEPEDL-ITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNLARSA 134 (185)
Q Consensus 67 ~~~~~~vsav~sg~~~s~~~~~~~-~s~~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkklaK~a 134 (185)
.+-+.-||.||.|+....--..+. -++.+.+|.+-....+...+.+-|+.++.+++++...+.+-..-
T Consensus 388 ~~~~a~VsvVG~gm~~~~gv~~~~f~aL~~~~I~ii~~~~s~~sis~vV~~~d~~~av~~LH~~f~~~~ 456 (810)
T PRK09466 388 REGLALVALVGAGVTRNPLHCHRFYQQLKDQPVEFIWQSEDGLSLVAVLRQGPTESLIQGLHQSLFRAE 456 (810)
T ss_pred eCCeEEEEEeCCCcccCccHHHHHHHHHHhCCCcEEEEeCCCcEEEEEEehHHHHHHHHHHHHHHhCcC
Confidence 345666999999986552222333 34666777777888888999999999999999999888876553
No 43
>PRK09084 aspartate kinase III; Validated
Probab=20.01 E-value=1.6e+02 Score=27.71 Aligned_cols=65 Identities=11% Similarity=0.104 Sum_probs=48.3
Q ss_pred eeeceeeceeccCCcccccCCcccc-ccccCcEEEEEecCCceEEEEEEeCHHHHHHHHHHHHHHH
Q 029914 66 VQHVLKTVSAVDSGVEVSITEPEDL-ITVKDAKIVVESQDEDKIQVRVDLTGDATQRVFDKVLTNL 130 (185)
Q Consensus 66 ~~~~~~~vsav~sg~~~s~~~~~~~-~s~~~MkV~Ve~le~~~ikL~VtVp~eeveka~dkalkkl 130 (185)
+..-+.-||.||.|+.....-..+. -++.+.++.+-....+++.+.+-|+.++.+++++...+.+
T Consensus 380 ~~~~va~IsvvG~gm~~~~gv~arif~aL~~~nI~~I~qgsSe~sIS~vV~~~d~~~al~~LH~~f 445 (448)
T PRK09084 380 VEEGLALVALIGNNLSKACGVAKRVFGVLEPFNIRMICYGASSHNLCFLVPESDAEQVVQALHQNL 445 (448)
T ss_pred EECCeEEEEEECCCcccCcChHHHHHHHHHhCCeEEEEEcCCCCcEEEEEcHHHHHHHHHHHHHHH
Confidence 3445666899999986653333333 3366677888888899999999999999999988876654
Done!