Query 039274
Match_columns 96
No_of_seqs 105 out of 308
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 08:04:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039274.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039274hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00280 potato_inhibit: Potat 100.0 1.3E-31 2.9E-36 169.2 5.8 63 34-96 1-63 (63)
2 PF11720 Inhibitor_I78: Peptid 99.7 1.8E-17 3.8E-22 103.0 2.5 54 35-92 4-57 (60)
3 PF03793 PASTA: PASTA domain; 78.7 6.3 0.00014 23.1 4.4 19 37-55 3-21 (63)
4 cd06573 PASTA PASTA domain. Th 59.1 20 0.00044 19.3 3.4 17 38-54 3-19 (53)
5 cd03477 Rieske_YhfW_C YhfW fam 44.9 27 0.00058 22.6 2.7 29 64-92 8-36 (91)
6 cd06575 PASTA_Pbp2x-like_2 PAS 43.8 37 0.0008 18.2 2.9 19 37-55 2-20 (54)
7 PF03413 PepSY: Peptidase prop 42.3 51 0.0011 18.6 3.4 48 44-91 3-62 (64)
8 PF06241 DUF1012: Protein of u 41.8 28 0.00061 26.7 2.8 29 35-67 97-126 (206)
9 PF13103 TonB_2: TonB C termin 41.1 28 0.0006 21.3 2.3 15 78-92 29-43 (85)
10 cd06577 PASTA_pknB PASTA domai 40.7 28 0.0006 19.1 2.1 19 37-55 2-20 (62)
11 cd06576 PASTA_Pbp2x-like_1 PAS 39.2 66 0.0014 17.4 3.5 28 38-67 3-30 (55)
12 cd03474 Rieske_T4moC Toluene-4 35.2 42 0.00092 21.6 2.5 29 64-92 10-38 (108)
13 smart00740 PASTA PASTA domain. 31.9 46 0.00099 18.5 2.1 20 36-55 6-25 (66)
14 PF14326 DUF4384: Domain of un 31.4 45 0.00097 20.9 2.1 29 64-92 3-35 (83)
15 PF11396 DUF2874: Protein of u 30.9 1.1E+02 0.0024 17.5 4.1 44 47-90 11-61 (61)
16 PF01436 NHL: NHL repeat; Int 29.6 62 0.0013 16.4 2.1 20 63-82 9-28 (28)
17 PF03544 TonB_C: Gram-negative 29.5 45 0.00097 19.8 1.8 15 78-92 19-33 (79)
18 TIGR01352 tonB_Cterm TonB fami 29.2 51 0.0011 19.2 2.0 16 78-93 13-28 (74)
19 PF09429 Wbp11: WW domain bind 28.5 55 0.0012 20.9 2.2 20 1-20 5-24 (78)
20 cd03531 Rieske_RO_Alpha_KSH Th 28.2 72 0.0016 21.2 2.8 29 64-92 11-39 (115)
21 PF08482 HrpB_C: ATP-dependent 28.1 59 0.0013 23.2 2.4 44 33-78 8-60 (133)
22 cd03469 Rieske_RO_Alpha_N Ries 27.9 73 0.0016 20.5 2.8 27 66-92 13-39 (118)
23 PRK13320 pantothenate kinase; 27.3 63 0.0014 24.5 2.7 39 36-74 91-129 (244)
24 TIGR00638 Mop molybdenum-pteri 27.2 33 0.00072 20.1 0.9 20 65-84 50-69 (69)
25 cd04337 Rieske_RO_Alpha_Cao Ca 26.2 82 0.0018 21.5 2.9 29 64-92 27-55 (129)
26 PF04225 OapA: Opacity-associa 25.9 56 0.0012 21.1 1.9 41 42-91 21-61 (85)
27 PF06691 DUF1189: Protein of u 25.1 1.4E+02 0.003 22.4 4.1 44 48-91 58-103 (250)
28 PRK13328 pantothenate kinase; 24.9 63 0.0014 24.7 2.3 38 38-75 97-134 (255)
29 cd03530 Rieske_NirD_small_Baci 24.6 87 0.0019 19.7 2.6 28 65-92 11-38 (98)
30 PF00367 PTS_EIIB: phosphotran 23.8 36 0.00079 18.7 0.6 20 70-89 15-34 (35)
31 PF08882 Acetone_carb_G: Aceto 22.7 37 0.00081 23.8 0.6 18 60-77 85-102 (112)
32 COG0391 Uncharacterized conser 22.5 79 0.0017 25.7 2.5 24 45-72 180-203 (323)
33 PRK13321 pantothenate kinase; 22.2 85 0.0018 23.6 2.5 39 36-74 101-139 (256)
34 PF02406 MmoB_DmpM: MmoB/DmpM 22.1 1.5E+02 0.0032 19.5 3.3 20 49-70 18-37 (87)
35 KOG0912 Thiol-disulfide isomer 21.0 1.1E+02 0.0024 25.4 3.0 18 61-78 76-93 (375)
36 PHA02087 hypothetical protein 20.5 1.1E+02 0.0024 20.0 2.4 22 73-94 38-61 (83)
37 PF02643 DUF192: Uncharacteriz 20.3 76 0.0016 21.1 1.7 17 74-92 48-64 (108)
No 1
>PF00280 potato_inhibit: Potato inhibitor I family; InterPro: IPR000864 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This family of proteinase inhibitors belong to MEROPS inhibitor family I13, clan IG. They inhibit peptidases of the S1 (IPR001254 from INTERPRO) and S8 (IPR000209 from INTERPRO) families []. Potato inhibitor type I sequences are not solely restricted to potatoes but are found in other plant species for example: barley endosperm chymotrypsin inhibitor [], and pumpkin trypsin inhibitor. Exceptions are found in leech's, e.g.Hirudo medicinalis (Medicinal leech), but not other metazoa []. In general, the proteins have retained a specificity towards chymotrypsin-like and elastase-like proteases []. Structurally these inhibitors are small (60 to 90 residues) and in contrast with other families of protease inhibitors, they lack disulphide bonds. The inhibitor is a wedge-shaped molecule, its pointed edge formed by the protease-binding loop, which contains the scissile bond. The loop binds tightly to the protease active site, subsequent cleavage of the scissile bond causing inhibition of the enzyme []. The inhibitors (designated type I and II) are synthesised in potato tubers, increasing in concentration as the tuber develops. Synthesis of the inhibitors throughout the plant is also induced by leaf damage; this systemic response being triggered by the release of a putative plant hormone []. Examples found in the bacteria and archaea are probable false positives.; GO: 0004867 serine-type endopeptidase inhibitor activity, 0009611 response to wounding; PDB: 1TEC_I 1SBN_I 1ACB_I 1EGP_A 3TEC_I 2SEC_I 1EGL_A 2TEC_I 1SIB_I 1MEE_I ....
Probab=99.97 E-value=1.3e-31 Score=169.20 Aligned_cols=63 Identities=60% Similarity=0.987 Sum_probs=59.4
Q ss_pred CCccccccCcchHHHHHHHHHHcCCCeEEEecCCccccCCCcCCeEEEEECCCCCEEecCcCC
Q 039274 34 KSSWPELVGVKGEVAAEIIMRENGKVVAIIVKEGFEVTMDYRCDRVWVWVDHHGIVKYTPRIG 96 (96)
Q Consensus 34 k~sWPELVG~~~~~A~~~I~~e~p~v~v~Vl~pGs~vTmDfr~dRV~V~vD~~g~V~~vP~vG 96 (96)
|+|||||||+++++|+++|++|||++++.+|++|+++|+|||||||+||+|++|+|+++|+||
T Consensus 1 K~sWPELVG~~~~~A~~~I~~e~P~v~v~vlp~gs~vt~df~~~RVrv~vd~~~~V~~~P~iG 63 (63)
T PF00280_consen 1 KTSWPELVGKSGEEAKAIIERENPDVTVVVLPEGSPVTMDFRCDRVRVFVDSNGIVVRVPRIG 63 (63)
T ss_dssp -SB-GGGTTSBHHHHHHHHHHHSTTSEEEEEETTSEEESSBETTEEEEEEETTSBBES-SEEE
T ss_pred CCCCchhcCCCHHHHHHHHHHHCCCCeEEEEeCCCCcCCCcCCCEEEEEECCCCeEEeCCCcC
Confidence 689999999999999999999999999999999999999999999999999999999999998
No 2
>PF11720 Inhibitor_I78: Peptidase inhibitor I78 family; InterPro: IPR021719 This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78.
Probab=99.68 E-value=1.8e-17 Score=103.04 Aligned_cols=54 Identities=31% Similarity=0.423 Sum_probs=45.3
Q ss_pred CccccccCcchHHHHHHHHHHcCCCeEEEecCCccccCCCcCCeEEEEECCCCCEEec
Q 039274 35 SSWPELVGVKGEVAAEIIMRENGKVVAIIVKEGFEVTMDYRCDRVWVWVDHHGIVKYT 92 (96)
Q Consensus 35 ~sWPELVG~~~~~A~~~I~~e~p~v~v~Vl~pGs~vTmDfr~dRV~V~vD~~g~V~~v 92 (96)
+....|||++++++...-. ...+|||+||+++|||||+|||||++|++|+|+++
T Consensus 4 ~~~q~lvGq~~~~~~~~~~----~~~~Rvi~Pg~~vTmDyr~dRLnv~~D~~g~I~~v 57 (60)
T PF11720_consen 4 AAAQSLVGQPASAAEREEL----AETVRVIRPGDAVTMDYRPDRLNVEVDDDGVITRV 57 (60)
T ss_pred HHHHHhhCCCccccccccc----ccceEEeCCCCcCcccCCCCcEEEEECCCCcEEEE
Confidence 5566789999987653211 44699999999999999999999999999999986
No 3
>PF03793 PASTA: PASTA domain; InterPro: IPR005543 The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (P71584 from SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan. PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [].; GO: 0008658 penicillin binding; PDB: 2ZC3_C 1QME_A 1RP5_B 2Z2M_C 2Z2L_F 2ZC4_C 1QMF_A 3M9G_A 3PY9_A 1K25_B ....
Probab=78.73 E-value=6.3 Score=23.12 Aligned_cols=19 Identities=32% Similarity=0.468 Sum_probs=15.3
Q ss_pred cccccCcchHHHHHHHHHH
Q 039274 37 WPELVGVKGEVAAEIIMRE 55 (96)
Q Consensus 37 WPELVG~~~~~A~~~I~~e 55 (96)
-|+|+|++.++|...+...
T Consensus 3 vPd~~g~~~~~a~~~l~~~ 21 (63)
T PF03793_consen 3 VPDLVGMTYDEAKSILEAA 21 (63)
T ss_dssp E-TTTTSBHHHHHHHHHHT
T ss_pred CCCcCCCcHHHHHHHHHHC
Confidence 4899999999999877664
No 4
>cd06573 PASTA PASTA domain. This domain is found at the C-termini of several Penicillin-binding proteins (PBPs) and bacterial serine/threonine kinases. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain.
Probab=59.08 E-value=20 Score=19.28 Aligned_cols=17 Identities=29% Similarity=0.540 Sum_probs=14.6
Q ss_pred ccccCcchHHHHHHHHH
Q 039274 38 PELVGVKGEVAAEIIMR 54 (96)
Q Consensus 38 PELVG~~~~~A~~~I~~ 54 (96)
|.++|.+..+|...+..
T Consensus 3 p~~~g~~~~~a~~~l~~ 19 (53)
T cd06573 3 PDLVGISKKDLEEQLYD 19 (53)
T ss_pred CcccCCcHHHHHHHHHc
Confidence 78999999999887765
No 5
>cd03477 Rieske_YhfW_C YhfW family, C-terminal Rieske domain; YhfW is a protein of unknown function with an N-terminal DadA-like (glycine/D-amino acid dehydrogenase) domain and a C-terminal Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. It is commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. YhfW is found in bacteria, some eukaryotes and archaea.
Probab=44.94 E-value=27 Score=22.57 Aligned_cols=29 Identities=17% Similarity=0.280 Sum_probs=21.2
Q ss_pred ecCCccccCCCcCCeEEEEECCCCCEEec
Q 039274 64 VKEGFEVTMDYRCDRVWVWVDHHGIVKYT 92 (96)
Q Consensus 64 l~pGs~vTmDfr~dRV~V~vD~~g~V~~v 92 (96)
|++|+.++.++.-..|-|+.+.+|.+..+
T Consensus 8 l~~g~~~~~~~~g~~v~v~r~~~g~~~A~ 36 (91)
T cd03477 8 LAPGEGGVVNIGGKRLAVYRDEDGVLHTV 36 (91)
T ss_pred cCCCCeEEEEECCEEEEEEECCCCCEEEE
Confidence 46777777777777788888777766554
No 6
>cd06575 PASTA_Pbp2x-like_2 PASTA domain of PBP2x-like proteins, second repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by acylating the active site serine. PBPs catalyze key steps in the synthesis of the peptidoglycan, such as the interconnecting of glycan chains (polymers of N-glucosamine and N-acetylmuramic acid residues) and the cross-linking (transpeptidation) of short stem peptides, which are attached to glycan chains. Peptidoglycan is essential in cell division and protects bacteria from osmotic shock and lysis. PBP2x is one of the two monofunctional high molecular mass PBPs in Streptococcus pneumoniae and has been seen as the primary PBP target in beta-lactam-resistant strains. The PASTA domain is found at the C-termini of several PBPs and bacterial serine/threonine kinases. The name PASTA is derived from PBP and Serine/Threonine
Probab=43.82 E-value=37 Score=18.20 Aligned_cols=19 Identities=21% Similarity=0.261 Sum_probs=15.0
Q ss_pred cccccCcchHHHHHHHHHH
Q 039274 37 WPELVGVKGEVAAEIIMRE 55 (96)
Q Consensus 37 WPELVG~~~~~A~~~I~~e 55 (96)
-|.++|.+.++|...+...
T Consensus 2 vp~~~g~~~~~a~~~l~~~ 20 (54)
T cd06575 2 MPDLTGWSKRDALKLLELL 20 (54)
T ss_pred CCCcCCCCHHHHHHHHHHC
Confidence 3789999999998777543
No 7
>PF03413 PepSY: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification. ; InterPro: IPR005075 This signature, PepSY, is found in the propeptide of members of the MEROPS peptidase family M4 (clan MA(E)), which contains the thermostable thermolysins (3.4.24.27 from EC), and related thermolabile neutral proteases (bacillolysins) (3.4.24.28 from EC) from various species of Bacillus. It is also in many non-peptidase proteins, including Bacillus subtilis YpeB protein - a regulator of SleB spore cortex lytic enzyme - and a large number of eubacterial and archaeal cell wall-associated and secreted proteins which are mostly annotated as 'hypothetical protein'. Many extracellular bacterial proteases are produced as proenzymes. The propeptides usually have a dual function, i.e. they function as an intramolecular chaperone required for the folding of the polypeptide and as an inhibitor preventing premature activation of the enzyme. Analysis of the propeptide region of the M4 family of peptidases reveals two regions of conservation, the PepSY domain and a second domain, proximate to the N terminus, the FTP domain (IPR011096 from INTERPRO), which is also found in isolation in the propeptide of eukaryotic peptidases belong to MEROPS peptidase family M36. Propeptide domain swapping experiments, for example swapping the propeptide domain of PA protease with that of vibrolysin, both propeptides contain the FTP and PepSY domains, allows the PA protease domain to fold correctly and inhibits the C-terminal autoprocessing activity. However, swapping the propeptide of PA protease for the thermolysin propeptide, does not facilitate the correct folding nor the processing of the chimaeric protein into an active peptidase []. Mutational analysis of the Pseudomonas aeruginosa elastase gene revealed two mutations in the propeptide which resulted in the loss of inhibitory activity but not chaperone activity: A-15V and T-153I (where +1 is defined as the first residue of the mature peptidase). Both mutations resulted in peptidase activity, the T-153V mutation being much less effective than the A-15I mutation [] in activating peptidase activity. The T-153V mutation lies N-terminal to the FTP domain while the A-15I mutation is C-terminal to the PepSY domain. Given the diverse range of other proteins, both domains occur in in isolation, the exact function of each is still unclear; though it has been proposed that the PepSY domain primarily has inhibitory activity and in conjunction with the FTP domain in chaperone activity. ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0005576 extracellular region; PDB: 2GU3_A 3NQZ_A 3NQY_A 2KGY_A.
Probab=42.34 E-value=51 Score=18.63 Aligned_cols=48 Identities=25% Similarity=0.182 Sum_probs=25.1
Q ss_pred chHHHHHHHHHHcCCCeEE-EecCC-c-----cccCCC----cCCeEEEEECCC-CCEEe
Q 039274 44 KGEVAAEIIMRENGKVVAI-IVKEG-F-----EVTMDY----RCDRVWVWVDHH-GIVKY 91 (96)
Q Consensus 44 ~~~~A~~~I~~e~p~v~v~-Vl~pG-s-----~vTmDf----r~dRV~V~vD~~-g~V~~ 91 (96)
+.++|..+.+...|+.... .+.++ . -+.... ......++||+. |.|..
T Consensus 3 s~~~A~~~A~~~~~~~~~~~~~~~~~~~~~~Y~v~~~~~~~~~~~~~~v~VDa~tG~Il~ 62 (64)
T PF03413_consen 3 SEEQAVEIALKQYPGKVISVELEEDENGRLVYEVEVVSDDDPDGGEYEVYVDAYTGEILS 62 (64)
T ss_dssp -HHHHHHHHHCCCCCEEEEEEEECC-TCEEEEEEEEEBTTSTTTEEEEEEEETTT--EEE
T ss_pred CHHHHHHHHHHHCCCCEEEEEEccccCCcEEEEEEEEEEecCCCCEEEEEEECCCCeEEE
Confidence 3567888888888887555 33433 1 122222 233355668864 76654
No 8
>PF06241 DUF1012: Protein of unknown function (DUF1012); InterPro: IPR010420 This entry represents the CASTOR/POLLUX/SYM8 family of ion channels, which are found in plants. They have been implicated in modulating the nuclear membrane envelope potential [].
Probab=41.83 E-value=28 Score=26.66 Aligned_cols=29 Identities=28% Similarity=0.524 Sum_probs=21.2
Q ss_pred CccccccCcchHHHHHHHHHHcCCCeEE-EecCC
Q 039274 35 SSWPELVGVKGEVAAEIIMRENGKVVAI-IVKEG 67 (96)
Q Consensus 35 ~sWPELVG~~~~~A~~~I~~e~p~v~v~-Vl~pG 67 (96)
.+||+|.|..+.+.. ...|++.+- +.+.|
T Consensus 97 ~~~P~L~Gm~y~dvr----~~Fpdav~CGv~r~G 126 (206)
T PF06241_consen 97 KRWPQLDGMKYRDVR----RSFPDAVVCGVKRDG 126 (206)
T ss_pred ecCcccCCcCHHHHH----hcCCcceeeeeeeCC
Confidence 579999999998654 677877544 55555
No 9
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=41.06 E-value=28 Score=21.33 Aligned_cols=15 Identities=27% Similarity=0.266 Sum_probs=11.9
Q ss_pred eEEEEECCCCCEEec
Q 039274 78 RVWVWVDHHGIVKYT 92 (96)
Q Consensus 78 RV~V~vD~~g~V~~v 92 (96)
.|.|.+|.+|.|+.+
T Consensus 29 ~V~i~i~~dG~v~~~ 43 (85)
T PF13103_consen 29 TVRITIDPDGRVISV 43 (85)
T ss_dssp EEEEEE-TTSBEEEE
T ss_pred EEEEEECCCCCEEEE
Confidence 689999999999754
No 10
>cd06577 PASTA_pknB PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis. PknB is a receptor-like transmembrane protein with an extracellular signal sensor domain (containing multiple PASTA domains) and an intracellular, eukaryotic serine/threonine kinase-like domain. The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBPs) and bacterial serine/threonine kinases. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain.
Probab=40.65 E-value=28 Score=19.05 Aligned_cols=19 Identities=21% Similarity=0.335 Sum_probs=15.4
Q ss_pred cccccCcchHHHHHHHHHH
Q 039274 37 WPELVGVKGEVAAEIIMRE 55 (96)
Q Consensus 37 WPELVG~~~~~A~~~I~~e 55 (96)
-|.|+|++.++|...+...
T Consensus 2 vp~~~g~~~~~a~~~l~~~ 20 (62)
T cd06577 2 VPDVVGMTLDEAKAALEAA 20 (62)
T ss_pred CCCcCCCCHHHHHHHHHHC
Confidence 3789999999998877544
No 11
>cd06576 PASTA_Pbp2x-like_1 PASTA domain of PBP2x-like proteins, first repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by acylating the active site serine. PBPs catalyze key steps in the synthesis of the peptidoglycan, such as the interconnecting of glycan chains (polymers of N-glucosamine and N-acetylmuramic acid residues) and the cross-linking (transpeptidation) of short stem peptides, which are connected to glycan chains. Peptidoglycan is essential in cell division and protects bacteria from osmotic shock and lysis. PBP2x is one of the two monofunctional high molecular mass PBPs in Streptococcus pneumoniae and has been seen as the primary PBP target in beta-lactam-resistant strains. The PASTA domain is found at the C-termini of several PBPs and bacterial serine/threonine kinases. The name PASTA is derived from PBP and Serine/Threonine
Probab=39.16 E-value=66 Score=17.41 Aligned_cols=28 Identities=18% Similarity=0.394 Sum_probs=18.6
Q ss_pred ccccCcchHHHHHHHHHHcCCCeEEEecCC
Q 039274 38 PELVGVKGEVAAEIIMRENGKVVAIIVKEG 67 (96)
Q Consensus 38 PELVG~~~~~A~~~I~~e~p~v~v~Vl~pG 67 (96)
|.++|.+..+|.+.+... +..+....+|
T Consensus 3 p~~~g~~~~~a~~~l~~~--g~~~~~~~~g 30 (55)
T cd06576 3 PDVTGKSVEEAKKELKEA--GLQPVVIGNG 30 (55)
T ss_pred CcccCCCHHHHHHHHHHC--CCEEEEeCCC
Confidence 789999999998777544 3334433333
No 12
>cd03474 Rieske_T4moC Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent hydroxylation of toluene to form p-cresol. T4mo consists of an NADH oxidoreductase (T4moF), a diiron hydroxylase (T4moH), a catalytic effector protein (T4moD), and a Rieske ferredoxin (T4moC). T4moC contains a Rieske domain and functions as an obligate electron carrier between T4moF and T4moH. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes.
Probab=35.17 E-value=42 Score=21.62 Aligned_cols=29 Identities=21% Similarity=0.113 Sum_probs=19.4
Q ss_pred ecCCccccCCCcCCeEEEEECCCCCEEec
Q 039274 64 VKEGFEVTMDYRCDRVWVWVDHHGIVKYT 92 (96)
Q Consensus 64 l~pGs~vTmDfr~dRV~V~vD~~g~V~~v 92 (96)
|++|.+.+..+...++.|+.+.+|.+..+
T Consensus 10 l~~g~~~~~~~~~~~~~~~~~~~g~~~A~ 38 (108)
T cd03474 10 VWEGEMELVDVDGEEVLLVAPEGGEFRAF 38 (108)
T ss_pred cCCCceEEEEECCeEEEEEEccCCeEEEE
Confidence 45677666666566677777777766554
No 13
>smart00740 PASTA PASTA domain.
Probab=31.93 E-value=46 Score=18.51 Aligned_cols=20 Identities=20% Similarity=0.433 Sum_probs=16.0
Q ss_pred ccccccCcchHHHHHHHHHH
Q 039274 36 SWPELVGVKGEVAAEIIMRE 55 (96)
Q Consensus 36 sWPELVG~~~~~A~~~I~~e 55 (96)
.-|.|+|++..+|...+...
T Consensus 6 ~vp~~~g~~~~~a~~~l~~~ 25 (66)
T smart00740 6 EVPDVIGLSKEEAKKLLKAL 25 (66)
T ss_pred eCCCcCCCCHHHHHHHHHHC
Confidence 46899999999998777543
No 14
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=31.43 E-value=45 Score=20.92 Aligned_cols=29 Identities=21% Similarity=0.448 Sum_probs=17.1
Q ss_pred ecCCccccCCCcCCe---EEE-EECCCCCEEec
Q 039274 64 VKEGFEVTMDYRCDR---VWV-WVDHHGIVKYT 92 (96)
Q Consensus 64 l~pGs~vTmDfr~dR---V~V-~vD~~g~V~~v 92 (96)
+..|+.+...++.+| |.| .+|++|.|+.+
T Consensus 3 ~~~Ge~v~~~~~~~~~~Yl~l~~~~~~G~v~~L 35 (83)
T PF14326_consen 3 YRVGERVRFRVTSNRDGYLYLFYIDADGKVTLL 35 (83)
T ss_pred ccCCCEEEEEEEeCCCeEEEEEEECCCCCEEEE
Confidence 345555555555444 444 47788888764
No 15
>PF11396 DUF2874: Protein of unknown function (DUF2874); InterPro: IPR021533 This bacterial family of proteins are probable periplasmic proteins with unknown function. There are between one and four copies of this domain per sequence. ; PDB: 3DUE_A 3U1W_B 3DB7_A 4DSD_A 3ELG_A.
Probab=30.91 E-value=1.1e+02 Score=17.53 Aligned_cols=44 Identities=14% Similarity=0.078 Sum_probs=29.5
Q ss_pred HHHHHHHHHcCCCeEE---Eec----CCccccCCCcCCeEEEEECCCCCEE
Q 039274 47 VAAEIIMRENGKVVAI---IVK----EGFEVTMDYRCDRVWVWVDHHGIVK 90 (96)
Q Consensus 47 ~A~~~I~~e~p~v~v~---Vl~----pGs~vTmDfr~dRV~V~vD~~g~V~ 90 (96)
.+...|....|+..+. ... ....+-+.-+.+...|++|.+|.+.
T Consensus 11 ~v~~~i~~~yp~~~i~~v~~~~~~~~~~Y~v~l~~~~~~~~v~fd~~G~~l 61 (61)
T PF11396_consen 11 AVKNAIKKNYPGAKIKEVEKETDPGGKYYEVELKKGGNEYEVYFDANGNWL 61 (61)
T ss_dssp HHHHHHHHHSTTSEEEEEEEEEETTEEEEEEEETETTTSEEEEEETTS-EE
T ss_pred HHHHHHHHHCCCCeEEEEEEEEcCCCCEEEEEEEEeCCeEEEEEcCCCCCC
Confidence 3567888999998765 222 2223445566788999999999763
No 16
>PF01436 NHL: NHL repeat; InterPro: IPR001258 The NHL repeat, named after NCL-1, HT2A and Lin-41, is found largely in a large number of eukaryotic and prokaryotic proteins. For example, the repeat is found in a variety of enzymes of the copper type II, ascorbate-dependent monooxygenase family which catalyse the C terminus alpha-amidation of biological peptides []. In many it occurs in tandem arrays, for example in the ringfinger beta-box, coiled-coil (RBCC) eukaryotic growth regulators []. The 'Brain Tumor' protein (Brat) is one such growth regulator that contains a 6-bladed NHL-repeat beta-propeller [, ]. The NHL repeats are also found in serine/threonine protein kinase (STPK) in diverse range of pathogenic bacteria. These STPK are transmembrane receptors with a intracellular N-terminal kinase domain and extracellular C-terminal sensor domain. In the STPK, PknD, from Mycobacterium tuberculosis, the sensor domain forms a rigid, six-bladed b-propeller composed of NHL repeats with a flexible tether to the transmembrane domain.; GO: 0005515 protein binding; PDB: 3FVZ_A 3FW0_A 1RWL_A 1RWI_A 1Q7F_A.
Probab=29.63 E-value=62 Score=16.38 Aligned_cols=20 Identities=25% Similarity=0.248 Sum_probs=16.0
Q ss_pred EecCCccccCCCcCCeEEEE
Q 039274 63 IVKEGFEVTMDYRCDRVWVW 82 (96)
Q Consensus 63 Vl~pGs~vTmDfr~dRV~V~ 82 (96)
+-+.|...-.|+..+||.+|
T Consensus 9 v~~~g~i~VaD~~n~rV~vf 28 (28)
T PF01436_consen 9 VDSDGNIYVADSGNHRVQVF 28 (28)
T ss_dssp EETTSEEEEEECCCTEEEEE
T ss_pred EeCCCCEEEEECCCCEEEEC
Confidence 44778888888999998876
No 17
>PF03544 TonB_C: Gram-negative bacterial TonB protein C-terminal; InterPro: IPR006260 The sequences in this set all contain a conserved C-terminal domain which is characteristic 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 repetitive 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 span the periplasm. Iron is essential for growth in both bacteria and mammals. Controlling the amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein molecules can accomplish this. Some bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores to scavenge iron from iron-binding host proteins []. The absence of free iron molecules in the surrounding environment triggers transcription of gene clusters that encode both siderophore-synthesis ezymes, and receptors that recognise iron-bound siderophores []. An example of the latter is Escherichia coli fepA, which resides in the outer envelope and captures iron-bound enterobactin []. To complete transport of bound iron across the inner membrane, a second receptor complex is needed. The major component of this is tonB, a 27kDa protein that facilitates energy transfer from the proton motive force to outer receptors. B-12 and colicin receptors also make use of the tonB system to drive active transport at the outer membrane.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016020 membrane, 0030288 outer membrane-bounded periplasmic space; PDB: 1U07_B 1IHR_A 2GRX_C 2GSK_B 1QXX_A 1XX3_A 2K9K_A.
Probab=29.47 E-value=45 Score=19.78 Aligned_cols=15 Identities=27% Similarity=0.129 Sum_probs=12.2
Q ss_pred eEEEEECCCCCEEec
Q 039274 78 RVWVWVDHHGIVKYT 92 (96)
Q Consensus 78 RV~V~vD~~g~V~~v 92 (96)
.|.+.+|++|.|..+
T Consensus 19 ~v~~~I~~~G~v~~~ 33 (79)
T PF03544_consen 19 VVEFTIDPDGRVSDV 33 (79)
T ss_dssp EEEEEEETTTEEEEE
T ss_pred EEEEEEeCCCCEEEE
Confidence 567889999988875
No 18
>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=29.16 E-value=51 Score=19.24 Aligned_cols=16 Identities=31% Similarity=0.217 Sum_probs=12.6
Q ss_pred eEEEEECCCCCEEecC
Q 039274 78 RVWVWVDHHGIVKYTP 93 (96)
Q Consensus 78 RV~V~vD~~g~V~~vP 93 (96)
.|.+.+|.+|.|+.+.
T Consensus 13 ~v~~~i~~~G~v~~~~ 28 (74)
T TIGR01352 13 VVRFTVDADGRVTSVS 28 (74)
T ss_pred EEEEEECCCCCEEEEE
Confidence 5678899999888753
No 19
>PF09429 Wbp11: WW domain binding protein 11; InterPro: IPR019007 Synonym(s): Rsp5 or WWP domain The WW domain is a short conserved region in a number of unrelated proteins, which folds as a stable, triple stranded beta-sheet. This short domain of approximately 40 amino acids, may be repeated up to four times in some proteins [, , , ]. The name WW or WWP derives from the presence of two signature tryptophan residues that are spaced 20-23 amino acids apart and are present in most WW domains known to date, as well as that of a conserved Pro. The WW domain binds to proteins with particular proline-motifs, [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs [, ]. It is frequently associated with other domains typical for proteins in signal transduction processes. A large variety of proteins containing the WW domain are known. These include; dystrophin, a multidomain cytoskeletal protein; utrophin, a dystrophin-like protein of unknown function; vertebrate YAP protein, substrate of an unknown serine kinase; Mus musculus (Mouse) NEDD-4, involved in the embryonic development and differentiation of the central nervous system; Saccharomyces cerevisiae (Baker's yeast) RSP5, similar to NEDD-4 in its molecular organisation; Rattus norvegicus (Rat) FE65, a transcription-factor activator expressed preferentially in liver; Nicotiana tabacum (Common tobacco) DB10 protein, amongst others. This entry represents WW domain-binding protein 11, which may play a role in the regulation of pre-mRNA processing. ; GO: 0006396 RNA processing
Probab=28.48 E-value=55 Score=20.95 Aligned_cols=20 Identities=45% Similarity=0.620 Sum_probs=15.9
Q ss_pred CchhHHHHHHHHHHHHHhhc
Q 039274 1 TPTIYFRKQLRQKKEKKEKK 20 (96)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~ 20 (96)
.||=-|||+.|+|.-||+|+
T Consensus 5 NP~da~RK~~kkKElkKnK~ 24 (78)
T PF09429_consen 5 NPTDAYRKEQKKKELKKNKK 24 (78)
T ss_pred CHHHHHHHHHHHHHHHHHHH
Confidence 47888999999887777664
No 20
>cd03531 Rieske_RO_Alpha_KSH The alignment model represents the N-terminal rieske iron-sulfur domain of KshA, the oxygenase component of 3-ketosteroid 9-alpha-hydroxylase (KSH). The terminal oxygenase component of KSH is a key enzyme in the microbial steroid degradation pathway, catalyzing the 9 alpha-hydroxylation of 4-androstene-3,17-dione (AD) and 1,4-androstadiene-3,17-dione (ADD). KSH is a two-component class IA monooxygenase, with terminal oxygenase (KshA) and oxygenase reductase (KshB) components. KSH activity has been found in many actino- and proteo- bacterial genera including Rhodococcus, Nocardia, Arthrobacter, Mycobacterium, and Burkholderia.
Probab=28.16 E-value=72 Score=21.17 Aligned_cols=29 Identities=14% Similarity=0.255 Sum_probs=19.9
Q ss_pred ecCCccccCCCcCCeEEEEECCCCCEEec
Q 039274 64 VKEGFEVTMDYRCDRVWVWVDHHGIVKYT 92 (96)
Q Consensus 64 l~pGs~vTmDfr~dRV~V~vD~~g~V~~v 92 (96)
|++|.+.+.+..-..+.|+-+.+|.|..+
T Consensus 11 l~~g~~~~~~~~g~~i~l~r~~~g~~~a~ 39 (115)
T cd03531 11 FRDGKPHGVEAFGTKLVVFADSDGALNVL 39 (115)
T ss_pred CCCCCeEEEEECCeEEEEEECCCCCEEEE
Confidence 35667766666667777777777776654
No 21
>PF08482 HrpB_C: ATP-dependent helicase C-terminal; InterPro: IPR013689 This domain is found near the C terminus of bacterial ATP-dependent helicases such as HrpB.
Probab=28.09 E-value=59 Score=23.20 Aligned_cols=44 Identities=20% Similarity=0.201 Sum_probs=29.4
Q ss_pred CCCccccccCcchHHHH---------HHHHHHcCCCeEEEecCCccccCCCcCCe
Q 039274 33 SKSSWPELVGVKGEVAA---------EIIMRENGKVVAIIVKEGFEVTMDYRCDR 78 (96)
Q Consensus 33 ~k~sWPELVG~~~~~A~---------~~I~~e~p~v~v~Vl~pGs~vTmDfr~dR 78 (96)
+.+++.+|-..+..+|. ..+.+..|. ...+|-|+.+..||..+.
T Consensus 8 g~~s~~~l~~~~l~~~L~~~L~~~~~~~Ld~~aP~--~~~~PsG~~~~I~Y~~~~ 60 (133)
T PF08482_consen 8 GVTSLKDLKKLDLLEALRSLLSWEQQQWLDRLAPE--HITLPSGRRIRIDYSDDG 60 (133)
T ss_pred CCCCHHHHhcCCHHHHHHHHCCHHHHHHHHHhCCC--eEEcCCCCEEEEEECCCC
Confidence 44556666666655553 345556564 467788999999998877
No 22
>cd03469 Rieske_RO_Alpha_N Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The oxygenase component may contain alpha and beta subunits, with the beta subunit having a purely structural function. Some oxygenase components contain only an alpha subunit. The oxygenase alpha subunit has two domains, an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from the reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Reduced pyridine nucleotide is used as the i
Probab=27.91 E-value=73 Score=20.53 Aligned_cols=27 Identities=22% Similarity=0.209 Sum_probs=16.1
Q ss_pred CCccccCCCcCCeEEEEECCCCCEEec
Q 039274 66 EGFEVTMDYRCDRVWVWVDHHGIVKYT 92 (96)
Q Consensus 66 pGs~vTmDfr~dRV~V~vD~~g~V~~v 92 (96)
+|+.++..+.-..|.|+-+.+|.|..+
T Consensus 13 ~g~~~~~~~~~~~i~v~r~~~g~~~a~ 39 (118)
T cd03469 13 PGDYVTLELGGEPLVLVRDRDGEVRAF 39 (118)
T ss_pred CCCEEEEEECCccEEEEECCCCCEEEE
Confidence 555555555556677777666665543
No 23
>PRK13320 pantothenate kinase; Reviewed
Probab=27.30 E-value=63 Score=24.53 Aligned_cols=39 Identities=15% Similarity=0.082 Sum_probs=28.9
Q ss_pred ccccccCcchHHHHHHHHHHcCCCeEEEecCCccccCCC
Q 039274 36 SWPELVGVKGEVAAEIIMRENGKVVAIIVKEGFEVTMDY 74 (96)
Q Consensus 36 sWPELVG~~~~~A~~~I~~e~p~v~v~Vl~pGs~vTmDf 74 (96)
.=|+-+|.+--.+........++-.+.|+--|++.|.|+
T Consensus 91 ~~p~~lG~DR~~~~~aa~~~~~~~~~lVID~GTA~Tid~ 129 (244)
T PRK13320 91 DTPETLGADRLALCAGARYLFPGKNVLAIDAGTAITYDV 129 (244)
T ss_pred cChhhcchhHHHHHHHHHHhcCCCCEEEEEcCCceEEEE
Confidence 345678988766655555555565688999999999995
No 24
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=27.21 E-value=33 Score=20.06 Aligned_cols=20 Identities=35% Similarity=0.262 Sum_probs=12.9
Q ss_pred cCCccccCCCcCCeEEEEEC
Q 039274 65 KEGFEVTMDYRCDRVWVWVD 84 (96)
Q Consensus 65 ~pGs~vTmDfr~dRV~V~vD 84 (96)
.+|+.+..-+.+..|.++.|
T Consensus 50 ~~G~~v~~~ik~~~v~l~~~ 69 (69)
T TIGR00638 50 KPGKEVYAVIKAPWVILAVD 69 (69)
T ss_pred CCCCEEEEEEECcEEEEecC
Confidence 46666666666666666654
No 25
>cd04337 Rieske_RO_Alpha_Cao Cao (chlorophyll a oxygenase) is a rieske non-heme iron-sulfur protein located within the plastid-envelope inner and thylakoid membranes, that catalyzes the conversion of chlorophyllide a to chlorophyllide b. CAO is found not only in plants but also in chlorophytes and prochlorophytes. This domain represents the N-terminal rieske domain of the oxygenase alpha subunit. ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Cao is closely related to several other plant RO's including Tic 55, a 55 kDa protein associated with protein transport through the inner
Probab=26.18 E-value=82 Score=21.45 Aligned_cols=29 Identities=14% Similarity=0.085 Sum_probs=19.5
Q ss_pred ecCCccccCCCcCCeEEEEECCCCCEEec
Q 039274 64 VKEGFEVTMDYRCDRVWVWVDHHGIVKYT 92 (96)
Q Consensus 64 l~pGs~vTmDfr~dRV~V~vD~~g~V~~v 92 (96)
|++|++.+.+..-..+-|+-+++|.|..+
T Consensus 27 l~~g~~~~~~v~g~~l~l~r~~~g~v~A~ 55 (129)
T cd04337 27 LKMDTMVPFELFGQPWVLFRDEDGTPGCI 55 (129)
T ss_pred CCCCCeEEEEECCcEEEEEECCCCcEEEE
Confidence 45677776666667777777777766543
No 26
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=25.95 E-value=56 Score=21.06 Aligned_cols=41 Identities=12% Similarity=0.127 Sum_probs=19.7
Q ss_pred CcchHHHHHHHHHHcCCCeEEEecCCccccCCCcCCeEEEEECCCCCEEe
Q 039274 42 GVKGEVAAEIIMRENGKVVAIIVKEGFEVTMDYRCDRVWVWVDHHGIVKY 91 (96)
Q Consensus 42 G~~~~~A~~~I~~e~p~v~v~Vl~pGs~vTmDfr~dRV~V~vD~~g~V~~ 91 (96)
|-++.+.-.++..+-.+....-|.||+.+ .+.+|++|.+..
T Consensus 21 gls~~dl~~v~~~~~~~k~L~~L~pGq~l---------~f~~d~~g~L~~ 61 (85)
T PF04225_consen 21 GLSASDLYAVLEADGEAKPLTRLKPGQTL---------EFQLDEDGQLTA 61 (85)
T ss_dssp T--HHHHHHHHHHGGGT--GGG--TT-EE---------EEEE-TTS-EEE
T ss_pred CCCHHHHHHHHhccCccchHhhCCCCCEE---------EEEECCCCCEEE
Confidence 77777777777776444444467788755 555555555543
No 27
>PF06691 DUF1189: Protein of unknown function (DUF1189); InterPro: IPR009574 This family consists of several hypothetical bacterial proteins of around 260 residues in length. The function of this family is unknown.
Probab=25.13 E-value=1.4e+02 Score=22.35 Aligned_cols=44 Identities=11% Similarity=0.086 Sum_probs=33.9
Q ss_pred HHHHHHHHcCCCeEE--EecCCccccCCCcCCeEEEEECCCCCEEe
Q 039274 48 AAEIIMRENGKVVAI--IVKEGFEVTMDYRCDRVWVWVDHHGIVKY 91 (96)
Q Consensus 48 A~~~I~~e~p~v~v~--Vl~pGs~vTmDfr~dRV~V~vD~~g~V~~ 91 (96)
....+.++-|+-++. .+.-++.-+.+++.+.+.+..|++|.+..
T Consensus 58 ~~~~i~~~iP~F~I~nG~L~~~~~~~i~~~~~~~~i~~D~~~~~~~ 103 (250)
T PF06691_consen 58 DQQKIENDIPDFTIENGKLTSDQSEPIIYQTNNFIIIFDPTGKVTE 103 (250)
T ss_pred hhhHHHhhCCCeEEECCcEecCCCCceEecCCcEEEEECCCCCcch
Confidence 345778889998877 66666666678888999999999887653
No 28
>PRK13328 pantothenate kinase; Reviewed
Probab=24.93 E-value=63 Score=24.73 Aligned_cols=38 Identities=16% Similarity=0.002 Sum_probs=29.9
Q ss_pred ccccCcchHHHHHHHHHHcCCCeEEEecCCccccCCCc
Q 039274 38 PELVGVKGEVAAEIIMRENGKVVAIIVKEGFEVTMDYR 75 (96)
Q Consensus 38 PELVG~~~~~A~~~I~~e~p~v~v~Vl~pGs~vTmDfr 75 (96)
|+=+|.+--.|.....+..|+-.+.|+--|+++|.|+=
T Consensus 97 p~~LG~DR~~a~vaA~~~~~~~~~lViD~GTA~TiD~v 134 (255)
T PRK13328 97 PAQLGSDRWAGLIGARAAFPGEHLLIATFGTATTLDAL 134 (255)
T ss_pred hhhccHHHHHHHHHHHHhcCCCCEEEEEcCCceEEEEE
Confidence 67799998777665656666666889999999999953
No 29
>cd03530 Rieske_NirD_small_Bacillus Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium.
Probab=24.57 E-value=87 Score=19.68 Aligned_cols=28 Identities=7% Similarity=-0.152 Sum_probs=14.5
Q ss_pred cCCccccCCCcCCeEEEEECCCCCEEec
Q 039274 65 KEGFEVTMDYRCDRVWVWVDHHGIVKYT 92 (96)
Q Consensus 65 ~pGs~vTmDfr~dRV~V~vD~~g~V~~v 92 (96)
++|......+....+-|+-+++|.+..+
T Consensus 11 ~~~~~~~~~~~g~~i~l~r~~~g~~~A~ 38 (98)
T cd03530 11 PPRGARKVQTGGGEIAVFRTADDEVFAL 38 (98)
T ss_pred CCCCcEEEEECCEEEEEEEeCCCCEEEE
Confidence 3444444444445566666665655443
No 30
>PF00367 PTS_EIIB: phosphotransferase system, EIIB; InterPro: IPR018113 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to enzyme-I (EI) of PTS which in turn transfers it to a phosphoryl carrier protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease which consists of at least three structurally distinct domains (IIA, IIB, and IIC) [] which can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA) carries the first permease-specific phoshorylation site, a histidine, which is phosphorylated by phospho-HPr. The second domain (IIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the permease. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate in a process catalyzed by the IIC domain; this process is coupled to the transmembrane transport of the sugar. This entry covers the phosphorylation site of EIIB domains. ; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity; PDB: 3IPJ_B 3BP3_A 1O2F_B 3BP8_C 1IBA_A.
Probab=23.80 E-value=36 Score=18.73 Aligned_cols=20 Identities=15% Similarity=0.106 Sum_probs=14.9
Q ss_pred ccCCCcCCeEEEEECCCCCE
Q 039274 70 VTMDYRCDRVWVWVDHHGIV 89 (96)
Q Consensus 70 vTmDfr~dRV~V~vD~~g~V 89 (96)
...+++.-|||+.+.+...|
T Consensus 15 ~~v~~C~TRLR~~v~d~~~V 34 (35)
T PF00367_consen 15 KSVTNCATRLRFTVKDDSKV 34 (35)
T ss_dssp EEEEE-SSEEEEEESTGGGS
T ss_pred HHHhcCcceEEEEecChhhC
Confidence 45588899999999887654
No 31
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=22.71 E-value=37 Score=23.77 Aligned_cols=18 Identities=17% Similarity=0.207 Sum_probs=15.3
Q ss_pred eEEEecCCccccCCCcCC
Q 039274 60 VAIIVKEGFEVTMDYRCD 77 (96)
Q Consensus 60 ~v~Vl~pGs~vTmDfr~d 77 (96)
.+..++||.+++-||-+|
T Consensus 85 evE~~~Pg~P~~hD~epD 102 (112)
T PF08882_consen 85 EVEAPPPGYPPIHDFEPD 102 (112)
T ss_pred EEccCCCCCCceEecccC
Confidence 466889999999999876
No 32
>COG0391 Uncharacterized conserved protein [Function unknown]
Probab=22.50 E-value=79 Score=25.65 Aligned_cols=24 Identities=25% Similarity=0.184 Sum_probs=18.0
Q ss_pred hHHHHHHHHHHcCCCeEEEecCCccccC
Q 039274 45 GEVAAEIIMRENGKVVAIIVKEGFEVTM 72 (96)
Q Consensus 45 ~~~A~~~I~~e~p~v~v~Vl~pGs~vTm 72 (96)
..+|.++|+.. ..++|-|||.+|-
T Consensus 180 ~~eaveAI~~A----D~IviGPgSl~TS 203 (323)
T COG0391 180 APEAVEAIKEA----DLIVIGPGSLFTS 203 (323)
T ss_pred CHHHHHHHHhC----CEEEEcCCccHhh
Confidence 44666677655 6899999999873
No 33
>PRK13321 pantothenate kinase; Reviewed
Probab=22.19 E-value=85 Score=23.62 Aligned_cols=39 Identities=28% Similarity=0.199 Sum_probs=27.0
Q ss_pred ccccccCcchHHHHHHHHHHcCCCeEEEecCCccccCCC
Q 039274 36 SWPELVGVKGEVAAEIIMRENGKVVAIIVKEGFEVTMDY 74 (96)
Q Consensus 36 sWPELVG~~~~~A~~~I~~e~p~v~v~Vl~pGs~vTmDf 74 (96)
.=|+-+|.+--.+........++..+.|+--|++.|.|+
T Consensus 101 ~~P~~lG~DR~a~~~aa~~~~~~~~~lvid~GTA~T~d~ 139 (256)
T PRK13321 101 DNPREVGADRIVNAVAARRLYPDRNLIVVDFGTATTFDC 139 (256)
T ss_pred CChhhccHHHHHHHHHHHHHcCCCCEEEEECCCceEEEE
Confidence 346778988544544444445554578999999999995
No 34
>PF02406 MmoB_DmpM: MmoB/DmpM family ; InterPro: IPR003454 This family consists of monooxygenase components such as MmoB methane monooxygenase (1.14.13.25 from EC) regulatory protein B. When MmoB is present at low concentration it converts methane monooxygenase from an oxidase to a hydroxylase and stabilises intermediates required for the activation of dioxygen []. Also found in this family is DmpM or Phenol hydroxylase (1.14.13.7 from EC) protein component P2, this protein lacks redox co-factors and is required for optimal turnover of Phenol hydroxylase []. Phenol hydroxylase catabolises phenol and some of its methylated derivatives in the first step of phenol biodegradation, and is required for growth on phenol. The multicomponent enzyme is made up of P0, P1, P2, P3, P4 and P5 polypeptides.; GO: 0004497 monooxygenase activity, 0006725 cellular aromatic compound metabolic process; PDB: 2INN_L 2INP_L 1CKV_A 3Q3M_H 3GE3_E 1G11_A 2BF2_B 3I5J_E 3Q3O_E 3I63_E ....
Probab=22.06 E-value=1.5e+02 Score=19.51 Aligned_cols=20 Identities=20% Similarity=0.127 Sum_probs=13.6
Q ss_pred HHHHHHHcCCCeEEEecCCccc
Q 039274 49 AEIIMRENGKVVAIIVKEGFEV 70 (96)
Q Consensus 49 ~~~I~~e~p~v~v~Vl~pGs~v 70 (96)
.++|..|||+ +.|...+.++
T Consensus 18 veai~~dNP~--v~V~d~~a~v 37 (87)
T PF02406_consen 18 VEAIEEDNPG--VTVEDRPAYV 37 (87)
T ss_dssp HHHHHHHSST--EEEEEESSEE
T ss_pred HHHHHhhCCC--eEEEecCCEE
Confidence 5789999999 4454444444
No 35
>KOG0912 consensus Thiol-disulfide isomerase and thioredoxin [Posttranslational modification, protein turnover, chaperones; Energy production and conversion]
Probab=20.96 E-value=1.1e+02 Score=25.45 Aligned_cols=18 Identities=22% Similarity=0.427 Sum_probs=13.0
Q ss_pred EEEecCCccccCCCcCCe
Q 039274 61 AIIVKEGFEVTMDYRCDR 78 (96)
Q Consensus 61 v~Vl~pGs~vTmDfr~dR 78 (96)
..|.+-|.++|..||..|
T Consensus 76 lKvfrnG~~~~rEYRg~R 93 (375)
T KOG0912|consen 76 LKVFRNGEMMKREYRGQR 93 (375)
T ss_pred eeeeeccchhhhhhccch
Confidence 346667888888888776
No 36
>PHA02087 hypothetical protein
Probab=20.50 E-value=1.1e+02 Score=20.02 Aligned_cols=22 Identities=18% Similarity=0.339 Sum_probs=16.1
Q ss_pred CCcCCeEEE--EECCCCCEEecCc
Q 039274 73 DYRCDRVWV--WVDHHGIVKYTPR 94 (96)
Q Consensus 73 Dfr~dRV~V--~vD~~g~V~~vP~ 94 (96)
.|++|.+.= .||++|.+..+|-
T Consensus 38 ~~d~nk~v~y~lvdsdg~~ielpe 61 (83)
T PHA02087 38 KFDPNKLVQYMLVDSDGVKIELPE 61 (83)
T ss_pred cCCCccceeEEEEcCCCcEEECCc
Confidence 466666544 4899999998873
No 37
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=20.25 E-value=76 Score=21.10 Aligned_cols=17 Identities=24% Similarity=0.378 Sum_probs=12.1
Q ss_pred CcCCeEEEEECCCCCEEec
Q 039274 74 YRCDRVWVWVDHHGIVKYT 92 (96)
Q Consensus 74 fr~dRV~V~vD~~g~V~~v 92 (96)
|.-| .+|+|++|+|+.+
T Consensus 48 ~pLD--i~fld~~g~Vv~i 64 (108)
T PF02643_consen 48 FPLD--IAFLDSDGRVVKI 64 (108)
T ss_dssp S-EE--EEEE-TTSBEEEE
T ss_pred eeEE--EEEECCCCeEEEE
Confidence 4455 7899999999875
Done!