Query 035225
Match_columns 70
No_of_seqs 102 out of 319
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 10:13:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035225.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035225hhsearch_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 1.8E-34 3.9E-39 166.0 5.3 63 8-70 1-63 (63)
2 PF11720 Inhibitor_I78: Peptid 99.8 2.6E-19 5.6E-24 101.6 2.2 57 6-66 1-57 (60)
3 PF03793 PASTA: PASTA domain; 77.6 2.1 4.6E-05 23.0 1.9 18 12-29 4-21 (63)
4 cd06573 PASTA PASTA domain. Th 68.6 12 0.00026 18.5 3.4 17 12-28 3-19 (53)
5 PF06241 DUF1012: Protein of u 64.5 7 0.00015 27.1 2.5 29 9-41 97-126 (206)
6 cd06577 PASTA_pknB PASTA domai 61.5 7.6 0.00016 19.6 1.8 18 12-29 3-20 (62)
7 PF03413 PepSY: Peptidase prop 53.3 23 0.0005 18.3 2.9 47 18-64 3-61 (64)
8 cd03477 Rieske_YhfW_C YhfW fam 49.5 19 0.00042 21.1 2.4 29 38-66 8-36 (91)
9 cd06575 PASTA_Pbp2x-like_2 PAS 49.5 16 0.00035 18.0 1.8 18 12-29 3-20 (54)
10 smart00740 PASTA PASTA domain. 49.3 16 0.00034 18.8 1.8 21 9-29 5-25 (66)
11 KOG0912 Thiol-disulfide isomer 47.0 22 0.00049 26.6 2.8 16 37-52 78-93 (375)
12 PF13103 TonB_2: TonB C termin 46.8 17 0.00037 20.3 1.8 17 50-66 27-43 (85)
13 cd06576 PASTA_Pbp2x-like_1 PAS 46.2 19 0.0004 18.0 1.8 18 12-29 3-20 (55)
14 TIGR00638 Mop molybdenum-pteri 44.0 14 0.0003 19.8 1.1 21 38-58 49-69 (69)
15 COG0391 Uncharacterized conser 43.7 22 0.00048 26.2 2.4 25 18-46 179-203 (323)
16 cd03474 Rieske_T4moC Toluene-4 41.0 29 0.00064 20.4 2.3 29 38-66 10-38 (108)
17 PF06691 DUF1189: Protein of u 39.9 53 0.0012 22.4 3.7 43 23-65 59-103 (250)
18 PF08482 HrpB_C: ATP-dependent 39.8 32 0.0007 22.2 2.4 47 4-52 5-60 (133)
19 PF04225 OapA: Opacity-associa 39.3 25 0.00053 20.7 1.7 32 16-47 21-52 (85)
20 PF03544 TonB_C: Gram-negative 36.9 24 0.00053 19.1 1.4 15 52-66 19-33 (79)
21 PF00367 PTS_EIIB: phosphotran 36.6 14 0.00031 18.4 0.3 20 44-63 15-34 (35)
22 TIGR01352 tonB_Cterm TonB fami 35.8 36 0.00079 18.2 2.0 15 52-66 13-27 (74)
23 KOG2819 Uncharacterized conser 35.0 85 0.0018 23.8 4.2 54 6-59 12-71 (413)
24 PRK13320 pantothenate kinase; 34.9 42 0.0009 23.2 2.5 39 11-49 92-130 (244)
25 PF13994 PgaD: PgaD-like prote 34.0 32 0.00069 21.8 1.7 17 49-65 122-138 (138)
26 PRK13328 pantothenate kinase; 33.9 39 0.00085 23.5 2.3 38 12-49 97-134 (255)
27 PF05380 Peptidase_A17: Pao re 33.1 41 0.00089 21.5 2.2 59 2-61 32-90 (159)
28 TIGR01819 F420_cofD LPPG:FO 2- 32.9 41 0.0009 24.5 2.3 25 18-46 172-196 (297)
29 cd04337 Rieske_RO_Alpha_Cao Ca 32.1 54 0.0012 20.3 2.5 29 38-66 27-55 (129)
30 cd03531 Rieske_RO_Alpha_KSH Th 32.1 53 0.0012 19.8 2.5 29 38-66 11-39 (115)
31 cd03469 Rieske_RO_Alpha_N Ries 31.7 55 0.0012 19.3 2.4 26 40-65 13-38 (118)
32 PRK11548 outer membrane biogen 31.6 49 0.0011 20.2 2.2 17 50-66 88-104 (113)
33 PRK14584 hmsS hemin storage sy 30.5 51 0.0011 21.9 2.3 18 49-66 120-137 (153)
34 PF11396 DUF2874: Protein of u 30.4 89 0.0019 16.3 3.2 43 22-64 12-61 (61)
35 PF04355 SmpA_OmlA: SmpA / Oml 30.0 50 0.0011 18.1 1.9 19 48-66 52-70 (71)
36 PRK13321 pantothenate kinase; 29.2 56 0.0012 22.4 2.4 39 11-49 102-140 (256)
37 PRK03760 hypothetical protein; 28.7 38 0.00081 21.1 1.4 13 54-66 63-75 (117)
38 PF14326 DUF4384: Domain of un 28.6 49 0.0011 18.8 1.8 29 38-66 3-35 (83)
39 cd03530 Rieske_NirD_small_Baci 28.4 64 0.0014 18.5 2.3 27 39-65 11-37 (98)
40 COG2815 Uncharacterized protei 27.6 1.8E+02 0.004 21.0 4.9 21 8-28 92-112 (303)
41 cd07186 CofD_like LPPG:FO 2-ph 27.1 60 0.0013 23.7 2.4 26 17-46 172-197 (303)
42 PHA02087 hypothetical protein 26.8 73 0.0016 18.8 2.3 22 47-68 38-61 (83)
43 PF08772 NOB1_Zn_bind: Nin one 26.6 35 0.00076 19.9 0.9 20 44-63 22-48 (73)
44 PF01933 UPF0052: Uncharacteri 26.4 74 0.0016 22.9 2.7 25 18-46 173-197 (300)
45 PF02643 DUF192: Uncharacteriz 26.2 41 0.0009 20.3 1.2 13 54-66 52-64 (108)
46 cd00340 GSH_Peroxidase Glutath 26.1 67 0.0014 19.9 2.2 16 51-66 123-138 (152)
47 PRK13606 LPPG:FO 2-phospho-L-l 25.8 66 0.0014 23.5 2.4 25 18-46 175-199 (303)
48 TIGR00671 baf pantothenate kin 25.1 69 0.0015 22.1 2.3 38 11-49 95-132 (243)
49 COG1430 Uncharacterized conser 25.0 49 0.0011 21.1 1.4 13 54-66 66-78 (126)
50 PRK13324 pantothenate kinase; 24.9 73 0.0016 22.4 2.4 38 12-49 103-140 (258)
51 PF06633 DUF1155: Protein of u 24.5 22 0.00049 18.5 -0.2 14 39-52 20-35 (42)
52 PF01436 NHL: NHL repeat; Int 24.2 73 0.0016 14.5 1.6 20 37-56 9-28 (28)
53 COG1264 PtsG Phosphotransferas 23.9 53 0.0011 19.4 1.3 21 43-63 17-37 (88)
54 PRK11251 DNA-binding transcrip 23.9 82 0.0018 19.6 2.3 17 50-66 77-93 (109)
55 PF13028 DUF3889: Protein of u 23.8 1.7E+02 0.0038 17.9 3.7 42 20-61 28-71 (97)
56 cd00212 PTS_IIB_glc PTS_IIB, P 23.7 66 0.0014 18.3 1.7 20 44-63 18-37 (78)
57 PF08882 Acetone_carb_G: Aceto 23.4 34 0.00073 21.7 0.4 17 35-51 86-102 (112)
58 PF08402 TOBE_2: TOBE domain; 22.6 33 0.00071 18.1 0.2 18 39-56 58-75 (75)
59 PF12357 PLD_C: Phospholipase 22.3 76 0.0016 18.6 1.8 13 55-67 45-57 (74)
60 PF14339 DUF4394: Domain of un 21.9 1E+02 0.0022 21.8 2.6 22 38-59 71-94 (236)
61 TIGR01826 CofD_related conserv 21.8 86 0.0019 22.9 2.3 25 17-45 161-185 (310)
62 PF08765 Mor: Mor transcriptio 21.4 34 0.00074 20.6 0.2 20 9-28 1-20 (108)
63 cd07044 CofD_YvcK Family of Co 21.0 91 0.002 22.6 2.3 24 18-45 164-187 (309)
64 PF11625 DUF3253: Protein of u 21.0 1.4E+02 0.0031 17.8 2.8 42 2-47 23-71 (83)
65 PF03309 Pan_kinase: Type III 20.7 59 0.0013 21.5 1.2 37 12-49 100-136 (206)
66 cd03480 Rieske_RO_Alpha_PaO Ri 20.4 94 0.002 19.5 2.1 27 39-65 28-55 (138)
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=100.00 E-value=1.8e-34 Score=165.99 Aligned_cols=63 Identities=54% Similarity=0.887 Sum_probs=59.4
Q ss_pred CCCcccccccchHHHHHHHHhhCCCCceEEecCCCcccCCccCCeEEEEeCCCCcEEcCCccC
Q 035225 8 KTSWPELVGEIGAVAAATIKLQNPIVNPIILMLGTPVTREFRCDRVWVWVDAIGRVSKPPVVG 70 (70)
Q Consensus 8 k~~WpelVG~~~~~A~~~I~~~~p~~~v~vl~pg~~vT~df~~~RV~v~vD~~g~V~~vP~iG 70 (70)
|+|||||||+++++|+++|++|||++++.++++|+++|+|||||||+||+|++|+|+++|+||
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 799999999999999999999999999999999999999999999999999999999999998
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=99.76 E-value=2.6e-19 Score=101.63 Aligned_cols=57 Identities=26% Similarity=0.311 Sum_probs=47.2
Q ss_pred CCCCCcccccccchHHHHHHHHhhCCCCceEEecCCCcccCCccCCeEEEEeCCCCcEEcC
Q 035225 6 SGKTSWPELVGEIGAVAAATIKLQNPIVNPIILMLGTPVTREFRCDRVWVWVDAIGRVSKP 66 (70)
Q Consensus 6 ~~k~~WpelVG~~~~~A~~~I~~~~p~~~v~vl~pg~~vT~df~~~RV~v~vD~~g~V~~v 66 (70)
=+.+....|||++++++...-. ...+|||+||+++|||||+|||||++|++|+|+++
T Consensus 1 C~A~~~q~lvGq~~~~~~~~~~----~~~~Rvi~Pg~~vTmDyr~dRLnv~~D~~g~I~~v 57 (60)
T PF11720_consen 1 CGAAAAQSLVGQPASAAEREEL----AETVRVIRPGDAVTMDYRPDRLNVEVDDDGVITRV 57 (60)
T ss_pred CCHHHHHHhhCCCccccccccc----ccceEEeCCCCcCcccCCCCcEEEEECCCCcEEEE
Confidence 0566778999999987644322 44689999999999999999999999999999875
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=77.58 E-value=2.1 Score=23.01 Aligned_cols=18 Identities=28% Similarity=0.383 Sum_probs=15.1
Q ss_pred ccccccchHHHHHHHHhh
Q 035225 12 PELVGEIGAVAAATIKLQ 29 (70)
Q Consensus 12 pelVG~~~~~A~~~I~~~ 29 (70)
|+|+|++..+|+..++..
T Consensus 4 Pd~~g~~~~~a~~~l~~~ 21 (63)
T PF03793_consen 4 PDLVGMTYDEAKSILEAA 21 (63)
T ss_dssp -TTTTSBHHHHHHHHHHT
T ss_pred CCcCCCcHHHHHHHHHHC
Confidence 899999999999877774
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=68.60 E-value=12 Score=18.52 Aligned_cols=17 Identities=24% Similarity=0.216 Sum_probs=14.8
Q ss_pred ccccccchHHHHHHHHh
Q 035225 12 PELVGEIGAVAAATIKL 28 (70)
Q Consensus 12 pelVG~~~~~A~~~I~~ 28 (70)
|.++|++..+|...++.
T Consensus 3 p~~~g~~~~~a~~~l~~ 19 (53)
T cd06573 3 PDLVGISKKDLEEQLYD 19 (53)
T ss_pred CcccCCcHHHHHHHHHc
Confidence 78999999999888775
No 5
>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=64.51 E-value=7 Score=27.06 Aligned_cols=29 Identities=21% Similarity=0.242 Sum_probs=21.1
Q ss_pred CCcccccccchHHHHHHHHhhCCCCceE-EecCC
Q 035225 9 TSWPELVGEIGAVAAATIKLQNPIVNPI-ILMLG 41 (70)
Q Consensus 9 ~~WpelVG~~~~~A~~~I~~~~p~~~v~-vl~pg 41 (70)
.+||+|-|..+.+ +....|++-+- +++.|
T Consensus 97 ~~~P~L~Gm~y~d----vr~~Fpdav~CGv~r~G 126 (206)
T PF06241_consen 97 KRWPQLDGMKYRD----VRRSFPDAVVCGVKRDG 126 (206)
T ss_pred ecCcccCCcCHHH----HHhcCCcceeeeeeeCC
Confidence 4799999999986 66677777543 54444
No 6
>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=61.55 E-value=7.6 Score=19.64 Aligned_cols=18 Identities=28% Similarity=0.381 Sum_probs=15.2
Q ss_pred ccccccchHHHHHHHHhh
Q 035225 12 PELVGEIGAVAAATIKLQ 29 (70)
Q Consensus 12 pelVG~~~~~A~~~I~~~ 29 (70)
|.|+|++..+|...+...
T Consensus 3 p~~~g~~~~~a~~~l~~~ 20 (62)
T cd06577 3 PDVVGMTLDEAKAALEAA 20 (62)
T ss_pred CCcCCCCHHHHHHHHHHC
Confidence 789999999998877654
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=53.31 E-value=23 Score=18.34 Aligned_cols=47 Identities=21% Similarity=0.005 Sum_probs=25.1
Q ss_pred chHHHHHHHHhhCCCCceE-EecCC-C-----cccCCc----cCCeEEEEeCC-CCcEE
Q 035225 18 IGAVAAATIKLQNPIVNPI-ILMLG-T-----PVTREF----RCDRVWVWVDA-IGRVS 64 (70)
Q Consensus 18 ~~~~A~~~I~~~~p~~~v~-vl~pg-~-----~vT~df----~~~RV~v~vD~-~g~V~ 64 (70)
+.++|..+.++..|+.... .+.+. . -+.... ......+++|+ +|.|.
T Consensus 3 s~~~A~~~A~~~~~~~~~~~~~~~~~~~~~~Y~v~~~~~~~~~~~~~~v~VDa~tG~Il 61 (64)
T PF03413_consen 3 SEEQAVEIALKQYPGKVISVELEEDENGRLVYEVEVVSDDDPDGGEYEVYVDAYTGEIL 61 (64)
T ss_dssp -HHHHHHHHHCCCCCEEEEEEEECC-TCEEEEEEEEEBTTSTTTEEEEEEEETTT--EE
T ss_pred CHHHHHHHHHHHCCCCEEEEEEccccCCcEEEEEEEEEEecCCCCEEEEEEECCCCeEE
Confidence 3568888888888887655 44443 1 122222 22335556887 46664
No 8
>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=49.50 E-value=19 Score=21.12 Aligned_cols=29 Identities=21% Similarity=0.161 Sum_probs=21.0
Q ss_pred ecCCCcccCCccCCeEEEEeCCCCcEEcC
Q 035225 38 LMLGTPVTREFRCDRVWVWVDAIGRVSKP 66 (70)
Q Consensus 38 l~pg~~vT~df~~~RV~v~vD~~g~V~~v 66 (70)
|++|+..+..+....|-|+-+.+|.+..+
T Consensus 8 l~~g~~~~~~~~g~~v~v~r~~~g~~~A~ 36 (91)
T cd03477 8 LAPGEGGVVNIGGKRLAVYRDEDGVLHTV 36 (91)
T ss_pred cCCCCeEEEEECCEEEEEEECCCCCEEEE
Confidence 47778777777777777777777766543
No 9
>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=49.47 E-value=16 Score=18.01 Aligned_cols=18 Identities=28% Similarity=0.300 Sum_probs=14.9
Q ss_pred ccccccchHHHHHHHHhh
Q 035225 12 PELVGEIGAVAAATIKLQ 29 (70)
Q Consensus 12 pelVG~~~~~A~~~I~~~ 29 (70)
|+++|++.++|...+...
T Consensus 3 p~~~g~~~~~a~~~l~~~ 20 (54)
T cd06575 3 PDLTGWSKRDALKLLELL 20 (54)
T ss_pred CCcCCCCHHHHHHHHHHC
Confidence 789999999998877544
No 10
>smart00740 PASTA PASTA domain.
Probab=49.33 E-value=16 Score=18.75 Aligned_cols=21 Identities=19% Similarity=0.245 Sum_probs=16.6
Q ss_pred CCcccccccchHHHHHHHHhh
Q 035225 9 TSWPELVGEIGAVAAATIKLQ 29 (70)
Q Consensus 9 ~~WpelVG~~~~~A~~~I~~~ 29 (70)
..=|+|+|++..+|...+...
T Consensus 5 ~~vp~~~g~~~~~a~~~l~~~ 25 (66)
T smart00740 5 VEVPDVIGLSKEEAKKLLKAL 25 (66)
T ss_pred eeCCCcCCCCHHHHHHHHHHC
Confidence 345899999999998877643
No 11
>KOG0912 consensus Thiol-disulfide isomerase and thioredoxin [Posttranslational modification, protein turnover, chaperones; Energy production and conversion]
Probab=47.03 E-value=22 Score=26.59 Aligned_cols=16 Identities=31% Similarity=0.582 Sum_probs=11.8
Q ss_pred EecCCCcccCCccCCe
Q 035225 37 ILMLGTPVTREFRCDR 52 (70)
Q Consensus 37 vl~pg~~vT~df~~~R 52 (70)
+.+-|.++|.+||..|
T Consensus 78 vfrnG~~~~rEYRg~R 93 (375)
T KOG0912|consen 78 VFRNGEMMKREYRGQR 93 (375)
T ss_pred eeeccchhhhhhccch
Confidence 5567777888888776
No 12
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=46.75 E-value=17 Score=20.34 Aligned_cols=17 Identities=29% Similarity=0.274 Sum_probs=12.0
Q ss_pred CCeEEEEeCCCCcEEcC
Q 035225 50 CDRVWVWVDAIGRVSKP 66 (70)
Q Consensus 50 ~~RV~v~vD~~g~V~~v 66 (70)
.-.|.|.+|.+|.|..+
T Consensus 27 ~~~V~i~i~~dG~v~~~ 43 (85)
T PF13103_consen 27 SVTVRITIDPDGRVISV 43 (85)
T ss_dssp -EEEEEEE-TTSBEEEE
T ss_pred EEEEEEEECCCCCEEEE
Confidence 34688899999999653
No 13
>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=46.24 E-value=19 Score=18.00 Aligned_cols=18 Identities=22% Similarity=0.324 Sum_probs=15.0
Q ss_pred ccccccchHHHHHHHHhh
Q 035225 12 PELVGEIGAVAAATIKLQ 29 (70)
Q Consensus 12 pelVG~~~~~A~~~I~~~ 29 (70)
|.++|++..+|...+...
T Consensus 3 p~~~g~~~~~a~~~l~~~ 20 (55)
T cd06576 3 PDVTGKSVEEAKKELKEA 20 (55)
T ss_pred CcccCCCHHHHHHHHHHC
Confidence 789999999998877654
No 14
>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=44.01 E-value=14 Score=19.83 Aligned_cols=21 Identities=29% Similarity=0.245 Sum_probs=14.7
Q ss_pred ecCCCcccCCccCCeEEEEeC
Q 035225 38 LMLGTPVTREFRCDRVWVWVD 58 (70)
Q Consensus 38 l~pg~~vT~df~~~RV~v~vD 58 (70)
|.+|+.+..-|.+..+.++.|
T Consensus 49 l~~G~~v~~~ik~~~v~l~~~ 69 (69)
T TIGR00638 49 LKPGKEVYAVIKAPWVILAVD 69 (69)
T ss_pred CCCCCEEEEEEECcEEEEecC
Confidence 457777777777777777654
No 15
>COG0391 Uncharacterized conserved protein [Function unknown]
Probab=43.74 E-value=22 Score=26.15 Aligned_cols=25 Identities=24% Similarity=0.236 Sum_probs=19.2
Q ss_pred chHHHHHHHHhhCCCCceEEecCCCcccC
Q 035225 18 IGAVAAATIKLQNPIVNPIILMLGTPVTR 46 (70)
Q Consensus 18 ~~~~A~~~I~~~~p~~~v~vl~pg~~vT~ 46 (70)
...+|.++|++. ..++|.||+.+|-
T Consensus 179 a~~eaveAI~~A----D~IviGPgSl~TS 203 (323)
T COG0391 179 AAPEAVEAIKEA----DLIVIGPGSLFTS 203 (323)
T ss_pred CCHHHHHHHHhC----CEEEEcCCccHhh
Confidence 445777778765 6889999999873
No 16
>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=40.99 E-value=29 Score=20.40 Aligned_cols=29 Identities=10% Similarity=0.003 Sum_probs=19.5
Q ss_pred ecCCCcccCCccCCeEEEEeCCCCcEEcC
Q 035225 38 LMLGTPVTREFRCDRVWVWVDAIGRVSKP 66 (70)
Q Consensus 38 l~pg~~vT~df~~~RV~v~vD~~g~V~~v 66 (70)
|++|.+.+..+...++-|+.+.+|.+..+
T Consensus 10 l~~g~~~~~~~~~~~~~~~~~~~g~~~A~ 38 (108)
T cd03474 10 VWEGEMELVDVDGEEVLLVAPEGGEFRAF 38 (108)
T ss_pred cCCCceEEEEECCeEEEEEEccCCeEEEE
Confidence 45677766666666677777777766543
No 17
>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=39.87 E-value=53 Score=22.41 Aligned_cols=43 Identities=14% Similarity=0.157 Sum_probs=34.2
Q ss_pred HHHHHhhCCCCceE--EecCCCcccCCccCCeEEEEeCCCCcEEc
Q 035225 23 AATIKLQNPIVNPI--ILMLGTPVTREFRCDRVWVWVDAIGRVSK 65 (70)
Q Consensus 23 ~~~I~~~~p~~~v~--vl~pg~~vT~df~~~RV~v~vD~~g~V~~ 65 (70)
...+.++-|+-+++ .+.-++..+.+|+.+.+.+..|.+|.+..
T Consensus 59 ~~~i~~~iP~F~I~nG~L~~~~~~~i~~~~~~~~i~~D~~~~~~~ 103 (250)
T PF06691_consen 59 QQKIENDIPDFTIENGKLTSDQSEPIIYQTNNFIIIFDPTGKVTE 103 (250)
T ss_pred hhHHHhhCCCeEEECCcEecCCCCceEecCCcEEEEECCCCCcch
Confidence 45788889998877 66666667778899999999999988653
No 18
>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=39.78 E-value=32 Score=22.23 Aligned_cols=47 Identities=23% Similarity=0.154 Sum_probs=32.6
Q ss_pred CCCCCCCcccccccchHHHH---------HHHHhhCCCCceEEecCCCcccCCccCCe
Q 035225 4 FCSGKTSWPELVGEIGAVAA---------ATIKLQNPIVNPIILMLGTPVTREFRCDR 52 (70)
Q Consensus 4 ~c~~k~~WpelVG~~~~~A~---------~~I~~~~p~~~v~vl~pg~~vT~df~~~R 52 (70)
.|.|.+++.+|-..+..+|. ..+.+..|. ...++-|+.+..||..+.
T Consensus 5 ~l~g~~s~~~l~~~~l~~~L~~~L~~~~~~~Ld~~aP~--~~~~PsG~~~~I~Y~~~~ 60 (133)
T PF08482_consen 5 YLSGVTSLKDLKKLDLLEALRSLLSWEQQQWLDRLAPE--HITLPSGRRIRIDYSDDG 60 (133)
T ss_pred HHcCCCCHHHHhcCCHHHHHHHHCCHHHHHHHHHhCCC--eEEcCCCCEEEEEECCCC
Confidence 35567777788777777764 234455444 246788999999998887
No 19
>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=39.29 E-value=25 Score=20.66 Aligned_cols=32 Identities=13% Similarity=0.021 Sum_probs=14.5
Q ss_pred ccchHHHHHHHHhhCCCCceEEecCCCcccCC
Q 035225 16 GEIGAVAAATIKLQNPIVNPIILMLGTPVTRE 47 (70)
Q Consensus 16 G~~~~~A~~~I~~~~p~~~v~vl~pg~~vT~d 47 (70)
|-++.+-.+.+..+-......-|+||+.+...
T Consensus 21 gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~ 52 (85)
T PF04225_consen 21 GLSASDLYAVLEADGEAKPLTRLKPGQTLEFQ 52 (85)
T ss_dssp T--HHHHHHHHHHGGGT--GGG--TT-EEEEE
T ss_pred CCCHHHHHHHHhccCccchHhhCCCCCEEEEE
Confidence 56666666666666444444567888765433
No 20
>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=36.89 E-value=24 Score=19.13 Aligned_cols=15 Identities=40% Similarity=0.304 Sum_probs=11.7
Q ss_pred eEEEEeCCCCcEEcC
Q 035225 52 RVWVWVDAIGRVSKP 66 (70)
Q Consensus 52 RV~v~vD~~g~V~~v 66 (70)
.|.+.+|.+|.|..+
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 467789999988764
No 21
>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=36.65 E-value=14 Score=18.43 Aligned_cols=20 Identities=15% Similarity=0.014 Sum_probs=14.6
Q ss_pred ccCCccCCeEEEEeCCCCcE
Q 035225 44 VTREFRCDRVWVWVDAIGRV 63 (70)
Q Consensus 44 vT~df~~~RV~v~vD~~g~V 63 (70)
...+.+.-|||+.+.+...|
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 45678889999999876543
No 22
>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=35.77 E-value=36 Score=18.16 Aligned_cols=15 Identities=47% Similarity=0.393 Sum_probs=11.7
Q ss_pred eEEEEeCCCCcEEcC
Q 035225 52 RVWVWVDAIGRVSKP 66 (70)
Q Consensus 52 RV~v~vD~~g~V~~v 66 (70)
.|.+.+|.+|.|+.+
T Consensus 13 ~v~~~i~~~G~v~~~ 27 (74)
T TIGR01352 13 VVRFTVDADGRVTSV 27 (74)
T ss_pred EEEEEECCCCCEEEE
Confidence 467788999988765
No 23
>KOG2819 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.98 E-value=85 Score=23.84 Aligned_cols=54 Identities=22% Similarity=0.327 Sum_probs=35.7
Q ss_pred CCCCCcccccccchHHHHHHHHhhCCCCceE-Ee-cCCCcc----cCCccCCeEEEEeCC
Q 035225 6 SGKTSWPELVGEIGAVAAATIKLQNPIVNPI-IL-MLGTPV----TREFRCDRVWVWVDA 59 (70)
Q Consensus 6 ~~k~~WpelVG~~~~~A~~~I~~~~p~~~v~-vl-~pg~~v----T~df~~~RV~v~vD~ 59 (70)
+|-+.|+=.+|.+..+|.++|++.-.-.+.+ |+ ..-++. ...+-.+=++++.|.
T Consensus 12 lg~~~~eF~lGMpi~qaiAiiqqh~riik~VqvlYsd~~Pl~~DiIinl~qdGirL~FD~ 71 (413)
T KOG2819|consen 12 LGSSQWEFVLGMPIAQAIAIIQQHPRIIKNVQVLYSDQDPLSHDIIINLPQDGIRLMFDP 71 (413)
T ss_pred cCCccceeEecChHHHHHHHHHhCccceeeEEEEEecCCCcceeEEEecCCCceEEEech
Confidence 3678899999999999999998876555544 44 223333 333445555555554
No 24
>PRK13320 pantothenate kinase; Reviewed
Probab=34.89 E-value=42 Score=23.22 Aligned_cols=39 Identities=23% Similarity=0.211 Sum_probs=29.0
Q ss_pred cccccccchHHHHHHHHhhCCCCceEEecCCCcccCCcc
Q 035225 11 WPELVGEIGAVAAATIKLQNPIVNPIILMLGTPVTREFR 49 (70)
Q Consensus 11 WpelVG~~~~~A~~~I~~~~p~~~v~vl~pg~~vT~df~ 49 (70)
=|+-+|.+--.+.....+..++....|+--|++.|.|+=
T Consensus 92 ~p~~lG~DR~~~~~aa~~~~~~~~~lVID~GTA~Tid~v 130 (244)
T PRK13320 92 TPETLGADRLALCAGARYLFPGKNVLAIDAGTAITYDVL 130 (244)
T ss_pred ChhhcchhHHHHHHHHHHhcCCCCEEEEEcCCceEEEEE
Confidence 357788887666555555556656789999999999963
No 25
>PF13994 PgaD: PgaD-like protein
Probab=34.04 E-value=32 Score=21.77 Aligned_cols=17 Identities=24% Similarity=0.292 Sum_probs=13.7
Q ss_pred cCCeEEEEeCCCCcEEc
Q 035225 49 RCDRVWVWVDAIGRVSK 65 (70)
Q Consensus 49 ~~~RV~v~vD~~g~V~~ 65 (70)
++..+.|+.|++|.|+.
T Consensus 122 ~~k~~~V~~d~~G~I~~ 138 (138)
T PF13994_consen 122 QAKVLTVHHDDHGRIIH 138 (138)
T ss_pred hCCeEEEEeCCCCCcCc
Confidence 46688899999998863
No 26
>PRK13328 pantothenate kinase; Reviewed
Probab=33.90 E-value=39 Score=23.55 Aligned_cols=38 Identities=18% Similarity=0.143 Sum_probs=30.2
Q ss_pred ccccccchHHHHHHHHhhCCCCceEEecCCCcccCCcc
Q 035225 12 PELVGEIGAVAAATIKLQNPIVNPIILMLGTPVTREFR 49 (70)
Q Consensus 12 pelVG~~~~~A~~~I~~~~p~~~v~vl~pg~~vT~df~ 49 (70)
|+=+|.+--.|.....+..|+....|+--|++.|.|+=
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 67789888777666666666766789999999999964
No 27
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=33.15 E-value=41 Score=21.50 Aligned_cols=59 Identities=14% Similarity=0.142 Sum_probs=37.5
Q ss_pred CCCCCCCCCcccccccchHHHHHHHHhhCCCCceEEecCCCcccCCccCCeEEEEeCCCC
Q 035225 2 ATFCSGKTSWPELVGEIGAVAAATIKLQNPIVNPIILMLGTPVTREFRCDRVWVWVDAIG 61 (70)
Q Consensus 2 ~~~c~~k~~WpelVG~~~~~A~~~I~~~~p~~~v~vl~pg~~vT~df~~~RV~v~vD~~g 61 (70)
+..|..+..|-+.+.......-..+.++.....-.-+|- .....+++.-.+.+|.|++.
T Consensus 32 q~lw~~~l~WD~~lp~el~~~w~~~~~~l~~~~~i~iPR-~i~~~~~~~~~L~~F~DAS~ 90 (159)
T PF05380_consen 32 QKLWQSKLDWDDPLPDELRKEWKKWLKELESLSPIRIPR-CIPISDYRSVELHVFCDASE 90 (159)
T ss_pred HhhhccccchhhhhhHHHHHHHHHHHHHHhhcccccCCc-ccccccccceeeeEeecccc
Confidence 445666788998888877777666666665543222222 22224566678889999873
No 28
>TIGR01819 F420_cofD LPPG:FO 2-phospho-L-lactate transferase. This model represents LPPG:Fo 2-phospho-L-lactate transferase, which catalyses the fourth step in the biosynthesis of coenzyme F420, a flavin derivative found in methanogens, the Mycobacteria, and several other lineages. This enzyme is characterized so far in Methanococcus jannaschii but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. The clade represented by this model is one of two major divisions of proteins in pfam model pfam01933.
Probab=32.86 E-value=41 Score=24.48 Aligned_cols=25 Identities=20% Similarity=0.373 Sum_probs=18.6
Q ss_pred chHHHHHHHHhhCCCCceEEecCCCcccC
Q 035225 18 IGAVAAATIKLQNPIVNPIILMLGTPVTR 46 (70)
Q Consensus 18 ~~~~A~~~I~~~~p~~~v~vl~pg~~vT~ 46 (70)
+..+|.++|++. .+++|.||+++|-
T Consensus 172 a~peal~AI~~A----D~IIlGPgsp~TS 196 (297)
T TIGR01819 172 IAPKVLEAIRKE----DNILIGPSNPITS 196 (297)
T ss_pred CCHHHHHHHHhC----CEEEECCCccHHH
Confidence 355667777765 4889999998874
No 29
>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=32.06 E-value=54 Score=20.34 Aligned_cols=29 Identities=21% Similarity=0.060 Sum_probs=20.2
Q ss_pred ecCCCcccCCccCCeEEEEeCCCCcEEcC
Q 035225 38 LMLGTPVTREFRCDRVWVWVDAIGRVSKP 66 (70)
Q Consensus 38 l~pg~~vT~df~~~RV~v~vD~~g~V~~v 66 (70)
|++|+..+.......+-|+-+++|.+..+
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 46777777777677777777777766543
No 30
>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=32.05 E-value=53 Score=19.84 Aligned_cols=29 Identities=21% Similarity=0.201 Sum_probs=19.4
Q ss_pred ecCCCcccCCccCCeEEEEeCCCCcEEcC
Q 035225 38 LMLGTPVTREFRCDRVWVWVDAIGRVSKP 66 (70)
Q Consensus 38 l~pg~~vT~df~~~RV~v~vD~~g~V~~v 66 (70)
|++|.+.+.+.....+-|+-+.+|.+..+
T Consensus 11 l~~g~~~~~~~~g~~i~l~r~~~g~~~a~ 39 (115)
T cd03531 11 FRDGKPHGVEAFGTKLVVFADSDGALNVL 39 (115)
T ss_pred CCCCCeEEEEECCeEEEEEECCCCCEEEE
Confidence 35677766666667777777777766543
No 31
>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=31.65 E-value=55 Score=19.29 Aligned_cols=26 Identities=27% Similarity=0.204 Sum_probs=15.7
Q ss_pred CCCcccCCccCCeEEEEeCCCCcEEc
Q 035225 40 LGTPVTREFRCDRVWVWVDAIGRVSK 65 (70)
Q Consensus 40 pg~~vT~df~~~RV~v~vD~~g~V~~ 65 (70)
+|+.++..+....+-|+-+.+|.|..
T Consensus 13 ~g~~~~~~~~~~~i~v~r~~~g~~~a 38 (118)
T cd03469 13 PGDYVTLELGGEPLVLVRDRDGEVRA 38 (118)
T ss_pred CCCEEEEEECCccEEEEECCCCCEEE
Confidence 56655555555666776666666554
No 32
>PRK11548 outer membrane biogenesis protein BamE; Provisional
Probab=31.63 E-value=49 Score=20.21 Aligned_cols=17 Identities=6% Similarity=0.054 Sum_probs=14.0
Q ss_pred CCeEEEEeCCCCcEEcC
Q 035225 50 CDRVWVWVDAIGRVSKP 66 (70)
Q Consensus 50 ~~RV~v~vD~~g~V~~v 66 (70)
..++.|+.|++|+|.++
T Consensus 88 ~~~l~V~Fd~~g~V~~i 104 (113)
T PRK11548 88 QQTLTLTFNSSGVLTNI 104 (113)
T ss_pred EEEEEEEECCCCeEEec
Confidence 34688999999999876
No 33
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=30.45 E-value=51 Score=21.87 Aligned_cols=18 Identities=11% Similarity=0.147 Sum_probs=15.3
Q ss_pred cCCeEEEEeCCCCcEEcC
Q 035225 49 RCDRVWVWVDAIGRVSKP 66 (70)
Q Consensus 49 ~~~RV~v~vD~~g~V~~v 66 (70)
.+..++|+.|++|.|..+
T Consensus 120 ~~kiltVh~De~G~Ii~V 137 (153)
T PRK14584 120 SGSCLTLYNDEHGHIIDV 137 (153)
T ss_pred hCCeEEEEECCCCCEEEe
Confidence 466889999999999876
No 34
>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=30.38 E-value=89 Score=16.29 Aligned_cols=43 Identities=19% Similarity=0.046 Sum_probs=28.2
Q ss_pred HHHHHHhhCCCCceE-EecCC----C--cccCCccCCeEEEEeCCCCcEE
Q 035225 22 AAATIKLQNPIVNPI-ILMLG----T--PVTREFRCDRVWVWVDAIGRVS 64 (70)
Q Consensus 22 A~~~I~~~~p~~~v~-vl~pg----~--~vT~df~~~RV~v~vD~~g~V~ 64 (70)
+...|....|+..+. +-... . -+-+.-+.+...|++|.+|.+.
T Consensus 12 v~~~i~~~yp~~~i~~v~~~~~~~~~~Y~v~l~~~~~~~~v~fd~~G~~l 61 (61)
T PF11396_consen 12 VKNAIKKNYPGAKIKEVEKETDPGGKYYEVELKKGGNEYEVYFDANGNWL 61 (61)
T ss_dssp HHHHHHHHSTTSEEEEEEEEEETTEEEEEEEETETTTSEEEEEETTS-EE
T ss_pred HHHHHHHHCCCCeEEEEEEEEcCCCCEEEEEEEEeCCeEEEEEcCCCCCC
Confidence 466888999998755 22221 1 3444456788999999999763
No 35
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=30.04 E-value=50 Score=18.07 Aligned_cols=19 Identities=21% Similarity=0.146 Sum_probs=15.2
Q ss_pred ccCCeEEEEeCCCCcEEcC
Q 035225 48 FRCDRVWVWVDAIGRVSKP 66 (70)
Q Consensus 48 f~~~RV~v~vD~~g~V~~v 66 (70)
....++.|+.|++|+|..+
T Consensus 52 ~~~~~l~V~Fd~~~~v~~~ 70 (71)
T PF04355_consen 52 NEQRQLKVYFDDDGVVKSI 70 (71)
T ss_dssp SCEEEEEEEECTTSBEEEE
T ss_pred cEEEEEEEEEcCCCEEEEe
Confidence 3467899999999999763
No 36
>PRK13321 pantothenate kinase; Reviewed
Probab=29.22 E-value=56 Score=22.42 Aligned_cols=39 Identities=28% Similarity=0.247 Sum_probs=27.1
Q ss_pred cccccccchHHHHHHHHhhCCCCceEEecCCCcccCCcc
Q 035225 11 WPELVGEIGAVAAATIKLQNPIVNPIILMLGTPVTREFR 49 (70)
Q Consensus 11 WpelVG~~~~~A~~~I~~~~p~~~v~vl~pg~~vT~df~ 49 (70)
=|+-+|.+--.+.....+..++..+.|+--|++.|.|+=
T Consensus 102 ~P~~lG~DR~a~~~aa~~~~~~~~~lvid~GTA~T~d~v 140 (256)
T PRK13321 102 NPREVGADRIVNAVAARRLYPDRNLIVVDFGTATTFDCV 140 (256)
T ss_pred ChhhccHHHHHHHHHHHHHcCCCCEEEEECCCceEEEEE
Confidence 367788885555444444455545789999999999963
No 37
>PRK03760 hypothetical protein; Provisional
Probab=28.75 E-value=38 Score=21.11 Aligned_cols=13 Identities=23% Similarity=0.302 Sum_probs=11.4
Q ss_pred EEEeCCCCcEEcC
Q 035225 54 WVWVDAIGRVSKP 66 (70)
Q Consensus 54 ~v~vD~~g~V~~v 66 (70)
-+|+|++|+|+++
T Consensus 63 iiFld~~g~Vv~i 75 (117)
T PRK03760 63 VIFLDSNRRVVDF 75 (117)
T ss_pred EEEECCCCeEEEE
Confidence 6799999999876
No 38
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=28.57 E-value=49 Score=18.85 Aligned_cols=29 Identities=24% Similarity=0.472 Sum_probs=18.1
Q ss_pred ecCCCcccCCccCCe---EEE-EeCCCCcEEcC
Q 035225 38 LMLGTPVTREFRCDR---VWV-WVDAIGRVSKP 66 (70)
Q Consensus 38 l~pg~~vT~df~~~R---V~v-~vD~~g~V~~v 66 (70)
++.|+.+...|+.+| |.| .+|.+|.|+.+
T Consensus 3 ~~~Ge~v~~~~~~~~~~Yl~l~~~~~~G~v~~L 35 (83)
T PF14326_consen 3 YRVGERVRFRVTSNRDGYLYLFYIDADGKVTLL 35 (83)
T ss_pred ccCCCEEEEEEEeCCCeEEEEEEECCCCCEEEE
Confidence 455666666666654 444 35888887764
No 39
>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=28.43 E-value=64 Score=18.49 Aligned_cols=27 Identities=11% Similarity=-0.116 Sum_probs=14.3
Q ss_pred cCCCcccCCccCCeEEEEeCCCCcEEc
Q 035225 39 MLGTPVTREFRCDRVWVWVDAIGRVSK 65 (70)
Q Consensus 39 ~pg~~vT~df~~~RV~v~vD~~g~V~~ 65 (70)
++|......+....+-|+-+++|.+..
T Consensus 11 ~~~~~~~~~~~g~~i~l~r~~~g~~~A 37 (98)
T cd03530 11 PPRGARKVQTGGGEIAVFRTADDEVFA 37 (98)
T ss_pred CCCCcEEEEECCEEEEEEEeCCCCEEE
Confidence 444444444445556666666565544
No 40
>COG2815 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.57 E-value=1.8e+02 Score=21.04 Aligned_cols=21 Identities=29% Similarity=0.292 Sum_probs=18.6
Q ss_pred CCCcccccccchHHHHHHHHh
Q 035225 8 KTSWPELVGEIGAVAAATIKL 28 (70)
Q Consensus 8 k~~WpelVG~~~~~A~~~I~~ 28 (70)
+..=|+++|.+.+||.+.++.
T Consensus 92 ~~~vpdv~Gl~~~eA~~~L~~ 112 (303)
T COG2815 92 YITVPDVVGLTIEEAVAKLKA 112 (303)
T ss_pred ceecCcccCCcHHHHHHHHHH
Confidence 457899999999999998887
No 41
>cd07186 CofD_like LPPG:FO 2-phospho-L-lactate transferase; important in F420 biosynthesis. CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis.
Probab=27.15 E-value=60 Score=23.67 Aligned_cols=26 Identities=19% Similarity=0.199 Sum_probs=19.5
Q ss_pred cchHHHHHHHHhhCCCCceEEecCCCcccC
Q 035225 17 EIGAVAAATIKLQNPIVNPIILMLGTPVTR 46 (70)
Q Consensus 17 ~~~~~A~~~I~~~~p~~~v~vl~pg~~vT~ 46 (70)
++..+|.++|.+. ..++|.||+++|-
T Consensus 172 ~~~p~vl~AI~~A----D~IVlGPgsp~TS 197 (303)
T cd07186 172 RPAPEVLEAIEDA----DLVIIGPSNPVTS 197 (303)
T ss_pred CCCHHHHHHHHhC----CEEEECCCccHHH
Confidence 4566777777765 5789999998874
No 42
>PHA02087 hypothetical protein
Probab=26.82 E-value=73 Score=18.79 Aligned_cols=22 Identities=23% Similarity=0.271 Sum_probs=16.3
Q ss_pred CccCCeEEE--EeCCCCcEEcCCc
Q 035225 47 EFRCDRVWV--WVDAIGRVSKPPV 68 (70)
Q Consensus 47 df~~~RV~v--~vD~~g~V~~vP~ 68 (70)
.|++|.+.= .||.+|++..+|-
T Consensus 38 ~~d~nk~v~y~lvdsdg~~ielpe 61 (83)
T PHA02087 38 KFDPNKLVQYMLVDSDGVKIELPE 61 (83)
T ss_pred cCCCccceeEEEEcCCCcEEECCc
Confidence 566776544 4799999998883
No 43
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=26.63 E-value=35 Score=19.85 Aligned_cols=20 Identities=40% Similarity=0.539 Sum_probs=8.1
Q ss_pred ccCCccCC-------eEEEEeCCCCcE
Q 035225 44 VTREFRCD-------RVWVWVDAIGRV 63 (70)
Q Consensus 44 vT~df~~~-------RV~v~vD~~g~V 63 (70)
++..|++. ||.+.+|++|.+
T Consensus 22 ~~k~FCp~CGn~TL~rvsvsv~~~G~~ 48 (73)
T PF08772_consen 22 MTKQFCPKCGNATLKRVSVSVDEDGKI 48 (73)
T ss_dssp SS--S-SSS--S--EEEE-B--SS---
T ss_pred CCceeCcccCCCcceEEEEEECCCCCE
Confidence 44556654 999999998865
No 44
>PF01933 UPF0052: Uncharacterised protein family UPF0052; InterPro: IPR002882 This entry contains LPPG:Fo 2-phospho-L-lactate transferase (CofD) and related sequences of unknown function belong to unidentified protein family UPF0052. CofD catalyses the fourth step in the biosynthesis of coenzyme F420, which is the transfer of the 2-phospholactate moiety from lactyl (2) diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) with the formation of the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) and GMP. F420 is a flavin derivative found in methanogens, Mycobacteria, and several other lineages. This enzyme is characterised so far in Methanocaldococcus jannaschii (Methanococcus jannaschii) [] but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. ; PDB: 2HZB_A 2O2Z_C 3CGW_A 3C3E_D 3C3D_D 2PPV_A 2P0Y_A 2Q7X_B.
Probab=26.37 E-value=74 Score=22.90 Aligned_cols=25 Identities=24% Similarity=0.187 Sum_probs=15.5
Q ss_pred chHHHHHHHHhhCCCCceEEecCCCcccC
Q 035225 18 IGAVAAATIKLQNPIVNPIILMLGTPVTR 46 (70)
Q Consensus 18 ~~~~A~~~I~~~~p~~~v~vl~pg~~vT~ 46 (70)
+..+|..+|++. ..+++.||++.|-
T Consensus 173 ~~p~~l~AI~~A----D~IiigPgs~~TS 197 (300)
T PF01933_consen 173 ANPEALEAIEEA----DLIIIGPGSLYTS 197 (300)
T ss_dssp B-HHHHHHHHH-----SEEEE-SS-CCCC
T ss_pred CCHHHHHHHHhC----CEEEEcCCCchhh
Confidence 345666777765 5789999998874
No 45
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=26.20 E-value=41 Score=20.34 Aligned_cols=13 Identities=38% Similarity=0.514 Sum_probs=10.2
Q ss_pred EEEeCCCCcEEcC
Q 035225 54 WVWVDAIGRVSKP 66 (70)
Q Consensus 54 ~v~vD~~g~V~~v 66 (70)
-+|+|++|+|+.+
T Consensus 52 i~fld~~g~Vv~i 64 (108)
T PF02643_consen 52 IAFLDSDGRVVKI 64 (108)
T ss_dssp EEEE-TTSBEEEE
T ss_pred EEEECCCCeEEEE
Confidence 6799999999875
No 46
>cd00340 GSH_Peroxidase Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per subunit, which is involved in catalysis. Different isoenzymes are known in mammals,which are involved in protection against reactive oxygen species, redox regulation of many metabolic processes, peroxinitrite scavenging, and modulation of inflammatory processes.
Probab=26.11 E-value=67 Score=19.89 Aligned_cols=16 Identities=31% Similarity=0.217 Sum_probs=13.1
Q ss_pred CeEEEEeCCCCcEEcC
Q 035225 51 DRVWVWVDAIGRVSKP 66 (70)
Q Consensus 51 ~RV~v~vD~~g~V~~v 66 (70)
+|-.+++|.+|+|+..
T Consensus 123 ~~ttflId~~G~i~~~ 138 (152)
T cd00340 123 NFTKFLVDRDGEVVKR 138 (152)
T ss_pred ccEEEEECCCCcEEEE
Confidence 4578999999999863
No 47
>PRK13606 LPPG:FO 2-phospho-L-lactate transferase; Provisional
Probab=25.77 E-value=66 Score=23.48 Aligned_cols=25 Identities=20% Similarity=0.234 Sum_probs=18.7
Q ss_pred chHHHHHHHHhhCCCCceEEecCCCcccC
Q 035225 18 IGAVAAATIKLQNPIVNPIILMLGTPVTR 46 (70)
Q Consensus 18 ~~~~A~~~I~~~~p~~~v~vl~pg~~vT~ 46 (70)
+..+|.++|.+. ..++|.||+++|-
T Consensus 175 a~p~vl~AI~~A----D~IiiGPgnp~TS 199 (303)
T PRK13606 175 PAPGVLEAIEEA----DAVIIGPSNPVTS 199 (303)
T ss_pred CCHHHHHHHHhC----CEEEECCCccHHh
Confidence 556677777664 4789999998874
No 48
>TIGR00671 baf pantothenate kinase, type III. This model describes a family of proteins found in a single copy in at least ten different early completed bacterial genomes. The only characterized member of the family is Bvg accessory factor (Baf), a protein required, in addition to the regulatory operon bvgAS, for heterologous transcription of the Bordetella pertussis toxin operon (ptx) in E. coli.
Probab=25.13 E-value=69 Score=22.08 Aligned_cols=38 Identities=18% Similarity=0.138 Sum_probs=29.0
Q ss_pred cccccccchHHHHHHHHhhCCCCceEEecCCCcccCCcc
Q 035225 11 WPELVGEIGAVAAATIKLQNPIVNPIILMLGTPVTREFR 49 (70)
Q Consensus 11 WpelVG~~~~~A~~~I~~~~p~~~v~vl~pg~~vT~df~ 49 (70)
=|+-+|.+--.|.....+..++ .+.|+--|++.|.|+=
T Consensus 95 ~p~~LG~DR~a~~~aA~~~~~~-~~lViD~GTA~Tid~v 132 (243)
T TIGR00671 95 SPKELGIDRVANALAAIKFYGF-NVVVVDAGTALTIDLV 132 (243)
T ss_pred ChhhccHHHHHHHHHHHHHcCC-CEEEEEcCCceEEEEE
Confidence 3567898887776666665655 5789999999999963
No 49
>COG1430 Uncharacterized conserved protein [Function unknown]
Probab=25.00 E-value=49 Score=21.14 Aligned_cols=13 Identities=31% Similarity=0.555 Sum_probs=10.8
Q ss_pred EEEeCCCCcEEcC
Q 035225 54 WVWVDAIGRVSKP 66 (70)
Q Consensus 54 ~v~vD~~g~V~~v 66 (70)
-+|+|++|+|+.+
T Consensus 66 iiFid~dg~i~~i 78 (126)
T COG1430 66 IIFIDSDGRVVDI 78 (126)
T ss_pred EEEEcCCCCEEEE
Confidence 5789999999875
No 50
>PRK13324 pantothenate kinase; Reviewed
Probab=24.91 E-value=73 Score=22.36 Aligned_cols=38 Identities=21% Similarity=0.255 Sum_probs=29.2
Q ss_pred ccccccchHHHHHHHHhhCCCCceEEecCCCcccCCcc
Q 035225 12 PELVGEIGAVAAATIKLQNPIVNPIILMLGTPVTREFR 49 (70)
Q Consensus 12 pelVG~~~~~A~~~I~~~~p~~~v~vl~pg~~vT~df~ 49 (70)
|+=+|.+--.+.....+..|+....|+--|++.|.|+=
T Consensus 103 p~~lG~DR~~~~vaA~~~~~~~~~iViD~GTA~T~d~v 140 (258)
T PRK13324 103 AHQVGADRIASCISAIADHPNKDLLIIDLGTATTFDLV 140 (258)
T ss_pred hhhccHHHHHHHHHHHHhcCCCCEEEEEcCCceEEEEE
Confidence 77788887777666666666666789999999999853
No 51
>PF06633 DUF1155: Protein of unknown function (DUF1155); InterPro: IPR009536 This family consists of several Cucumber mosaic virus ORF IIB proteins. The function of this family is unknown.
Probab=24.50 E-value=22 Score=18.52 Aligned_cols=14 Identities=36% Similarity=0.375 Sum_probs=10.6
Q ss_pred cCCC--cccCCccCCe
Q 035225 39 MLGT--PVTREFRCDR 52 (70)
Q Consensus 39 ~pg~--~vT~df~~~R 52 (70)
.||. +.||||+.+-
T Consensus 20 ~pg~wfa~t~df~k~~ 35 (42)
T PF06633_consen 20 EPGTWFADTMDFRKKH 35 (42)
T ss_pred CCCchhhhhhhhhhhh
Confidence 5665 7999998764
No 52
>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=24.16 E-value=73 Score=14.51 Aligned_cols=20 Identities=20% Similarity=0.109 Sum_probs=14.2
Q ss_pred EecCCCcccCCccCCeEEEE
Q 035225 37 ILMLGTPVTREFRCDRVWVW 56 (70)
Q Consensus 37 vl~pg~~vT~df~~~RV~v~ 56 (70)
+-+.|...-.|+..+||.+|
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 34667777778888888765
No 53
>COG1264 PtsG Phosphotransferase system IIB components [Carbohydrate transport and metabolism]
Probab=23.94 E-value=53 Score=19.44 Aligned_cols=21 Identities=24% Similarity=0.215 Sum_probs=17.1
Q ss_pred cccCCccCCeEEEEeCCCCcE
Q 035225 43 PVTREFRCDRVWVWVDAIGRV 63 (70)
Q Consensus 43 ~vT~df~~~RV~v~vD~~g~V 63 (70)
....+.+.-|||+.+.+...|
T Consensus 17 I~~~~~C~TRLR~~v~D~s~V 37 (88)
T COG1264 17 IVSVDHCATRLRVTVKDESKV 37 (88)
T ss_pred HhhhhcCcceEEEEEcChhhc
Confidence 456789999999999887665
No 54
>PRK11251 DNA-binding transcriptional activator OsmE; Provisional
Probab=23.92 E-value=82 Score=19.57 Aligned_cols=17 Identities=24% Similarity=0.374 Sum_probs=14.2
Q ss_pred CCeEEEEeCCCCcEEcC
Q 035225 50 CDRVWVWVDAIGRVSKP 66 (70)
Q Consensus 50 ~~RV~v~vD~~g~V~~v 66 (70)
..++.|+.|++|+|++.
T Consensus 77 ~~~~tV~Fd~~G~V~~~ 93 (109)
T PRK11251 77 AQTYFVSFDDTGHVDNK 93 (109)
T ss_pred eEEEEEEECCCCCEEec
Confidence 46788999999999874
No 55
>PF13028 DUF3889: Protein of unknown function (DUF3889)
Probab=23.79 E-value=1.7e+02 Score=17.86 Aligned_cols=42 Identities=19% Similarity=0.327 Sum_probs=28.6
Q ss_pred HHHHHHHHhhCCCCceE-EecCCCcc-cCCccCCeEEEEeCCCC
Q 035225 20 AVAAATIKLQNPIVNPI-ILMLGTPV-TREFRCDRVWVWVDAIG 61 (70)
Q Consensus 20 ~~A~~~I~~~~p~~~v~-vl~pg~~v-T~df~~~RV~v~vD~~g 61 (70)
.-|...++.++|++.+. .+..|..- +-+--.+.-.|++.++|
T Consensus 28 rlA~~~~k~~Yp~a~v~DY~~vGr~~~~~~~t~e~Fkl~l~~~~ 71 (97)
T PF13028_consen 28 RLAVQETKEKYPGAEVVDYLYVGRTKVNDEQTVEKFKLWLREGG 71 (97)
T ss_pred HHHHHHHHHHCCCCEEeeeeeecceecCCcceEEEEEEEEEcCC
Confidence 45677899999999988 77777643 33335566666665544
No 56
>cd00212 PTS_IIB_glc PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation
Probab=23.69 E-value=66 Score=18.29 Aligned_cols=20 Identities=20% Similarity=0.239 Sum_probs=15.1
Q ss_pred ccCCccCCeEEEEeCCCCcE
Q 035225 44 VTREFRCDRVWVWVDAIGRV 63 (70)
Q Consensus 44 vT~df~~~RV~v~vD~~g~V 63 (70)
...+.+..|+|+.+++...|
T Consensus 18 ~~v~~c~TRLRv~l~d~~~v 37 (78)
T cd00212 18 VSLDHCATRLRLTVKDESKV 37 (78)
T ss_pred ccccccccEEEEEEeCchhc
Confidence 34577889999999876544
No 57
>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=23.37 E-value=34 Score=21.70 Aligned_cols=17 Identities=24% Similarity=0.196 Sum_probs=14.2
Q ss_pred eEEecCCCcccCCccCC
Q 035225 35 PIILMLGTPVTREFRCD 51 (70)
Q Consensus 35 v~vl~pg~~vT~df~~~ 51 (70)
++.++||.+++-||-+|
T Consensus 86 vE~~~Pg~P~~hD~epD 102 (112)
T PF08882_consen 86 VEAPPPGYPPIHDFEPD 102 (112)
T ss_pred EccCCCCCCceEecccC
Confidence 55789999999998776
No 58
>PF08402 TOBE_2: TOBE domain; InterPro: IPR013611 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (e.g. P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT). Found in ABC transporters immediately after the ATPase domain. A strong RPE motif is found at the presumed N terminus of the domain. ; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1Q12_A 1Q1B_C 2AWN_D 3RLF_B 3PUX_B 2R6G_B 3PUV_B 1Q1E_A 3PV0_B 2AWO_A ....
Probab=22.56 E-value=33 Score=18.07 Aligned_cols=18 Identities=22% Similarity=0.259 Sum_probs=8.8
Q ss_pred cCCCcccCCccCCeEEEE
Q 035225 39 MLGTPVTREFRCDRVWVW 56 (70)
Q Consensus 39 ~pg~~vT~df~~~RV~v~ 56 (70)
.+|+.+...|+++++.+|
T Consensus 58 ~~G~~v~l~~~~~~~~vf 75 (75)
T PF08402_consen 58 EPGDEVRLSWDPDDAHVF 75 (75)
T ss_dssp -TTSEEEEEEEGGGEEEE
T ss_pred CCCCEEEEEECcccEEeC
Confidence 345555555555555443
No 59
>PF12357 PLD_C: Phospholipase D C terminal ; InterPro: IPR024632 Phospholipase D (PLD) catalyses the hydrolysis of the phosphodiester bond of glycerophospholipids to generate phosphatidic acid and a free head group. Phospholipase D activities have been detected in simple to complex organisms from viruses and bacteria to yeast, plants, and mammals []. In higher organisms, PLD specifically catalyzes the hydrolysis of phosphatidylcholine (PC) to phosphatidic acid (PA) and choline and is activated in response to stimulators of vesicle transport, endocytosis, exocytosis, cell migration, and mitosis. This entry represents the C-terminal domain of eukaryotic phospholipase D. The domain is approximately 70 amino acids in length and contains a conserved FPD sequence motif.
Probab=22.35 E-value=76 Score=18.63 Aligned_cols=13 Identities=46% Similarity=0.598 Sum_probs=11.0
Q ss_pred EEeCCCCcEEcCC
Q 035225 55 VWVDAIGRVSKPP 67 (70)
Q Consensus 55 v~vD~~g~V~~vP 67 (70)
|.|+.+|.|..+|
T Consensus 45 v~V~~dG~V~~Lp 57 (74)
T PF12357_consen 45 VQVDRDGKVTPLP 57 (74)
T ss_pred eEEcCCCCEeeCC
Confidence 6788999999876
No 60
>PF14339 DUF4394: Domain of unknown function (DUF4394)
Probab=21.86 E-value=1e+02 Score=21.76 Aligned_cols=22 Identities=27% Similarity=0.380 Sum_probs=16.6
Q ss_pred ecCCCcccCCccC--CeEEEEeCC
Q 035225 38 LMLGTPVTREFRC--DRVWVWVDA 59 (70)
Q Consensus 38 l~pg~~vT~df~~--~RV~v~vD~ 59 (70)
-..|..+..|||| ||+||.-+.
T Consensus 71 al~g~~~gvDFNP~aDRlRvvs~~ 94 (236)
T PF14339_consen 71 ALSGTAFGVDFNPAADRLRVVSNT 94 (236)
T ss_pred cccCceEEEecCcccCcEEEEccC
Confidence 3457788889997 899988554
No 61
>TIGR01826 CofD_related conserved hypothetical protein, cofD-related. This model represents a subfamily of conserved hypothetical proteins that forms a sister group to the family of CofD, (TIGR01819), LPPG:Fo 2-phospho-L-lactate transferase, an enzyme of cytochrome F420 biosynthesis. Both this family and TIGR01819 are within the scope of the pfam model pfam01933.
Probab=21.78 E-value=86 Score=22.87 Aligned_cols=25 Identities=28% Similarity=0.161 Sum_probs=17.6
Q ss_pred cchHHHHHHHHhhCCCCceEEecCCCccc
Q 035225 17 EIGAVAAATIKLQNPIVNPIILMLGTPVT 45 (70)
Q Consensus 17 ~~~~~A~~~I~~~~p~~~v~vl~pg~~vT 45 (70)
+...+|.++|++. ..+++.||+..|
T Consensus 161 ~a~~~al~AI~~A----DlIvlgPGSlyT 185 (310)
T TIGR01826 161 PALREAVEAIREA----DLIILGPGSLYT 185 (310)
T ss_pred CCCHHHHHHHHhC----CEEEECCCcCHH
Confidence 3445666777754 578999999776
No 62
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=21.40 E-value=34 Score=20.64 Aligned_cols=20 Identities=40% Similarity=0.810 Sum_probs=11.4
Q ss_pred CCcccccccchHHHHHHHHh
Q 035225 9 TSWPELVGEIGAVAAATIKL 28 (70)
Q Consensus 9 ~~WpelVG~~~~~A~~~I~~ 28 (70)
+.||||++.-.+......++
T Consensus 1 ~r~~e~l~~l~~~i~~~l~~ 20 (108)
T PF08765_consen 1 SRWPELLSELADVIAAELER 20 (108)
T ss_dssp --HHHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHHHHH
Confidence 35888887776665444443
No 63
>cd07044 CofD_YvcK Family of CofD-like proteins and proteins related to YvcK. CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis. YvcK from Bacillus subtilis is a member of a family of mostly uncharacterized proteins and has been proposed to play a role in carbon metabolism, since its function is essential for growth on intermediates of the Krebs cycle and pentose phosphate pathway. Both families appear to have a conserved phosphate binding site, but ha
Probab=20.99 E-value=91 Score=22.64 Aligned_cols=24 Identities=17% Similarity=0.145 Sum_probs=17.1
Q ss_pred chHHHHHHHHhhCCCCceEEecCCCccc
Q 035225 18 IGAVAAATIKLQNPIVNPIILMLGTPVT 45 (70)
Q Consensus 18 ~~~~A~~~I~~~~p~~~v~vl~pg~~vT 45 (70)
+..+|..+|.+. ..+++.||+..|
T Consensus 164 ~~~~~l~AI~~A----DlIvlgPGSlyT 187 (309)
T cd07044 164 PSREVLEAIEKA----DNIVIGPGSLYT 187 (309)
T ss_pred CCHHHHHHHHhC----CEEEECCCcCHH
Confidence 345666677664 478999999876
No 64
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=20.97 E-value=1.4e+02 Score=17.76 Aligned_cols=42 Identities=29% Similarity=0.479 Sum_probs=22.8
Q ss_pred CCCCC-------CCCCcccccccchHHHHHHHHhhCCCCceEEecCCCcccCC
Q 035225 2 ATFCS-------GKTSWPELVGEIGAVAAATIKLQNPIVNPIILMLGTPVTRE 47 (70)
Q Consensus 2 ~~~c~-------~k~~WpelVG~~~~~A~~~I~~~~p~~~v~vl~pg~~vT~d 47 (70)
.+.|| +-..|-+|...--..|......- .++|...|.++..+
T Consensus 23 ktiCPSevARal~~~~WR~lm~~vR~~A~~L~~~G----~i~I~qkG~~Vdp~ 71 (83)
T PF11625_consen 23 KTICPSEVARALGPDDWRDLMPPVRAAARRLARAG----RIEITQKGKPVDPE 71 (83)
T ss_dssp --B-HHHHHHHH-TTS-GGGHHHHHHHHHHHHHTT----SEEEEETTEE--TT
T ss_pred CccCHHHHHHHHCchhhHHHHHHHHHHHHHHHHCC----cEEEEECCEecCcc
Confidence 35677 34569999887666554333322 47788999887444
No 65
>PF03309 Pan_kinase: Type III pantothenate kinase; InterPro: IPR004619 Pantothenate kinase (PanK or CoaA) catalyses the first step of the universal five step coenzyme A (CoA) biosynthesis pathway. CoA is a ubiquitous and essential cofactor in all living organsims. Pantothenate kinase catalyses the first and rate limiting step in the CoA biosynthetic pathway, which involves transferring a phosphoryl group from ATP to pantothenate, also known as vitamin B5. Three distinct types of pantothenate kinase enzymes have been identified: type I PanK enzymes are typified by the E. coli CoaA protein, type II enzymes are primarily found in eukaryotic organisms whilst type III enzymes have a wider phylogenic distribution and are not feedback inhibited by CoA []. This entry represents the type III pantothenate kinase family, such as that found in Helicobacter pylori. PanK III enzymes have a much wider phylogenic distribution than PanK I, and differs significantly in biochemical activity. PanK III enzymes are are not feedback inhibited by CoA concentration (which is also the case for PanK II enzymes), and PanK III enzymes have an unusually high Km for ATP []. ; GO: 0045893 positive regulation of transcription, DNA-dependent; PDB: 2GTD_E 3BF1_F 3BEX_D 3BF3_F 2NRH_B 2H3G_X 3DJC_J 2F9T_A 2F9W_A.
Probab=20.72 E-value=59 Score=21.51 Aligned_cols=37 Identities=19% Similarity=0.098 Sum_probs=27.4
Q ss_pred ccccccchHHHHHHHHhhCCCCceEEecCCCcccCCcc
Q 035225 12 PELVGEIGAVAAATIKLQNPIVNPIILMLGTPVTREFR 49 (70)
Q Consensus 12 pelVG~~~~~A~~~I~~~~p~~~v~vl~pg~~vT~df~ 49 (70)
|+-+|.+--.+.....+.. +....|+--|++.|.|+=
T Consensus 100 p~~LG~DR~~~~~aa~~~~-~~~~lViD~GTA~Tid~v 136 (206)
T PF03309_consen 100 PSQLGVDRWAAAIAARKLY-GQPCLVIDAGTATTIDVV 136 (206)
T ss_dssp GGGS-HHHHHHHHHHHHHH-TSSEEEEEESSEEEEEEE
T ss_pred hhHhhHHHHHHHHHHHHhc-CCCEEEEEcCCeEEEEEE
Confidence 7889998877766555544 455789999999999964
No 66
>cd03480 Rieske_RO_Alpha_PaO Rieske non-heme iron oxygenase (RO) family, Pheophorbide a oxygenase (PaO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of a small subfamily of enzymes found in plants as well as oxygenic cyanobacterial photosynthesizers including LLS1 (lethal leaf spot 1, also known as PaO) and ACD1 (accelerated cell death 1). 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. PaO expression increases upon physical wounding of plant leaves and is thought to catalyze a key step in chlorophyll degradation. The
Probab=20.37 E-value=94 Score=19.46 Aligned_cols=27 Identities=11% Similarity=0.126 Sum_probs=14.4
Q ss_pred cCCCcccCCccCCeEEEEeCC-CCcEEc
Q 035225 39 MLGTPVTREFRCDRVWVWVDA-IGRVSK 65 (70)
Q Consensus 39 ~pg~~vT~df~~~RV~v~vD~-~g~V~~ 65 (70)
++|.+.+.++.-..+-|+-|. +|.+..
T Consensus 28 ~~g~~~~~~~~g~~i~v~r~~~dG~~~A 55 (138)
T cd03480 28 DPSRPTPFTLLGRDLVIWWDRNSQQWRA 55 (138)
T ss_pred CCCCcEEEEECCeeEEEEEECCCCEEEE
Confidence 445555555555555565553 555543
Done!