Query 044806
Match_columns 70
No_of_seqs 106 out of 315
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 06:57:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044806.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044806hhsearch_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 1.4E-34 3E-39 167.1 5.2 63 8-70 1-63 (63)
2 PF11720 Inhibitor_I78: Peptid 99.7 2.5E-18 5.4E-23 97.9 2.3 54 9-66 4-57 (60)
3 PF03793 PASTA: PASTA domain; 78.4 1.9 4E-05 23.3 1.8 18 12-29 4-21 (63)
4 cd06573 PASTA PASTA domain. Th 71.0 8.9 0.00019 19.0 3.2 17 12-28 3-19 (53)
5 PF03413 PepSY: Peptidase prop 70.0 11 0.00025 19.6 3.6 48 18-65 3-62 (64)
6 cd06577 PASTA_pknB PASTA domai 63.7 6.4 0.00014 20.0 1.8 18 12-29 3-20 (62)
7 cd03477 Rieske_YhfW_C YhfW fam 58.9 13 0.00029 21.9 2.8 29 38-66 8-36 (91)
8 PF14326 DUF4384: Domain of un 55.9 13 0.00028 21.4 2.3 29 38-66 3-35 (83)
9 PF13103 TonB_2: TonB C termin 55.2 13 0.00028 20.9 2.2 17 50-66 27-43 (85)
10 cd06575 PASTA_Pbp2x-like_2 PAS 51.7 14 0.0003 18.3 1.8 18 12-29 3-20 (54)
11 smart00740 PASTA PASTA domain. 51.6 14 0.00029 19.1 1.8 19 10-28 6-24 (66)
12 PF06691 DUF1189: Protein of u 51.5 30 0.00066 23.7 3.9 43 23-65 59-103 (250)
13 PF06241 DUF1012: Protein of u 50.2 19 0.00041 25.1 2.7 29 9-41 97-126 (206)
14 cd06576 PASTA_Pbp2x-like_1 PAS 49.8 15 0.00032 18.4 1.7 18 12-29 3-20 (55)
15 PHA03066 Hypothetical protein; 48.3 62 0.0013 20.5 4.6 41 19-64 35-81 (110)
16 cd03474 Rieske_T4moC Toluene-4 48.0 23 0.0005 20.9 2.6 29 38-66 10-38 (108)
17 TIGR00638 Mop molybdenum-pteri 46.7 12 0.00025 20.2 1.1 21 38-58 49-69 (69)
18 KOG0912 Thiol-disulfide isomer 45.6 25 0.00053 26.5 2.8 17 36-52 77-93 (375)
19 PF08482 HrpB_C: ATP-dependent 45.6 19 0.00042 23.4 2.1 46 5-52 6-60 (133)
20 cd03469 Rieske_RO_Alpha_N Ries 43.4 36 0.00078 20.2 2.9 27 40-66 13-39 (118)
21 TIGR01352 tonB_Cterm TonB fami 42.4 24 0.00052 19.0 1.9 16 52-67 13-28 (74)
22 cd03531 Rieske_RO_Alpha_KSH Th 42.3 36 0.00077 20.7 2.9 29 38-66 11-39 (115)
23 cd04337 Rieske_RO_Alpha_Cao Ca 41.6 38 0.00082 21.1 2.9 30 37-66 26-55 (129)
24 PF03544 TonB_C: Gram-negative 41.3 23 0.0005 19.3 1.8 15 52-66 19-33 (79)
25 PF04225 OapA: Opacity-associa 39.4 24 0.00053 20.7 1.7 32 16-47 21-52 (85)
26 COG0391 Uncharacterized conser 39.3 30 0.00066 25.5 2.5 25 18-46 179-203 (323)
27 cd03530 Rieske_NirD_small_Baci 37.3 45 0.00098 19.2 2.7 28 39-66 11-38 (98)
28 PF11396 DUF2874: Protein of u 35.5 71 0.0015 16.7 3.9 43 22-64 12-61 (61)
29 PHA02087 hypothetical protein 33.1 54 0.0012 19.5 2.4 22 47-68 38-61 (83)
30 PRK14584 hmsS hemin storage sy 32.1 50 0.0011 22.0 2.5 22 45-66 116-137 (153)
31 PF13994 PgaD: PgaD-like prote 31.4 34 0.00074 21.7 1.5 18 48-65 121-138 (138)
32 PF04355 SmpA_OmlA: SmpA / Oml 31.2 57 0.0012 17.9 2.3 19 48-66 52-70 (71)
33 cd00340 GSH_Peroxidase Glutath 30.9 55 0.0012 20.3 2.5 16 51-66 123-138 (152)
34 PF08402 TOBE_2: TOBE domain; 30.6 25 0.00054 18.6 0.7 18 39-56 58-75 (75)
35 PRK13320 pantothenate kinase; 30.1 58 0.0012 22.6 2.6 38 11-48 92-129 (244)
36 PRK03760 hypothetical protein; 30.0 41 0.0009 21.0 1.7 13 54-66 63-75 (117)
37 TIGR01819 F420_cofD LPPG:FO 2- 29.8 53 0.0012 24.0 2.5 24 19-46 173-196 (297)
38 KOG0544 FKBP-type peptidyl-pro 29.7 91 0.002 19.6 3.2 27 32-58 2-28 (108)
39 PF01436 NHL: NHL repeat; Int 29.7 57 0.0012 14.9 1.8 20 37-56 9-28 (28)
40 PF02643 DUF192: Uncharacteriz 28.8 45 0.00098 20.2 1.7 13 54-66 52-64 (108)
41 PRK11548 outer membrane biogen 28.7 60 0.0013 19.9 2.3 17 50-66 88-104 (113)
42 PF06519 TolA: TolA C-terminal 28.5 46 0.001 20.1 1.7 17 50-66 38-54 (96)
43 PF00367 PTS_EIIB: phosphotran 28.3 23 0.00049 17.7 0.3 20 44-63 15-34 (35)
44 PRK13328 pantothenate kinase; 28.2 57 0.0012 22.8 2.3 38 12-49 97-134 (255)
45 PF13028 DUF3889: Protein of u 28.2 1.4E+02 0.003 18.4 3.8 42 19-60 27-70 (97)
46 COG1430 Uncharacterized conser 27.1 52 0.0011 21.1 1.8 13 54-66 66-78 (126)
47 cd03480 Rieske_RO_Alpha_PaO Ri 25.7 76 0.0017 20.0 2.4 28 39-66 28-56 (138)
48 PLN03213 repressor of silencin 25.3 17 0.00037 29.1 -0.7 18 5-22 324-341 (759)
49 PRK00522 tpx lipid hydroperoxi 25.1 67 0.0015 20.5 2.1 17 50-66 130-146 (167)
50 cd07186 CofD_like LPPG:FO 2-ph 25.0 75 0.0016 23.3 2.5 26 17-46 172-197 (303)
51 PF06633 DUF1155: Protein of u 25.0 22 0.00048 18.6 -0.2 14 39-52 20-35 (42)
52 PF08882 Acetone_carb_G: Aceto 24.7 35 0.00075 21.7 0.7 18 34-51 85-102 (112)
53 PRK09510 tolA cell envelope in 24.3 64 0.0014 24.4 2.1 16 51-66 328-343 (387)
54 COG1596 Wza Periplasmic protei 24.2 74 0.0016 22.0 2.3 41 13-56 89-130 (239)
55 PF02406 MmoB_DmpM: MmoB/DmpM 24.2 81 0.0018 18.9 2.2 20 23-44 18-37 (87)
56 PF01933 UPF0052: Uncharacteri 23.9 88 0.0019 22.6 2.7 24 19-46 174-197 (300)
57 PRK13321 pantothenate kinase; 23.9 83 0.0018 21.6 2.5 38 11-48 102-139 (256)
58 PRK11251 DNA-binding transcrip 23.8 87 0.0019 19.5 2.4 17 50-66 77-93 (109)
59 COG5428 Uncharacterized conser 23.5 1.6E+02 0.0036 17.1 3.6 29 38-66 16-45 (69)
60 PF00899 ThiF: ThiF family; I 22.9 1.8E+02 0.0039 17.6 3.7 30 12-41 50-80 (135)
61 KOG4442 Clathrin coat binding 22.8 32 0.00069 28.2 0.3 17 36-52 224-240 (729)
62 COG1225 Bcp Peroxiredoxin [Pos 22.8 82 0.0018 20.9 2.2 18 49-66 118-135 (157)
63 COG2815 Uncharacterized protei 22.6 2.3E+02 0.005 20.6 4.6 22 7-28 91-112 (303)
64 PRK13606 LPPG:FO 2-phospho-L-l 22.5 89 0.0019 22.9 2.5 25 18-46 175-199 (303)
65 PF14339 DUF4394: Domain of un 22.5 1.1E+02 0.0023 21.7 2.9 21 38-58 71-93 (236)
66 PF02575 YbaB_DNA_bd: YbaB/Ebf 22.2 78 0.0017 18.2 1.8 15 52-66 31-45 (93)
67 TIGR02540 gpx7 putative glutat 22.0 94 0.002 19.2 2.3 16 51-66 120-135 (153)
68 cd03478 Rieske_AIFL_N AIFL (ap 22.0 1.1E+02 0.0023 17.5 2.4 27 38-65 9-35 (95)
69 PRK09437 bcp thioredoxin-depen 21.8 88 0.0019 19.2 2.1 15 52-66 121-135 (154)
70 PF12357 PLD_C: Phospholipase 21.7 86 0.0019 18.5 1.9 13 55-67 45-57 (74)
71 cd04338 Rieske_RO_Alpha_Tic55 21.5 1.3E+02 0.0029 18.7 2.9 28 39-66 28-55 (134)
72 TIGR01826 CofD_related conserv 21.2 96 0.0021 22.7 2.5 24 18-45 162-185 (310)
73 cd07044 CofD_YvcK Family of Co 20.6 1E+02 0.0022 22.5 2.5 24 18-45 164-187 (309)
74 cd03479 Rieske_RO_Alpha_PhDO_l 20.3 1.4E+02 0.003 18.8 2.8 29 38-66 31-60 (144)
75 cd03529 Rieske_NirD Assimilato 20.1 1.2E+02 0.0027 17.7 2.4 25 39-63 11-35 (103)
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=1.4e-34 Score=167.10 Aligned_cols=63 Identities=60% Similarity=0.916 Sum_probs=59.4
Q ss_pred CCCCccccccchHHHHHHHHhhCCCCeEEEecCCCccccCccCCcEEEEeCCCCcEEecCcCC
Q 044806 8 KSSWPELVGVEGKVAAETIERENPIVSAHILLEGSIVFLDRYCRRVYVWVDTNGIVVDVPTIG 70 (70)
Q Consensus 8 k~~WpeLVG~~~~~A~~~I~~d~p~~~v~vl~pg~~vTmDyr~dRV~v~vD~~g~V~~vP~vG 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=99.72 E-value=2.5e-18 Score=97.90 Aligned_cols=54 Identities=24% Similarity=0.308 Sum_probs=44.6
Q ss_pred CCCccccccchHHHHHHHHhhCCCCeEEEecCCCccccCccCCcEEEEeCCCCcEEec
Q 044806 9 SSWPELVGVEGKVAAETIERENPIVSAHILLEGSIVFLDRYCRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 9 ~~WpeLVG~~~~~A~~~I~~d~p~~~v~vl~pg~~vTmDyr~dRV~v~vD~~g~V~~v 66 (70)
+....|||++++++...-. ...+||++||+++|||||+|||||++|++|+|+++
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 3456899999876653322 34579999999999999999999999999999975
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=78.45 E-value=1.9 Score=23.30 Aligned_cols=18 Identities=33% Similarity=0.516 Sum_probs=14.9
Q ss_pred ccccccchHHHHHHHHhh
Q 044806 12 PELVGVEGKVAAETIERE 29 (70)
Q Consensus 12 peLVG~~~~~A~~~I~~d 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 899999999999877763
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=71.03 E-value=8.9 Score=19.05 Aligned_cols=17 Identities=35% Similarity=0.569 Sum_probs=14.8
Q ss_pred ccccccchHHHHHHHHh
Q 044806 12 PELVGVEGKVAAETIER 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 78999999999887765
No 5
>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=69.96 E-value=11 Score=19.64 Aligned_cols=48 Identities=21% Similarity=0.120 Sum_probs=27.1
Q ss_pred chHHHHHHHHhhCCCCeEE-EecCC-C-----ccccCc----cCCcEEEEeCCC-CcEEe
Q 044806 18 EGKVAAETIERENPIVSAH-ILLEG-S-----IVFLDR----YCRRVYVWVDTN-GIVVD 65 (70)
Q Consensus 18 ~~~~A~~~I~~d~p~~~v~-vl~pg-~-----~vTmDy----r~dRV~v~vD~~-g~V~~ 65 (70)
+.++|.++.++..|+.... .+.+. . -+.... ......+++|+. |.|..
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 4568888888888887665 44443 2 133222 233456669974 88765
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=63.75 E-value=6.4 Score=19.97 Aligned_cols=18 Identities=28% Similarity=0.486 Sum_probs=15.2
Q ss_pred ccccccchHHHHHHHHhh
Q 044806 12 PELVGVEGKVAAETIERE 29 (70)
Q Consensus 12 peLVG~~~~~A~~~I~~d 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
>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=58.88 E-value=13 Score=21.90 Aligned_cols=29 Identities=24% Similarity=0.337 Sum_probs=21.8
Q ss_pred ecCCCccccCccCCcEEEEeCCCCcEEec
Q 044806 38 LLEGSIVFLDRYCRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 38 l~pg~~vTmDyr~dRV~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 57888888888788888888777766654
No 8
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=55.92 E-value=13 Score=21.40 Aligned_cols=29 Identities=24% Similarity=0.406 Sum_probs=18.9
Q ss_pred ecCCCccccCccCCc---EEE-EeCCCCcEEec
Q 044806 38 LLEGSIVFLDRYCRR---VYV-WVDTNGIVVDV 66 (70)
Q Consensus 38 l~pg~~vTmDyr~dR---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 456676666666655 444 37888888774
No 9
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=55.21 E-value=13 Score=20.95 Aligned_cols=17 Identities=29% Similarity=0.468 Sum_probs=12.1
Q ss_pred CCcEEEEeCCCCcEEec
Q 044806 50 CRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 50 ~dRV~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 44688899999999754
No 10
>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=51.71 E-value=14 Score=18.30 Aligned_cols=18 Identities=28% Similarity=0.366 Sum_probs=14.9
Q ss_pred ccccccchHHHHHHHHhh
Q 044806 12 PELVGVEGKVAAETIERE 29 (70)
Q Consensus 12 peLVG~~~~~A~~~I~~d 29 (70)
|+++|++.++|...+...
T Consensus 3 p~~~g~~~~~a~~~l~~~ 20 (54)
T cd06575 3 PDLTGWSKRDALKLLELL 20 (54)
T ss_pred CCcCCCCHHHHHHHHHHC
Confidence 789999999998777543
No 11
>smart00740 PASTA PASTA domain.
Probab=51.64 E-value=14 Score=19.06 Aligned_cols=19 Identities=16% Similarity=0.438 Sum_probs=15.6
Q ss_pred CCccccccchHHHHHHHHh
Q 044806 10 SWPELVGVEGKVAAETIER 28 (70)
Q Consensus 10 ~WpeLVG~~~~~A~~~I~~ 28 (70)
.=|+|+|++..+|...+..
T Consensus 6 ~vp~~~g~~~~~a~~~l~~ 24 (66)
T smart00740 6 EVPDVIGLSKEEAKKLLKA 24 (66)
T ss_pred eCCCcCCCCHHHHHHHHHH
Confidence 4589999999999877754
No 12
>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=51.54 E-value=30 Score=23.69 Aligned_cols=43 Identities=16% Similarity=0.159 Sum_probs=34.9
Q ss_pred HHHHHhhCCCCeEE--EecCCCccccCccCCcEEEEeCCCCcEEe
Q 044806 23 AETIERENPIVSAH--ILLEGSIVFLDRYCRRVYVWVDTNGIVVD 65 (70)
Q Consensus 23 ~~~I~~d~p~~~v~--vl~pg~~vTmDyr~dRV~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 45788899999887 67666667778999999999999988653
No 13
>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=50.24 E-value=19 Score=25.09 Aligned_cols=29 Identities=24% Similarity=0.516 Sum_probs=20.1
Q ss_pred CCCccccccchHHHHHHHHhhCCCCeEE-EecCC
Q 044806 9 SSWPELVGVEGKVAAETIERENPIVSAH-ILLEG 41 (70)
Q Consensus 9 ~~WpeLVG~~~~~A~~~I~~d~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 3699999999874 55666777443 55555
No 14
>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=49.84 E-value=15 Score=18.44 Aligned_cols=18 Identities=17% Similarity=0.385 Sum_probs=14.9
Q ss_pred ccccccchHHHHHHHHhh
Q 044806 12 PELVGVEGKVAAETIERE 29 (70)
Q Consensus 12 peLVG~~~~~A~~~I~~d 29 (70)
|+++|.+..+|.+.+...
T Consensus 3 p~~~g~~~~~a~~~l~~~ 20 (55)
T cd06576 3 PDVTGKSVEEAKKELKEA 20 (55)
T ss_pred CcccCCCHHHHHHHHHHC
Confidence 789999999998777654
No 15
>PHA03066 Hypothetical protein; Provisional
Probab=48.30 E-value=62 Score=20.54 Aligned_cols=41 Identities=12% Similarity=0.178 Sum_probs=23.4
Q ss_pred hHHHHHHHHhh---CCCC--eEEEecCCCccccCccCCcEEEEeCCC-CcEE
Q 044806 19 GKVAAETIERE---NPIV--SAHILLEGSIVFLDRYCRRVYVWVDTN-GIVV 64 (70)
Q Consensus 19 ~~~A~~~I~~d---~p~~--~v~vl~pg~~vTmDyr~dRV~v~vD~~-g~V~ 64 (70)
...+.++|++. -|-. ++.+..|+.+ .++.|++++|+. |+|+
T Consensus 35 l~~e~~~ik~~d~~~P~~~~t~lF~~~~~~-----~~~~v~~~Yds~~~~Vt 81 (110)
T PHA03066 35 LNRENAIIKQRNDEFPTTLNTIIFTDPETV-----ISTQVNTYYNSSIGTVT 81 (110)
T ss_pred hhHHHHHHHhhhccCCcccceEEecCCCCc-----ccceEEEEEcCcCCeEE
Confidence 33444455552 3322 2345566654 478889998876 5554
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=48.00 E-value=23 Score=20.92 Aligned_cols=29 Identities=17% Similarity=0.217 Sum_probs=20.5
Q ss_pred ecCCCccccCccCCcEEEEeCCCCcEEec
Q 044806 38 LLEGSIVFLDRYCRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 38 l~pg~~vTmDyr~dRV~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 46677777777666777888877776654
No 17
>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=46.68 E-value=12 Score=20.20 Aligned_cols=21 Identities=29% Similarity=0.197 Sum_probs=14.5
Q ss_pred ecCCCccccCccCCcEEEEeC
Q 044806 38 LLEGSIVFLDRYCRRVYVWVD 58 (70)
Q Consensus 38 l~pg~~vTmDyr~dRV~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 18
>KOG0912 consensus Thiol-disulfide isomerase and thioredoxin [Posttranslational modification, protein turnover, chaperones; Energy production and conversion]
Probab=45.60 E-value=25 Score=26.49 Aligned_cols=17 Identities=12% Similarity=0.258 Sum_probs=12.4
Q ss_pred EEecCCCccccCccCCc
Q 044806 36 HILLEGSIVFLDRYCRR 52 (70)
Q Consensus 36 ~vl~pg~~vTmDyr~dR 52 (70)
.+.+-|.++|.+||..|
T Consensus 77 KvfrnG~~~~rEYRg~R 93 (375)
T KOG0912|consen 77 KVFRNGEMMKREYRGQR 93 (375)
T ss_pred eeeeccchhhhhhccch
Confidence 35667778888888776
No 19
>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=45.56 E-value=19 Score=23.37 Aligned_cols=46 Identities=20% Similarity=0.138 Sum_probs=32.4
Q ss_pred CCCCCCCccccccchHHHH---------HHHHhhCCCCeEEEecCCCccccCccCCc
Q 044806 5 CKGKSSWPELVGVEGKVAA---------ETIERENPIVSAHILLEGSIVFLDRYCRR 52 (70)
Q Consensus 5 ~~~k~~WpeLVG~~~~~A~---------~~I~~d~p~~~v~vl~pg~~vTmDyr~dR 52 (70)
|.+.++.-+|-..+..+|. ..+.+..|. ...++-|+.+..||..+.
T Consensus 6 l~g~~s~~~l~~~~l~~~L~~~L~~~~~~~Ld~~aP~--~~~~PsG~~~~I~Y~~~~ 60 (133)
T PF08482_consen 6 LSGVTSLKDLKKLDLLEALRSLLSWEQQQWLDRLAPE--HITLPSGRRIRIDYSDDG 60 (133)
T ss_pred HcCCCCHHHHhcCCHHHHHHHHCCHHHHHHHHHhCCC--eEEcCCCCEEEEEECCCC
Confidence 5566777777777766664 345555554 357788999999998877
No 20
>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=43.35 E-value=36 Score=20.17 Aligned_cols=27 Identities=22% Similarity=0.185 Sum_probs=17.8
Q ss_pred CCCccccCccCCcEEEEeCCCCcEEec
Q 044806 40 EGSIVFLDRYCRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 40 pg~~vTmDyr~dRV~v~vD~~g~V~~v 66 (70)
+|+.++..+....+-|+-+.+|.|..+
T Consensus 13 ~g~~~~~~~~~~~i~v~r~~~g~~~a~ 39 (118)
T cd03469 13 PGDYVTLELGGEPLVLVRDRDGEVRAF 39 (118)
T ss_pred CCCEEEEEECCccEEEEECCCCCEEEE
Confidence 666666666666777777767766553
No 21
>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=42.36 E-value=24 Score=18.98 Aligned_cols=16 Identities=38% Similarity=0.397 Sum_probs=12.0
Q ss_pred cEEEEeCCCCcEEecC
Q 044806 52 RVYVWVDTNGIVVDVP 67 (70)
Q Consensus 52 RV~v~vD~~g~V~~vP 67 (70)
.|.+.+|++|.|..+.
T Consensus 13 ~v~~~i~~~G~v~~~~ 28 (74)
T TIGR01352 13 VVRFTVDADGRVTSVS 28 (74)
T ss_pred EEEEEECCCCCEEEEE
Confidence 4567889999887653
No 22
>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=42.32 E-value=36 Score=20.68 Aligned_cols=29 Identities=14% Similarity=0.339 Sum_probs=20.8
Q ss_pred ecCCCccccCccCCcEEEEeCCCCcEEec
Q 044806 38 LLEGSIVFLDRYCRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 38 l~pg~~vTmDyr~dRV~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 46677777777777788887777777654
No 23
>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=41.58 E-value=38 Score=21.13 Aligned_cols=30 Identities=13% Similarity=0.150 Sum_probs=22.3
Q ss_pred EecCCCccccCccCCcEEEEeCCCCcEEec
Q 044806 37 ILLEGSIVFLDRYCRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 37 vl~pg~~vTmDyr~dRV~v~vD~~g~V~~v 66 (70)
=|++|++.+.+.....+-|+-+++|.+..+
T Consensus 26 el~~g~~~~~~v~g~~l~l~r~~~g~v~A~ 55 (129)
T cd04337 26 DLKMDTMVPFELFGQPWVLFRDEDGTPGCI 55 (129)
T ss_pred HCCCCCeEEEEECCcEEEEEECCCCcEEEE
Confidence 356788888887778888888777776654
No 24
>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=41.28 E-value=23 Score=19.30 Aligned_cols=15 Identities=40% Similarity=0.448 Sum_probs=11.7
Q ss_pred cEEEEeCCCCcEEec
Q 044806 52 RVYVWVDTNGIVVDV 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 367789999988864
No 25
>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=39.43 E-value=24 Score=20.75 Aligned_cols=32 Identities=13% Similarity=0.145 Sum_probs=13.4
Q ss_pred ccchHHHHHHHHhhCCCCeEEEecCCCccccC
Q 044806 16 GVEGKVAAETIERENPIVSAHILLEGSIVFLD 47 (70)
Q Consensus 16 G~~~~~A~~~I~~d~p~~~v~vl~pg~~vTmD 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 55555555555555333334467888766443
No 26
>COG0391 Uncharacterized conserved protein [Function unknown]
Probab=39.31 E-value=30 Score=25.52 Aligned_cols=25 Identities=20% Similarity=0.214 Sum_probs=18.6
Q ss_pred chHHHHHHHHhhCCCCeEEEecCCCcccc
Q 044806 18 EGKVAAETIERENPIVSAHILLEGSIVFL 46 (70)
Q Consensus 18 ~~~~A~~~I~~d~p~~~v~vl~pg~~vTm 46 (70)
...+|.++|++ +..+++-|||.+|-
T Consensus 179 a~~eaveAI~~----AD~IviGPgSl~TS 203 (323)
T COG0391 179 AAPEAVEAIKE----ADLIVIGPGSLFTS 203 (323)
T ss_pred CCHHHHHHHHh----CCEEEEcCCccHhh
Confidence 34566777776 36789999999873
No 27
>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=37.31 E-value=45 Score=19.23 Aligned_cols=28 Identities=7% Similarity=-0.027 Sum_probs=16.0
Q ss_pred cCCCccccCccCCcEEEEeCCCCcEEec
Q 044806 39 LEGSIVFLDRYCRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 39 ~pg~~vTmDyr~dRV~v~vD~~g~V~~v 66 (70)
++|......+....+-|+-+++|.+..+
T Consensus 11 ~~~~~~~~~~~g~~i~l~r~~~g~~~A~ 38 (98)
T cd03530 11 PPRGARKVQTGGGEIAVFRTADDEVFAL 38 (98)
T ss_pred CCCCcEEEEECCEEEEEEEeCCCCEEEE
Confidence 4555544455556666776666665543
No 28
>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=35.52 E-value=71 Score=16.74 Aligned_cols=43 Identities=21% Similarity=0.196 Sum_probs=29.1
Q ss_pred HHHHHHhhCCCCeEE-EecCC------CccccCccCCcEEEEeCCCCcEE
Q 044806 22 AAETIERENPIVSAH-ILLEG------SIVFLDRYCRRVYVWVDTNGIVV 64 (70)
Q Consensus 22 A~~~I~~d~p~~~v~-vl~pg------~~vTmDyr~dRV~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 456888889999764 22221 23445566789999999999763
No 29
>PHA02087 hypothetical protein
Probab=33.12 E-value=54 Score=19.45 Aligned_cols=22 Identities=18% Similarity=0.422 Sum_probs=15.9
Q ss_pred CccCCcEEE--EeCCCCcEEecCc
Q 044806 47 DRYCRRVYV--WVDTNGIVVDVPT 68 (70)
Q Consensus 47 Dyr~dRV~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 466666543 4899999999873
No 30
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=32.11 E-value=50 Score=21.99 Aligned_cols=22 Identities=18% Similarity=0.253 Sum_probs=17.3
Q ss_pred ccCccCCcEEEEeCCCCcEEec
Q 044806 45 FLDRYCRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 45 TmDyr~dRV~v~vD~~g~V~~v 66 (70)
..=-.+..++|+.|+.|.|+.+
T Consensus 116 ~qLr~~kiltVh~De~G~Ii~V 137 (153)
T PRK14584 116 AQLKSGSCLTLYNDEHGHIIDV 137 (153)
T ss_pred HHHHhCCeEEEEECCCCCEEEe
Confidence 3334577889999999999887
No 31
>PF13994 PgaD: PgaD-like protein
Probab=31.36 E-value=34 Score=21.70 Aligned_cols=18 Identities=22% Similarity=0.397 Sum_probs=14.2
Q ss_pred ccCCcEEEEeCCCCcEEe
Q 044806 48 RYCRRVYVWVDTNGIVVD 65 (70)
Q Consensus 48 yr~dRV~v~vD~~g~V~~ 65 (70)
=++..+.|+.|++|.|++
T Consensus 121 r~~k~~~V~~d~~G~I~~ 138 (138)
T PF13994_consen 121 RQAKVLTVHHDDHGRIIH 138 (138)
T ss_pred HhCCeEEEEeCCCCCcCc
Confidence 357788999999998863
No 32
>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=31.16 E-value=57 Score=17.88 Aligned_cols=19 Identities=26% Similarity=0.538 Sum_probs=15.6
Q ss_pred ccCCcEEEEeCCCCcEEec
Q 044806 48 RYCRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 48 yr~dRV~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 4467899999999999864
No 33
>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=30.91 E-value=55 Score=20.33 Aligned_cols=16 Identities=31% Similarity=0.287 Sum_probs=13.4
Q ss_pred CcEEEEeCCCCcEEec
Q 044806 51 RRVYVWVDTNGIVVDV 66 (70)
Q Consensus 51 dRV~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 4579999999999864
No 34
>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=30.65 E-value=25 Score=18.60 Aligned_cols=18 Identities=22% Similarity=0.050 Sum_probs=10.0
Q ss_pred cCCCccccCccCCcEEEE
Q 044806 39 LEGSIVFLDRYCRRVYVW 56 (70)
Q Consensus 39 ~pg~~vTmDyr~dRV~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 456666666666655554
No 35
>PRK13320 pantothenate kinase; Reviewed
Probab=30.09 E-value=58 Score=22.58 Aligned_cols=38 Identities=16% Similarity=0.126 Sum_probs=28.1
Q ss_pred CccccccchHHHHHHHHhhCCCCeEEEecCCCccccCc
Q 044806 11 WPELVGVEGKVAAETIERENPIVSAHILLEGSIVFLDR 48 (70)
Q Consensus 11 WpeLVG~~~~~A~~~I~~d~p~~~v~vl~pg~~vTmDy 48 (70)
=|+-+|.+--.+.....+..++-...|+--|++.|.|+
T Consensus 92 ~p~~lG~DR~~~~~aa~~~~~~~~~lVID~GTA~Tid~ 129 (244)
T PRK13320 92 TPETLGADRLALCAGARYLFPGKNVLAIDAGTAITYDV 129 (244)
T ss_pred ChhhcchhHHHHHHHHHHhcCCCCEEEEEcCCceEEEE
Confidence 35778888766665555555555578999999999996
No 36
>PRK03760 hypothetical protein; Provisional
Probab=30.05 E-value=41 Score=20.99 Aligned_cols=13 Identities=38% Similarity=0.657 Sum_probs=11.5
Q ss_pred EEEeCCCCcEEec
Q 044806 54 YVWVDTNGIVVDV 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 37
>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=29.81 E-value=53 Score=23.99 Aligned_cols=24 Identities=13% Similarity=0.116 Sum_probs=17.7
Q ss_pred hHHHHHHHHhhCCCCeEEEecCCCcccc
Q 044806 19 GKVAAETIERENPIVSAHILLEGSIVFL 46 (70)
Q Consensus 19 ~~~A~~~I~~d~p~~~v~vl~pg~~vTm 46 (70)
..+|.++|++. .+++|.||+++|-
T Consensus 173 ~peal~AI~~A----D~IIlGPgsp~TS 196 (297)
T TIGR01819 173 APKVLEAIRKE----DNILIGPSNPITS 196 (297)
T ss_pred CHHHHHHHHhC----CEEEECCCccHHH
Confidence 45666677763 4789999999874
No 38
>KOG0544 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=29.71 E-value=91 Score=19.63 Aligned_cols=27 Identities=15% Similarity=0.074 Sum_probs=22.7
Q ss_pred CCeEEEecCCCccccCccCCcEEEEeC
Q 044806 32 IVSAHILLEGSIVFLDRYCRRVYVWVD 58 (70)
Q Consensus 32 ~~~v~vl~pg~~vTmDyr~dRV~v~vD 58 (70)
++...+|.||+-.|.-=+.+.|.+++-
T Consensus 2 Gv~~~~i~~Gdg~tfpK~Gqtvt~hYt 28 (108)
T KOG0544|consen 2 GVEKQVISPGDGRTFPKKGQTVTVHYT 28 (108)
T ss_pred CceeEEeeCCCCcccCCCCCEEEEEEE
Confidence 356779999999999999999999853
No 39
>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=29.69 E-value=57 Score=14.94 Aligned_cols=20 Identities=30% Similarity=0.363 Sum_probs=14.9
Q ss_pred EecCCCccccCccCCcEEEE
Q 044806 37 ILLEGSIVFLDRYCRRVYVW 56 (70)
Q Consensus 37 vl~pg~~vTmDyr~dRV~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 44677777788888888775
No 40
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=28.75 E-value=45 Score=20.24 Aligned_cols=13 Identities=31% Similarity=0.713 Sum_probs=10.4
Q ss_pred EEEeCCCCcEEec
Q 044806 54 YVWVDTNGIVVDV 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 41
>PRK11548 outer membrane biogenesis protein BamE; Provisional
Probab=28.70 E-value=60 Score=19.88 Aligned_cols=17 Identities=6% Similarity=0.366 Sum_probs=14.3
Q ss_pred CCcEEEEeCCCCcEEec
Q 044806 50 CRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 50 ~dRV~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 45788999999999876
No 42
>PF06519 TolA: TolA C-terminal; InterPro: IPR014161 TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cut-offs are based largely on conserved operon structure. The Tol-Pal complex is required for maintaining outer membrane integrity, and is also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins OmpC, PhoE and LamB.; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2X9A_D 3QDP_A 3QDR_A 1TOL_A 1S62_A.
Probab=28.51 E-value=46 Score=20.11 Aligned_cols=17 Identities=29% Similarity=0.489 Sum_probs=13.6
Q ss_pred CCcEEEEeCCCCcEEec
Q 044806 50 CRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 50 ~dRV~v~vD~~g~V~~v 66 (70)
.-+|+|.+..+|.|..+
T Consensus 38 ~C~v~i~l~~dG~v~~v 54 (96)
T PF06519_consen 38 ECRVRIRLAPDGLVLSV 54 (96)
T ss_dssp -EEEEEEEETTSEEEEE
T ss_pred EEEEEEEECCCCcEEEe
Confidence 44788899999999876
No 43
>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=28.32 E-value=23 Score=17.73 Aligned_cols=20 Identities=15% Similarity=0.111 Sum_probs=14.7
Q ss_pred cccCccCCcEEEEeCCCCcE
Q 044806 44 VFLDRYCRRVYVWVDTNGIV 63 (70)
Q Consensus 44 vTmDyr~dRV~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 45678889999999877654
No 44
>PRK13328 pantothenate kinase; Reviewed
Probab=28.22 E-value=57 Score=22.80 Aligned_cols=38 Identities=18% Similarity=0.106 Sum_probs=29.3
Q ss_pred ccccccchHHHHHHHHhhCCCCeEEEecCCCccccCcc
Q 044806 12 PELVGVEGKVAAETIERENPIVSAHILLEGSIVFLDRY 49 (70)
Q Consensus 12 peLVG~~~~~A~~~I~~d~p~~~v~vl~pg~~vTmDyr 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 67789888777665555566656789999999999963
No 45
>PF13028 DUF3889: Protein of unknown function (DUF3889)
Probab=28.18 E-value=1.4e+02 Score=18.40 Aligned_cols=42 Identities=17% Similarity=0.336 Sum_probs=27.8
Q ss_pred hHHHHHHHHhhCCCCeEE-EecCCCccccCc-cCCcEEEEeCCC
Q 044806 19 GKVAAETIERENPIVSAH-ILLEGSIVFLDR-YCRRVYVWVDTN 60 (70)
Q Consensus 19 ~~~A~~~I~~d~p~~~v~-vl~pg~~vTmDy-r~dRV~v~vD~~ 60 (70)
+.-|...++++.|++.+. .+..|..---|- -.+.-.|++.++
T Consensus 27 grlA~~~~k~~Yp~a~v~DY~~vGr~~~~~~~t~e~Fkl~l~~~ 70 (97)
T PF13028_consen 27 GRLAVQETKEKYPGAEVVDYLYVGRTKVNDEQTVEKFKLWLREG 70 (97)
T ss_pred HHHHHHHHHHHCCCCEEeeeeeecceecCCcceEEEEEEEEEcC
Confidence 345778899999999987 777777533333 455555555544
No 46
>COG1430 Uncharacterized conserved protein [Function unknown]
Probab=27.09 E-value=52 Score=21.12 Aligned_cols=13 Identities=38% Similarity=0.930 Sum_probs=11.0
Q ss_pred EEEeCCCCcEEec
Q 044806 54 YVWVDTNGIVVDV 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 47
>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=25.72 E-value=76 Score=19.95 Aligned_cols=28 Identities=11% Similarity=0.057 Sum_probs=17.0
Q ss_pred cCCCccccCccCCcEEEEeCC-CCcEEec
Q 044806 39 LEGSIVFLDRYCRRVYVWVDT-NGIVVDV 66 (70)
Q Consensus 39 ~pg~~vTmDyr~dRV~v~vD~-~g~V~~v 66 (70)
++|++.+.++....+-|+-|. +|.+..+
T Consensus 28 ~~g~~~~~~~~g~~i~v~r~~~dG~~~A~ 56 (138)
T cd03480 28 DPSRPTPFTLLGRDLVIWWDRNSQQWRAF 56 (138)
T ss_pred CCCCcEEEEECCeeEEEEEECCCCEEEEE
Confidence 556666666666666666654 6665543
No 48
>PLN03213 repressor of silencing 3; Provisional
Probab=25.33 E-value=17 Score=29.08 Aligned_cols=18 Identities=28% Similarity=0.383 Sum_probs=14.9
Q ss_pred CCCCCCCccccccchHHH
Q 044806 5 CKGKSSWPELVGVEGKVA 22 (70)
Q Consensus 5 ~~~k~~WpeLVG~~~~~A 22 (70)
-.+|++|-||||.....+
T Consensus 324 WSQKSSWreLvg~~~nn~ 341 (759)
T PLN03213 324 WSQKSSWKSLMANGNSND 341 (759)
T ss_pred hhhcchHHHHhccCCCCc
Confidence 458999999999987655
No 49
>PRK00522 tpx lipid hydroperoxide peroxidase; Provisional
Probab=25.06 E-value=67 Score=20.50 Aligned_cols=17 Identities=29% Similarity=0.210 Sum_probs=14.1
Q ss_pred CCcEEEEeCCCCcEEec
Q 044806 50 CRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 50 ~dRV~v~vD~~g~V~~v 66 (70)
+.|-.+.+|.+|+|..+
T Consensus 130 ~~r~tfvId~~G~I~~~ 146 (167)
T PRK00522 130 LARAVFVLDENNKVVYS 146 (167)
T ss_pred eeeEEEEECCCCeEEEE
Confidence 35788999999999875
No 50
>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=24.99 E-value=75 Score=23.27 Aligned_cols=26 Identities=19% Similarity=0.040 Sum_probs=19.0
Q ss_pred cchHHHHHHHHhhCCCCeEEEecCCCcccc
Q 044806 17 VEGKVAAETIERENPIVSAHILLEGSIVFL 46 (70)
Q Consensus 17 ~~~~~A~~~I~~d~p~~~v~vl~pg~~vTm 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 4455667777763 4789999998874
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=24.96 E-value=22 Score=18.64 Aligned_cols=14 Identities=14% Similarity=0.048 Sum_probs=10.3
Q ss_pred cCCC--ccccCccCCc
Q 044806 39 LEGS--IVFLDRYCRR 52 (70)
Q Consensus 39 ~pg~--~vTmDyr~dR 52 (70)
.||. +.||||+.+-
T Consensus 20 ~pg~wfa~t~df~k~~ 35 (42)
T PF06633_consen 20 EPGTWFADTMDFRKKH 35 (42)
T ss_pred CCCchhhhhhhhhhhh
Confidence 4565 7899998764
No 52
>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=24.73 E-value=35 Score=21.73 Aligned_cols=18 Identities=11% Similarity=-0.189 Sum_probs=14.7
Q ss_pred eEEEecCCCccccCccCC
Q 044806 34 SAHILLEGSIVFLDRYCR 51 (70)
Q Consensus 34 ~v~vl~pg~~vTmDyr~d 51 (70)
.++.++||-+++-||-+|
T Consensus 85 evE~~~Pg~P~~hD~epD 102 (112)
T PF08882_consen 85 EVEAPPPGYPPIHDFEPD 102 (112)
T ss_pred EEccCCCCCCceEecccC
Confidence 356889999999998876
No 53
>PRK09510 tolA cell envelope integrity inner membrane protein TolA; Provisional
Probab=24.29 E-value=64 Score=24.42 Aligned_cols=16 Identities=13% Similarity=0.385 Sum_probs=14.0
Q ss_pred CcEEEEeCCCCcEEec
Q 044806 51 RRVYVWVDTNGIVVDV 66 (70)
Q Consensus 51 dRV~v~vD~~g~V~~v 66 (70)
-+|+|.++++|.|+.+
T Consensus 328 c~VrI~LapDG~V~sV 343 (387)
T PRK09510 328 CTLRIKLAPDGTLLDI 343 (387)
T ss_pred EEEEEEEcCCCcEEee
Confidence 5689999999999976
No 54
>COG1596 Wza Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]
Probab=24.20 E-value=74 Score=21.97 Aligned_cols=41 Identities=12% Similarity=0.003 Sum_probs=28.8
Q ss_pred cccccchHHHHHHHHhhCCCCeEEEecCCCcccc-CccCCcEEEE
Q 044806 13 ELVGVEGKVAAETIERENPIVSAHILLEGSIVFL-DRYCRRVYVW 56 (70)
Q Consensus 13 eLVG~~~~~A~~~I~~d~p~~~v~vl~pg~~vTm-Dyr~dRV~v~ 56 (70)
...|++..+....|...... ....|...|++ .||+.+|.|-
T Consensus 89 ~vaG~T~~el~~~I~~~L~~---~~~~P~v~V~v~~~rp~~v~V~ 130 (239)
T COG1596 89 PVAGKTLEELQSEIADRLAG---YLVNPQVSVEVAQYRPQKVFVS 130 (239)
T ss_pred EecCCCHHHHHHHHHHHHHh---hccCCCeEEEEcccCCcEEEEe
Confidence 45788888888888776555 34466666665 7888877774
No 55
>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=24.16 E-value=81 Score=18.86 Aligned_cols=20 Identities=35% Similarity=0.399 Sum_probs=13.2
Q ss_pred HHHHHhhCCCCeEEEecCCCcc
Q 044806 23 AETIERENPIVSAHILLEGSIV 44 (70)
Q Consensus 23 ~~~I~~d~p~~~v~vl~pg~~v 44 (70)
.++|.+|||++ .|...+.++
T Consensus 18 veai~~dNP~v--~V~d~~a~v 37 (87)
T PF02406_consen 18 VEAIEEDNPGV--TVEDRPAYV 37 (87)
T ss_dssp HHHHHHHSSTE--EEEEESSEE
T ss_pred HHHHHhhCCCe--EEEecCCEE
Confidence 57899999994 344444443
No 56
>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=23.90 E-value=88 Score=22.57 Aligned_cols=24 Identities=29% Similarity=0.231 Sum_probs=14.6
Q ss_pred hHHHHHHHHhhCCCCeEEEecCCCcccc
Q 044806 19 GKVAAETIERENPIVSAHILLEGSIVFL 46 (70)
Q Consensus 19 ~~~A~~~I~~d~p~~~v~vl~pg~~vTm 46 (70)
..+|.++|++. ..+++.||+++|-
T Consensus 174 ~p~~l~AI~~A----D~IiigPgs~~TS 197 (300)
T PF01933_consen 174 NPEALEAIEEA----DLIIIGPGSLYTS 197 (300)
T ss_dssp -HHHHHHHHH-----SEEEE-SS-CCCC
T ss_pred CHHHHHHHHhC----CEEEEcCCCchhh
Confidence 44566677763 5789999998873
No 57
>PRK13321 pantothenate kinase; Reviewed
Probab=23.87 E-value=83 Score=21.64 Aligned_cols=38 Identities=24% Similarity=0.191 Sum_probs=26.3
Q ss_pred CccccccchHHHHHHHHhhCCCCeEEEecCCCccccCc
Q 044806 11 WPELVGVEGKVAAETIERENPIVSAHILLEGSIVFLDR 48 (70)
Q Consensus 11 WpeLVG~~~~~A~~~I~~d~p~~~v~vl~pg~~vTmDy 48 (70)
=|+-+|.+--.+.....+..++....|+--|++.|.|+
T Consensus 102 ~P~~lG~DR~a~~~aa~~~~~~~~~lvid~GTA~T~d~ 139 (256)
T PRK13321 102 NPREVGADRIVNAVAARRLYPDRNLIVVDFGTATTFDC 139 (256)
T ss_pred ChhhccHHHHHHHHHHHHHcCCCCEEEEECCCceEEEE
Confidence 36778888555544444445553567899999999996
No 58
>PRK11251 DNA-binding transcriptional activator OsmE; Provisional
Probab=23.83 E-value=87 Score=19.54 Aligned_cols=17 Identities=24% Similarity=0.327 Sum_probs=14.4
Q ss_pred CCcEEEEeCCCCcEEec
Q 044806 50 CRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 50 ~dRV~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 56789999999999874
No 59
>COG5428 Uncharacterized conserved small protein [Function unknown]
Probab=23.53 E-value=1.6e+02 Score=17.11 Aligned_cols=29 Identities=24% Similarity=0.314 Sum_probs=21.7
Q ss_pred ecCC-CccccCccCCcEEEEeCCCCcEEec
Q 044806 38 LLEG-SIVFLDRYCRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 38 l~pg-~~vTmDyr~dRV~v~vD~~g~V~~v 66 (70)
+.+| +...+.==.+-+.|.+|.+|+|.-+
T Consensus 16 ~~~~~~~~dt~e~~edi~Idide~GkV~Gi 45 (69)
T COG5428 16 LEEGKVVEDTIELGEDILIDIDENGKVIGI 45 (69)
T ss_pred EecCcceeehhhcCCcEEEEecCCCcEEEE
Confidence 3444 6777766677899999999998754
No 60
>PF00899 ThiF: ThiF family; InterPro: IPR000594 Ubiquitin-activating enzyme (E1 enzyme) [, ] activates ubiquitin by first adenylating with ATP its C-terminal glycine residue and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thiolester and free AMP. Later the ubiquitin moiety is transferred to a cysteine residue on one of the many forms of ubiquitin- conjugating enzymes (E2). The family of ubiquitin-activating enzymes shares in its catalytic domain significant similarity with a large family of NAD/FAD-binding proteins. This domain is based on the common NAD/FAD-binding fold and finds members of several families, including UBA ubiquitin activating enzymes; the hesA/moeB/thiF family; NADH peroxidases; the LDH family; sarcosin oxidase; phytoene dehydrogenases; alanine dehydrogenases; hydroxyacyl-CoA dehydrogenases and many other NAD/FAD dependent dehydrogenases and oxidases.; GO: 0003824 catalytic activity; PDB: 1ZKM_D 1ZUD_3 1ZFN_D 1R4M_G 2NVU_A 1R4N_C 3DBR_A 3DBH_C 3DBL_G 1YOV_A ....
Probab=22.86 E-value=1.8e+02 Score=17.61 Aligned_cols=30 Identities=30% Similarity=0.295 Sum_probs=22.4
Q ss_pred ccccccchHHH-HHHHHhhCCCCeEEEecCC
Q 044806 12 PELVGVEGKVA-AETIERENPIVSAHILLEG 41 (70)
Q Consensus 12 peLVG~~~~~A-~~~I~~d~p~~~v~vl~pg 41 (70)
++-+|++-.+| ++.+.+.+|.+++..++..
T Consensus 50 ~~~vG~~Ka~~~~~~l~~~np~~~v~~~~~~ 80 (135)
T PF00899_consen 50 EEDVGKNKAEAAKERLQEINPDVEVEAIPEK 80 (135)
T ss_dssp GGGTTSBHHHHHHHHHHHHSTTSEEEEEESH
T ss_pred cccchhHHHHHHHHHHHHhcCceeeeeeecc
Confidence 46789885555 5689999999998765543
No 61
>KOG4442 consensus Clathrin coat binding protein/Huntingtin interacting protein HIP1, involved in regulation of endocytosis [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.77 E-value=32 Score=28.17 Aligned_cols=17 Identities=18% Similarity=0.309 Sum_probs=15.5
Q ss_pred EEecCCCccccCccCCc
Q 044806 36 HILLEGSIVFLDRYCRR 52 (70)
Q Consensus 36 ~vl~pg~~vTmDyr~dR 52 (70)
++|+||.-.|.||+-+|
T Consensus 224 k~I~~GEEITFDYqf~r 240 (729)
T KOG4442|consen 224 KVIKPGEEITFDYQFDR 240 (729)
T ss_pred cccCCCceeeEeccccc
Confidence 58999999999999876
No 62
>COG1225 Bcp Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=22.76 E-value=82 Score=20.85 Aligned_cols=18 Identities=22% Similarity=0.204 Sum_probs=15.9
Q ss_pred cCCcEEEEeCCCCcEEec
Q 044806 49 YCRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 49 r~dRV~v~vD~~g~V~~v 66 (70)
-..|....+|++|+|..+
T Consensus 118 ~~~R~TfvId~dG~I~~~ 135 (157)
T COG1225 118 GIERSTFVIDPDGKIRYV 135 (157)
T ss_pred cccceEEEECCCCeEEEE
Confidence 378999999999999875
No 63
>COG2815 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.56 E-value=2.3e+02 Score=20.62 Aligned_cols=22 Identities=18% Similarity=0.283 Sum_probs=19.0
Q ss_pred CCCCCccccccchHHHHHHHHh
Q 044806 7 GKSSWPELVGVEGKVAAETIER 28 (70)
Q Consensus 7 ~k~~WpeLVG~~~~~A~~~I~~ 28 (70)
.+..=|+++|.+.++|.+.++.
T Consensus 91 ~~~~vpdv~Gl~~~eA~~~L~~ 112 (303)
T COG2815 91 QYITVPDVVGLTIEEAVAKLKA 112 (303)
T ss_pred cceecCcccCCcHHHHHHHHHH
Confidence 4457799999999999988887
No 64
>PRK13606 LPPG:FO 2-phospho-L-lactate transferase; Provisional
Probab=22.54 E-value=89 Score=22.90 Aligned_cols=25 Identities=24% Similarity=0.106 Sum_probs=18.2
Q ss_pred chHHHHHHHHhhCCCCeEEEecCCCcccc
Q 044806 18 EGKVAAETIERENPIVSAHILLEGSIVFL 46 (70)
Q Consensus 18 ~~~~A~~~I~~d~p~~~v~vl~pg~~vTm 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 455666777653 4789999998874
No 65
>PF14339 DUF4394: Domain of unknown function (DUF4394)
Probab=22.53 E-value=1.1e+02 Score=21.70 Aligned_cols=21 Identities=24% Similarity=0.167 Sum_probs=16.2
Q ss_pred ecCCCccccCccC--CcEEEEeC
Q 044806 38 LLEGSIVFLDRYC--RRVYVWVD 58 (70)
Q Consensus 38 l~pg~~vTmDyr~--dRV~v~vD 58 (70)
-..|..+..|||| ||+||.-+
T Consensus 71 al~g~~~gvDFNP~aDRlRvvs~ 93 (236)
T PF14339_consen 71 ALSGTAFGVDFNPAADRLRVVSN 93 (236)
T ss_pred cccCceEEEecCcccCcEEEEcc
Confidence 3557788889997 89998744
No 66
>PF02575 YbaB_DNA_bd: YbaB/EbfC DNA-binding family; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta []. YbaB is co-transcribed with RecR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.; PDB: 1PUG_B 3F42_B 1YBX_B 1J8B_A.
Probab=22.17 E-value=78 Score=18.23 Aligned_cols=15 Identities=53% Similarity=0.578 Sum_probs=10.7
Q ss_pred cEEEEeCCCCcEEec
Q 044806 52 RVYVWVDTNGIVVDV 66 (70)
Q Consensus 52 RV~v~vD~~g~V~~v 66 (70)
-|+|.+|.+|.|..+
T Consensus 31 ~V~V~v~g~g~v~~i 45 (93)
T PF02575_consen 31 LVTVTVNGNGEVVDI 45 (93)
T ss_dssp TEEEEEETTS-EEEE
T ss_pred EEEEEEecCceEEEE
Confidence 567888888888765
No 67
>TIGR02540 gpx7 putative glutathione peroxidase Gpx7. This model represents one of several families of known and probable glutathione peroxidases. This family is restricted to animals and designated GPX7.
Probab=21.98 E-value=94 Score=19.24 Aligned_cols=16 Identities=25% Similarity=0.196 Sum_probs=13.4
Q ss_pred CcEEEEeCCCCcEEec
Q 044806 51 RRVYVWVDTNGIVVDV 66 (70)
Q Consensus 51 dRV~v~vD~~g~V~~v 66 (70)
+|-.+.+|.+|+|...
T Consensus 120 ~~~tflID~~G~v~~~ 135 (153)
T TIGR02540 120 NFWKYLVNPEGQVVKF 135 (153)
T ss_pred ccEEEEEcCCCcEEEE
Confidence 5668999999999874
No 68
>cd03478 Rieske_AIFL_N AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. AIFL shares 35% homology with human AIF (apoptosis-inducing factor), mainly in the Pyr_redox domain. AIFL is predominantly localized to the mitochondria. AIFL induces apoptosis in a caspase-dependent manner.
Probab=21.97 E-value=1.1e+02 Score=17.50 Aligned_cols=27 Identities=22% Similarity=0.149 Sum_probs=15.6
Q ss_pred ecCCCccccCccCCcEEEEeCCCCcEEe
Q 044806 38 LLEGSIVFLDRYCRRVYVWVDTNGIVVD 65 (70)
Q Consensus 38 l~pg~~vTmDyr~dRV~v~vD~~g~V~~ 65 (70)
|++|++...++....|-|+-+ +|.+..
T Consensus 9 l~~g~~~~~~~~~~~v~v~r~-~g~~~A 35 (95)
T cd03478 9 LGDGEMKEVDVGDGKVLLVRQ-GGEVHA 35 (95)
T ss_pred CCCCCEEEEEeCCcEEEEEEE-CCEEEE
Confidence 456666666666666666544 455443
No 69
>PRK09437 bcp thioredoxin-dependent thiol peroxidase; Reviewed
Probab=21.77 E-value=88 Score=19.20 Aligned_cols=15 Identities=27% Similarity=0.565 Sum_probs=12.9
Q ss_pred cEEEEeCCCCcEEec
Q 044806 52 RVYVWVDTNGIVVDV 66 (70)
Q Consensus 52 RV~v~vD~~g~V~~v 66 (70)
|..+.+|++|+|...
T Consensus 121 ~~~~lid~~G~i~~~ 135 (154)
T PRK09437 121 RISFLIDADGKIEHV 135 (154)
T ss_pred eEEEEECCCCEEEEE
Confidence 677899999999875
No 70
>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=21.75 E-value=86 Score=18.47 Aligned_cols=13 Identities=46% Similarity=0.703 Sum_probs=10.8
Q ss_pred EEeCCCCcEEecC
Q 044806 55 VWVDTNGIVVDVP 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 5588999999876
No 71
>cd04338 Rieske_RO_Alpha_Tic55 Tic55 is a 55kDa LLS1-related non-heme iron oxygenase associated with protein transport through the plant inner chloroplast membrane. This domain represents the N-terminal Rieske domain of the Tic55 oxygenase alpha subunit. Tic55 is closely related to 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), Ptc52, 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.
Probab=21.47 E-value=1.3e+02 Score=18.71 Aligned_cols=28 Identities=18% Similarity=0.161 Sum_probs=16.0
Q ss_pred cCCCccccCccCCcEEEEeCCCCcEEec
Q 044806 39 LEGSIVFLDRYCRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 39 ~pg~~vTmDyr~dRV~v~vD~~g~V~~v 66 (70)
++|...+.+.....+-|+-|.+|.+..+
T Consensus 28 ~~~~~~~~~v~g~~ivl~r~~~G~v~A~ 55 (134)
T cd04338 28 PTDAPLGLSVYDEPFVLFRDQNGQLRCL 55 (134)
T ss_pred CCCCCEEEEECCceEEEEEcCCCCEEEE
Confidence 4555555555556666666666666543
No 72
>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=21.18 E-value=96 Score=22.68 Aligned_cols=24 Identities=29% Similarity=0.231 Sum_probs=17.0
Q ss_pred chHHHHHHHHhhCCCCeEEEecCCCccc
Q 044806 18 EGKVAAETIERENPIVSAHILLEGSIVF 45 (70)
Q Consensus 18 ~~~~A~~~I~~d~p~~~v~vl~pg~~vT 45 (70)
...+|.++|++ +..+++.|||..|
T Consensus 162 a~~~al~AI~~----ADlIvlgPGSlyT 185 (310)
T TIGR01826 162 ALREAVEAIRE----ADLIILGPGSLYT 185 (310)
T ss_pred CCHHHHHHHHh----CCEEEECCCcCHH
Confidence 34566667765 3578999999866
No 73
>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=20.55 E-value=1e+02 Score=22.48 Aligned_cols=24 Identities=21% Similarity=0.299 Sum_probs=16.7
Q ss_pred chHHHHHHHHhhCCCCeEEEecCCCccc
Q 044806 18 EGKVAAETIERENPIVSAHILLEGSIVF 45 (70)
Q Consensus 18 ~~~~A~~~I~~d~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 344566667663 478999999876
No 74
>cd03479 Rieske_RO_Alpha_PhDO_like Rieske non-heme iron oxygenase (RO) family, Phthalate 4,5-dioxygenase (PhDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of PhDO and similar proteins including 3-chlorobenzoate 3,4-dioxygenase (CBDO), phenoxybenzoate dioxygenase (POB-dioxygenase) and 3-nitrobenzoate oxygenase (MnbA). 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. PhDO and CBDO are two-component RO systems, containing oxygenase and reductase components. PhDO catalyzes the dihydroxylation of phthalate to form th
Probab=20.25 E-value=1.4e+02 Score=18.81 Aligned_cols=29 Identities=24% Similarity=0.229 Sum_probs=18.8
Q ss_pred ec-CCCccccCccCCcEEEEeCCCCcEEec
Q 044806 38 LL-EGSIVFLDRYCRRVYVWVDTNGIVVDV 66 (70)
Q Consensus 38 l~-pg~~vTmDyr~dRV~v~vD~~g~V~~v 66 (70)
|+ +|+..+..+....+-|+-+.+|.+..+
T Consensus 31 L~~~g~~~~~~~~g~~i~v~r~~~G~v~A~ 60 (144)
T cd03479 31 LTEDGQPVRVRLLGEDLVAFRDTSGRVGLL 60 (144)
T ss_pred CCCCCCEEEEEECCcEEEEEEeCCCCEEEE
Confidence 45 577666666666677777777766554
No 75
>cd03529 Rieske_NirD Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while fungal proteins have a C-terminal Rieske domain in addition to several other domains. The fungal NirD is involved in nutrient acquisition, functioning at the soil/fungus interface to control nutrient exchange between the fungus and the host plant. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The Rieske [2Fe-2S] cluster is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In this family, only a few members contain these residues. Other members may have lost the ability to bind the Rieske [2Fe-2S] cluster.
Probab=20.08 E-value=1.2e+02 Score=17.67 Aligned_cols=25 Identities=16% Similarity=-0.113 Sum_probs=11.7
Q ss_pred cCCCccccCccCCcEEEEeCCCCcE
Q 044806 39 LEGSIVFLDRYCRRVYVWVDTNGIV 63 (70)
Q Consensus 39 ~pg~~vTmDyr~dRV~v~vD~~g~V 63 (70)
++|..+.......++-|+.+.+|.+
T Consensus 11 ~~g~~~~~~~~g~~i~l~r~~~g~~ 35 (103)
T cd03529 11 PPGSGVAALVGDTQIAIFRLPGREV 35 (103)
T ss_pred CCCCcEEEEECCEEEEEEEeCCCeE
Confidence 3444444444444555555544444
Done!