Query 040548
Match_columns 71
No_of_seqs 106 out of 366
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 09:29:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040548.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040548hhsearch_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 4.1E-33 8.9E-38 161.0 5.9 63 9-71 1-63 (63)
2 PF11720 Inhibitor_I78: Peptid 99.8 5.3E-20 1.1E-24 104.9 2.8 56 8-67 2-57 (60)
3 PF03793 PASTA: PASTA domain; 75.9 2.8 6.1E-05 22.6 2.1 19 12-30 3-21 (63)
4 cd06573 PASTA PASTA domain. Th 63.6 17 0.00037 18.0 3.6 18 12-29 2-19 (53)
5 cd06577 PASTA_pknB PASTA domai 60.0 9.3 0.0002 19.4 2.0 19 12-30 2-20 (62)
6 PF03413 PepSY: Peptidase prop 50.3 36 0.00079 17.6 3.7 48 19-66 3-62 (64)
7 PF13103 TonB_2: TonB C termin 48.1 21 0.00047 20.0 2.4 18 50-67 26-43 (85)
8 cd03477 Rieske_YhfW_C YhfW fam 47.8 31 0.00066 20.3 3.1 28 39-66 8-35 (91)
9 smart00740 PASTA PASTA domain. 47.6 19 0.00042 18.5 2.0 21 10-30 5-25 (66)
10 cd06575 PASTA_Pbp2x-like_2 PAS 47.5 20 0.00043 17.7 2.0 19 12-30 2-20 (54)
11 PF14326 DUF4384: Domain of un 46.3 27 0.00058 20.1 2.6 28 39-66 3-34 (83)
12 cd06576 PASTA_Pbp2x-like_1 PAS 45.6 22 0.00047 17.8 2.0 19 12-30 2-20 (55)
13 TIGR00638 Mop molybdenum-pteri 44.0 17 0.00036 19.6 1.4 21 39-59 49-69 (69)
14 PF00367 PTS_EIIB: phosphotran 40.1 13 0.00029 18.6 0.6 21 44-64 14-34 (35)
15 TIGR01352 tonB_Cterm TonB fami 39.3 34 0.00073 18.4 2.2 16 53-68 13-28 (74)
16 PF03544 TonB_C: Gram-negative 38.9 29 0.00063 18.9 1.9 15 53-67 19-33 (79)
17 KOG0912 Thiol-disulfide isomer 37.5 40 0.00087 25.4 2.9 18 36-53 76-93 (375)
18 PF06691 DUF1189: Protein of u 36.6 73 0.0016 21.8 4.0 43 23-65 58-102 (250)
19 PF04355 SmpA_OmlA: SmpA / Oml 36.2 47 0.001 18.3 2.5 19 49-67 52-70 (71)
20 cd03474 Rieske_T4moC Toluene-4 35.3 58 0.0012 19.2 3.0 28 39-66 10-37 (108)
21 PF04225 OapA: Opacity-associa 34.0 59 0.0013 19.1 2.8 33 17-49 21-53 (85)
22 cd03531 Rieske_RO_Alpha_KSH Th 33.5 72 0.0016 19.3 3.2 29 39-67 11-39 (115)
23 cd04337 Rieske_RO_Alpha_Cao Ca 33.0 74 0.0016 19.8 3.3 29 38-66 26-54 (129)
24 cd03469 Rieske_RO_Alpha_N Ries 32.2 79 0.0017 18.7 3.2 26 41-66 13-38 (118)
25 COG0391 Uncharacterized conser 31.5 45 0.00097 24.7 2.4 24 20-47 180-203 (323)
26 PRK11548 outer membrane biogen 31.4 53 0.0012 20.1 2.4 17 51-67 88-104 (113)
27 PF11625 DUF3253: Protein of u 30.8 43 0.00093 20.1 1.8 42 3-48 24-71 (83)
28 cd03530 Rieske_NirD_small_Baci 27.2 94 0.002 17.8 2.9 28 39-66 10-37 (98)
29 PF00899 ThiF: ThiF family; I 26.6 1.4E+02 0.0031 18.1 3.8 30 13-42 50-80 (135)
30 COG1264 PtsG Phosphotransferas 26.1 43 0.00093 19.9 1.3 21 44-64 17-37 (88)
31 PHA02087 hypothetical protein 25.9 83 0.0018 18.6 2.4 22 48-69 38-61 (83)
32 COG1614 CdhC CO dehydrogenase/ 25.7 17 0.00037 27.7 -0.7 40 1-41 315-356 (470)
33 COG1430 Uncharacterized conser 25.6 59 0.0013 20.9 1.9 13 55-67 66-78 (126)
34 PRK14584 hmsS hemin storage sy 25.6 80 0.0017 21.0 2.6 19 49-67 119-137 (153)
35 PRK11251 DNA-binding transcrip 25.5 79 0.0017 19.7 2.4 17 51-67 77-93 (109)
36 KOG2819 Uncharacterized conser 25.5 1.7E+02 0.0037 22.3 4.5 53 8-60 13-71 (413)
37 PRK03760 hypothetical protein; 25.5 58 0.0013 20.3 1.8 13 55-67 63-75 (117)
38 PF13994 PgaD: PgaD-like prote 25.4 53 0.0012 20.8 1.7 16 50-65 122-137 (138)
39 COG1596 Wza Periplasmic protei 25.4 88 0.0019 21.6 2.9 41 14-57 89-130 (239)
40 PF06241 DUF1012: Protein of u 25.2 82 0.0018 22.0 2.6 21 10-34 97-117 (206)
41 PF02643 DUF192: Uncharacteriz 24.6 63 0.0014 19.6 1.8 13 55-67 52-64 (108)
42 COG2815 Uncharacterized protei 23.7 1.2E+02 0.0026 22.0 3.4 22 8-29 91-112 (303)
43 PF14599 zinc_ribbon_6: Zinc-r 23.7 89 0.0019 17.6 2.2 26 43-68 18-43 (61)
44 cd00340 GSH_Peroxidase Glutath 23.6 89 0.0019 19.4 2.4 16 52-67 123-138 (152)
45 PF06519 TolA: TolA C-terminal 23.5 72 0.0016 19.3 1.9 17 51-67 38-54 (96)
46 TIGR02480 fliN flagellar motor 23.5 1E+02 0.0022 17.5 2.5 24 37-60 27-51 (77)
47 PF11396 DUF2874: Protein of u 23.3 1.3E+02 0.0028 15.7 4.0 43 23-65 12-61 (61)
48 PF08402 TOBE_2: TOBE domain; 23.0 41 0.00089 17.7 0.7 18 40-57 58-75 (75)
49 cd00212 PTS_IIB_glc PTS_IIB, P 22.9 69 0.0015 18.3 1.7 19 46-64 19-37 (78)
50 TIGR01819 F420_cofD LPPG:FO 2- 22.5 79 0.0017 23.1 2.3 24 20-47 173-196 (297)
51 COG5428 Uncharacterized conser 22.0 1.8E+02 0.0039 17.0 3.8 28 40-67 18-45 (69)
52 PF09363 XFP_C: XFP C-terminal 21.5 1E+02 0.0023 21.4 2.6 24 22-45 52-75 (203)
53 PF06633 DUF1155: Protein of u 21.1 27 0.00059 18.3 -0.3 14 40-53 20-35 (42)
54 KOG4442 Clathrin coat binding 21.0 42 0.00091 27.5 0.6 18 36-53 223-240 (729)
55 PF08882 Acetone_carb_G: Aceto 21.0 43 0.00094 21.3 0.6 18 35-52 85-102 (112)
56 cd05744 Ig_Myotilin_C_like Imm 21.0 1.6E+02 0.0034 16.0 4.0 29 32-62 11-39 (75)
57 PRK09510 tolA cell envelope in 20.5 90 0.002 23.7 2.3 17 51-67 327-343 (387)
58 PF01436 NHL: NHL repeat; Int 20.4 1.1E+02 0.0024 13.9 2.3 21 37-57 8-28 (28)
59 PF02575 YbaB_DNA_bd: YbaB/Ebf 20.1 94 0.002 17.9 1.9 16 52-67 30-45 (93)
60 PRK13320 pantothenate kinase; 20.1 1.3E+02 0.0028 20.8 2.9 39 12-50 92-130 (244)
No 1
>PF00280 potato_inhibit: Potato inhibitor I family; InterPro: IPR000864 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This family of proteinase inhibitors belong to MEROPS inhibitor family I13, clan IG. They inhibit peptidases of the S1 (IPR001254 from INTERPRO) and S8 (IPR000209 from INTERPRO) families []. Potato inhibitor type I sequences are not solely restricted to potatoes but are found in other plant species for example: barley endosperm chymotrypsin inhibitor [], and pumpkin trypsin inhibitor. Exceptions are found in leech's, e.g.Hirudo medicinalis (Medicinal leech), but not other metazoa []. In general, the proteins have retained a specificity towards chymotrypsin-like and elastase-like proteases []. Structurally these inhibitors are small (60 to 90 residues) and in contrast with other families of protease inhibitors, they lack disulphide bonds. The inhibitor is a wedge-shaped molecule, its pointed edge formed by the protease-binding loop, which contains the scissile bond. The loop binds tightly to the protease active site, subsequent cleavage of the scissile bond causing inhibition of the enzyme []. The inhibitors (designated type I and II) are synthesised in potato tubers, increasing in concentration as the tuber develops. Synthesis of the inhibitors throughout the plant is also induced by leaf damage; this systemic response being triggered by the release of a putative plant hormone []. Examples found in the bacteria and archaea are probable false positives.; GO: 0004867 serine-type endopeptidase inhibitor activity, 0009611 response to wounding; PDB: 1TEC_I 1SBN_I 1ACB_I 1EGP_A 3TEC_I 2SEC_I 1EGL_A 2TEC_I 1SIB_I 1MEE_I ....
Probab=99.98 E-value=4.1e-33 Score=160.97 Aligned_cols=63 Identities=63% Similarity=1.030 Sum_probs=59.3
Q ss_pred CCcchhccCCCHHHHHHHHHHhCCCccEEEecCCceecCcccCCeeEEEECCCCcEEecccCC
Q 040548 9 KGSWPELVGMNGEAAAHIIMAENPKVGATTVDENAIVTADFRCDRVRVFVNDHGIVTRVPRIG 71 (71)
Q Consensus 9 k~~wpelVG~~~~~A~~~i~~~~p~~~vrvl~pg~~vTmDy~~~RV~v~vD~~g~V~~vP~iG 71 (71)
|++||||||+++++|+++|++|||++++.+|++|+++|+||||+||+||+|++|+|+++|+||
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=99.79 E-value=5.3e-20 Score=104.87 Aligned_cols=56 Identities=34% Similarity=0.475 Sum_probs=47.5
Q ss_pred CCCcchhccCCCHHHHHHHHHHhCCCccEEEecCCceecCcccCCeeEEEECCCCcEEec
Q 040548 8 GKGSWPELVGMNGEAAAHIIMAENPKVGATTVDENAIVTADFRCDRVRVFVNDHGIVTRV 67 (71)
Q Consensus 8 ~k~~wpelVG~~~~~A~~~i~~~~p~~~vrvl~pg~~vTmDy~~~RV~v~vD~~g~V~~v 67 (71)
+++..+.|||++++++...-. ...+||++||+++|||||++||||++|++|+|+++
T Consensus 2 ~A~~~q~lvGq~~~~~~~~~~----~~~~Rvi~Pg~~vTmDyr~dRLnv~~D~~g~I~~v 57 (60)
T PF11720_consen 2 GAAAAQSLVGQPASAAEREEL----AETVRVIRPGDAVTMDYRPDRLNVEVDDDGVITRV 57 (60)
T ss_pred CHHHHHHhhCCCccccccccc----ccceEEeCCCCcCcccCCCCcEEEEECCCCcEEEE
Confidence 578889999999887543211 33699999999999999999999999999999985
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=75.93 E-value=2.8 Score=22.60 Aligned_cols=19 Identities=42% Similarity=0.601 Sum_probs=15.3
Q ss_pred chhccCCCHHHHHHHHHHh
Q 040548 12 WPELVGMNGEAAAHIIMAE 30 (71)
Q Consensus 12 wpelVG~~~~~A~~~i~~~ 30 (71)
-|+|+|++..+|+..++..
T Consensus 3 vPd~~g~~~~~a~~~l~~~ 21 (63)
T PF03793_consen 3 VPDLVGMTYDEAKSILEAA 21 (63)
T ss_dssp E-TTTTSBHHHHHHHHHHT
T ss_pred CCCcCCCcHHHHHHHHHHC
Confidence 5899999999999877664
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=63.58 E-value=17 Score=17.96 Aligned_cols=18 Identities=22% Similarity=0.455 Sum_probs=15.0
Q ss_pred chhccCCCHHHHHHHHHH
Q 040548 12 WPELVGMNGEAAAHIIMA 29 (71)
Q Consensus 12 wpelVG~~~~~A~~~i~~ 29 (71)
-|.++|++..+|...++.
T Consensus 2 ~p~~~g~~~~~a~~~l~~ 19 (53)
T cd06573 2 VPDLVGISKKDLEEQLYD 19 (53)
T ss_pred CCcccCCcHHHHHHHHHc
Confidence 378999999999887765
No 5
>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=60.05 E-value=9.3 Score=19.36 Aligned_cols=19 Identities=32% Similarity=0.461 Sum_probs=15.5
Q ss_pred chhccCCCHHHHHHHHHHh
Q 040548 12 WPELVGMNGEAAAHIIMAE 30 (71)
Q Consensus 12 wpelVG~~~~~A~~~i~~~ 30 (71)
-|.|+|++..+|...+++.
T Consensus 2 vp~~~g~~~~~a~~~l~~~ 20 (62)
T cd06577 2 VPDVVGMTLDEAKAALEAA 20 (62)
T ss_pred CCCcCCCCHHHHHHHHHHC
Confidence 3789999999998877554
No 6
>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=50.28 E-value=36 Score=17.63 Aligned_cols=48 Identities=19% Similarity=0.251 Sum_probs=25.0
Q ss_pred CHHHHHHHHHHhCCCccEE-EecCC-c-----eecCcc----cCCeeEEEECC-CCcEEe
Q 040548 19 NGEAAAHIIMAENPKVGAT-TVDEN-A-----IVTADF----RCDRVRVFVND-HGIVTR 66 (71)
Q Consensus 19 ~~~~A~~~i~~~~p~~~vr-vl~pg-~-----~vTmDy----~~~RV~v~vD~-~g~V~~ 66 (71)
+.++|.+++++..|+.... .+.+. . -+.... ......+++|+ +|.|.+
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 3567888888888886544 33333 1 222222 23335566886 477754
No 7
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=48.10 E-value=21 Score=20.00 Aligned_cols=18 Identities=28% Similarity=0.353 Sum_probs=12.3
Q ss_pred cCCeeEEEECCCCcEEec
Q 040548 50 RCDRVRVFVNDHGIVTRV 67 (71)
Q Consensus 50 ~~~RV~v~vD~~g~V~~v 67 (71)
..-.|.|.+|.+|.|+.+
T Consensus 26 ~~~~V~i~i~~dG~v~~~ 43 (85)
T PF13103_consen 26 LSVTVRITIDPDGRVISV 43 (85)
T ss_dssp --EEEEEEE-TTSBEEEE
T ss_pred cEEEEEEEECCCCCEEEE
Confidence 345688899999999754
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=47.78 E-value=31 Score=20.33 Aligned_cols=28 Identities=11% Similarity=0.277 Sum_probs=20.7
Q ss_pred ecCCceecCcccCCeeEEEECCCCcEEe
Q 040548 39 VDENAIVTADFRCDRVRVFVNDHGIVTR 66 (71)
Q Consensus 39 l~pg~~vTmDy~~~RV~v~vD~~g~V~~ 66 (71)
|++|+..+..+....|-|+.+.+|.+..
T Consensus 8 l~~g~~~~~~~~g~~v~v~r~~~g~~~A 35 (91)
T cd03477 8 LAPGEGGVVNIGGKRLAVYRDEDGVLHT 35 (91)
T ss_pred cCCCCeEEEEECCEEEEEEECCCCCEEE
Confidence 5778888877777788788776666554
No 9
>smart00740 PASTA PASTA domain.
Probab=47.60 E-value=19 Score=18.47 Aligned_cols=21 Identities=24% Similarity=0.457 Sum_probs=16.6
Q ss_pred CcchhccCCCHHHHHHHHHHh
Q 040548 10 GSWPELVGMNGEAAAHIIMAE 30 (71)
Q Consensus 10 ~~wpelVG~~~~~A~~~i~~~ 30 (71)
..-|.|+|++..+|...+...
T Consensus 5 ~~vp~~~g~~~~~a~~~l~~~ 25 (66)
T smart00740 5 VEVPDVIGLSKEEAKKLLKAL 25 (66)
T ss_pred eeCCCcCCCCHHHHHHHHHHC
Confidence 456899999999998776543
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=47.47 E-value=20 Score=17.70 Aligned_cols=19 Identities=21% Similarity=0.356 Sum_probs=15.1
Q ss_pred chhccCCCHHHHHHHHHHh
Q 040548 12 WPELVGMNGEAAAHIIMAE 30 (71)
Q Consensus 12 wpelVG~~~~~A~~~i~~~ 30 (71)
-|.++|++.++|...+...
T Consensus 2 vp~~~g~~~~~a~~~l~~~ 20 (54)
T cd06575 2 MPDLTGWSKRDALKLLELL 20 (54)
T ss_pred CCCcCCCCHHHHHHHHHHC
Confidence 3789999999998876544
No 11
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=46.28 E-value=27 Score=20.07 Aligned_cols=28 Identities=18% Similarity=0.272 Sum_probs=17.3
Q ss_pred ecCCceecCcccCCe---eEE-EECCCCcEEe
Q 040548 39 VDENAIVTADFRCDR---VRV-FVNDHGIVTR 66 (71)
Q Consensus 39 l~pg~~vTmDy~~~R---V~v-~vD~~g~V~~ 66 (71)
++.|+.+...++.+| |.| .+|.+|.|++
T Consensus 3 ~~~Ge~v~~~~~~~~~~Yl~l~~~~~~G~v~~ 34 (83)
T PF14326_consen 3 YRVGERVRFRVTSNRDGYLYLFYIDADGKVTL 34 (83)
T ss_pred ccCCCEEEEEEEeCCCeEEEEEEECCCCCEEE
Confidence 455666666665554 444 3777887776
No 12
>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=45.60 E-value=22 Score=17.83 Aligned_cols=19 Identities=21% Similarity=0.303 Sum_probs=15.2
Q ss_pred chhccCCCHHHHHHHHHHh
Q 040548 12 WPELVGMNGEAAAHIIMAE 30 (71)
Q Consensus 12 wpelVG~~~~~A~~~i~~~ 30 (71)
-|.++|++..+|.+.+...
T Consensus 2 ~p~~~g~~~~~a~~~l~~~ 20 (55)
T cd06576 2 VPDVTGKSVEEAKKELKEA 20 (55)
T ss_pred CCcccCCCHHHHHHHHHHC
Confidence 3789999999998776554
No 13
>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=44.03 E-value=17 Score=19.58 Aligned_cols=21 Identities=19% Similarity=0.131 Sum_probs=14.7
Q ss_pred ecCCceecCcccCCeeEEEEC
Q 040548 39 VDENAIVTADFRCDRVRVFVN 59 (71)
Q Consensus 39 l~pg~~vTmDy~~~RV~v~vD 59 (71)
|.+|+.+..-+.+..+.++.|
T Consensus 49 l~~G~~v~~~ik~~~v~l~~~ 69 (69)
T TIGR00638 49 LKPGKEVYAVIKAPWVILAVD 69 (69)
T ss_pred CCCCCEEEEEEECcEEEEecC
Confidence 457777777777777777654
No 14
>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=40.08 E-value=13 Score=18.60 Aligned_cols=21 Identities=29% Similarity=0.306 Sum_probs=15.5
Q ss_pred eecCcccCCeeEEEECCCCcE
Q 040548 44 IVTADFRCDRVRVFVNDHGIV 64 (71)
Q Consensus 44 ~vTmDy~~~RV~v~vD~~g~V 64 (71)
....+++..||++.+.+...|
T Consensus 14 I~~v~~C~TRLR~~v~d~~~V 34 (35)
T PF00367_consen 14 IKSVTNCATRLRFTVKDDSKV 34 (35)
T ss_dssp EEEEEE-SSEEEEEESTGGGS
T ss_pred HHHHhcCcceEEEEecChhhC
Confidence 456788899999999876554
No 15
>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=39.30 E-value=34 Score=18.38 Aligned_cols=16 Identities=44% Similarity=0.488 Sum_probs=12.2
Q ss_pred eeEEEECCCCcEEecc
Q 040548 53 RVRVFVNDHGIVTRVP 68 (71)
Q Consensus 53 RV~v~vD~~g~V~~vP 68 (71)
.|.+.+|.+|.|+.+.
T Consensus 13 ~v~~~i~~~G~v~~~~ 28 (74)
T TIGR01352 13 VVRFTVDADGRVTSVS 28 (74)
T ss_pred EEEEEECCCCCEEEEE
Confidence 4677889999888753
No 16
>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=38.93 E-value=29 Score=18.88 Aligned_cols=15 Identities=27% Similarity=0.377 Sum_probs=11.8
Q ss_pred eeEEEECCCCcEEec
Q 040548 53 RVRVFVNDHGIVTRV 67 (71)
Q Consensus 53 RV~v~vD~~g~V~~v 67 (71)
.|.+.+|.+|.|..+
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 467789999988864
No 17
>KOG0912 consensus Thiol-disulfide isomerase and thioredoxin [Posttranslational modification, protein turnover, chaperones; Energy production and conversion]
Probab=37.45 E-value=40 Score=25.40 Aligned_cols=18 Identities=11% Similarity=0.366 Sum_probs=12.7
Q ss_pred EEEecCCceecCcccCCe
Q 040548 36 ATTVDENAIVTADFRCDR 53 (71)
Q Consensus 36 vrvl~pg~~vTmDy~~~R 53 (71)
.-+.+-|.++|.+||..|
T Consensus 76 lKvfrnG~~~~rEYRg~R 93 (375)
T KOG0912|consen 76 LKVFRNGEMMKREYRGQR 93 (375)
T ss_pred eeeeeccchhhhhhccch
Confidence 345667777888888776
No 18
>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=36.55 E-value=73 Score=21.83 Aligned_cols=43 Identities=12% Similarity=0.191 Sum_probs=32.8
Q ss_pred HHHHHHHhCCCccEE--EecCCceecCcccCCeeEEEECCCCcEE
Q 040548 23 AAHIIMAENPKVGAT--TVDENAIVTADFRCDRVRVFVNDHGIVT 65 (71)
Q Consensus 23 A~~~i~~~~p~~~vr--vl~pg~~vTmDy~~~RV~v~vD~~g~V~ 65 (71)
....+.++-|+-++. .|.-++..+.+|..+.+.+..|++|.+.
T Consensus 58 ~~~~i~~~iP~F~I~nG~L~~~~~~~i~~~~~~~~i~~D~~~~~~ 102 (250)
T PF06691_consen 58 DQQKIENDIPDFTIENGKLTSDQSEPIIYQTNNFIIIFDPTGKVT 102 (250)
T ss_pred hhhHHHhhCCCeEEECCcEecCCCCceEecCCcEEEEECCCCCcc
Confidence 355688888987665 5555666677889999999999988765
No 19
>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=36.18 E-value=47 Score=18.26 Aligned_cols=19 Identities=21% Similarity=0.573 Sum_probs=15.6
Q ss_pred ccCCeeEEEECCCCcEEec
Q 040548 49 FRCDRVRVFVNDHGIVTRV 67 (71)
Q Consensus 49 y~~~RV~v~vD~~g~V~~v 67 (71)
....++.|+.|++++|..+
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 20
>cd03474 Rieske_T4moC Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent hydroxylation of toluene to form p-cresol. T4mo consists of an NADH oxidoreductase (T4moF), a diiron hydroxylase (T4moH), a catalytic effector protein (T4moD), and a Rieske ferredoxin (T4moC). T4moC contains a Rieske domain and functions as an obligate electron carrier between T4moF and T4moH. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes.
Probab=35.29 E-value=58 Score=19.18 Aligned_cols=28 Identities=18% Similarity=0.169 Sum_probs=18.6
Q ss_pred ecCCceecCcccCCeeEEEECCCCcEEe
Q 040548 39 VDENAIVTADFRCDRVRVFVNDHGIVTR 66 (71)
Q Consensus 39 l~pg~~vTmDy~~~RV~v~vD~~g~V~~ 66 (71)
|++|.+.+..+...++-|+.+.+|.+.-
T Consensus 10 l~~g~~~~~~~~~~~~~~~~~~~g~~~A 37 (108)
T cd03474 10 VWEGEMELVDVDGEEVLLVAPEGGEFRA 37 (108)
T ss_pred cCCCceEEEEECCeEEEEEEccCCeEEE
Confidence 4567776666666667777777776554
No 21
>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=34.04 E-value=59 Score=19.10 Aligned_cols=33 Identities=9% Similarity=0.169 Sum_probs=15.9
Q ss_pred CCCHHHHHHHHHHhCCCccEEEecCCceecCcc
Q 040548 17 GMNGEAAAHIIMAENPKVGATTVDENAIVTADF 49 (71)
Q Consensus 17 G~~~~~A~~~i~~~~p~~~vrvl~pg~~vTmDy 49 (71)
|.++.+-...+..+-......-|+||+.+....
T Consensus 21 gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~ 53 (85)
T PF04225_consen 21 GLSASDLYAVLEADGEAKPLTRLKPGQTLEFQL 53 (85)
T ss_dssp T--HHHHHHHHHHGGGT--GGG--TT-EEEEEE
T ss_pred CCCHHHHHHHHhccCccchHhhCCCCCEEEEEE
Confidence 677777666666664443455678887655443
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=33.54 E-value=72 Score=19.33 Aligned_cols=29 Identities=10% Similarity=0.187 Sum_probs=20.2
Q ss_pred ecCCceecCcccCCeeEEEECCCCcEEec
Q 040548 39 VDENAIVTADFRCDRVRVFVNDHGIVTRV 67 (71)
Q Consensus 39 l~pg~~vTmDy~~~RV~v~vD~~g~V~~v 67 (71)
|++|.+.+.+.....+-|+-+.+|.+.-+
T Consensus 11 l~~g~~~~~~~~g~~i~l~r~~~g~~~a~ 39 (115)
T cd03531 11 FRDGKPHGVEAFGTKLVVFADSDGALNVL 39 (115)
T ss_pred CCCCCeEEEEECCeEEEEEECCCCCEEEE
Confidence 46677777777777777877777766543
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=32.95 E-value=74 Score=19.78 Aligned_cols=29 Identities=10% Similarity=0.171 Sum_probs=21.8
Q ss_pred EecCCceecCcccCCeeEEEECCCCcEEe
Q 040548 38 TVDENAIVTADFRCDRVRVFVNDHGIVTR 66 (71)
Q Consensus 38 vl~pg~~vTmDy~~~RV~v~vD~~g~V~~ 66 (71)
=|++|++.+.+.....+-|+-+++|.+.-
T Consensus 26 el~~g~~~~~~v~g~~l~l~r~~~g~v~A 54 (129)
T cd04337 26 DLKMDTMVPFELFGQPWVLFRDEDGTPGC 54 (129)
T ss_pred HCCCCCeEEEEECCcEEEEEECCCCcEEE
Confidence 35778888888877888888777776654
No 24
>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=32.23 E-value=79 Score=18.66 Aligned_cols=26 Identities=15% Similarity=0.202 Sum_probs=16.3
Q ss_pred CCceecCcccCCeeEEEECCCCcEEe
Q 040548 41 ENAIVTADFRCDRVRVFVNDHGIVTR 66 (71)
Q Consensus 41 pg~~vTmDy~~~RV~v~vD~~g~V~~ 66 (71)
+|+.++..+....+-|+-+.+|.|..
T Consensus 13 ~g~~~~~~~~~~~i~v~r~~~g~~~a 38 (118)
T cd03469 13 PGDYVTLELGGEPLVLVRDRDGEVRA 38 (118)
T ss_pred CCCEEEEEECCccEEEEECCCCCEEE
Confidence 66666555556667777766665544
No 25
>COG0391 Uncharacterized conserved protein [Function unknown]
Probab=31.55 E-value=45 Score=24.67 Aligned_cols=24 Identities=13% Similarity=0.192 Sum_probs=17.5
Q ss_pred HHHHHHHHHHhCCCccEEEecCCceecC
Q 040548 20 GEAAAHIIMAENPKVGATTVDENAIVTA 47 (71)
Q Consensus 20 ~~~A~~~i~~~~p~~~vrvl~pg~~vTm 47 (71)
..+|.++|++. ...++.||+++|-
T Consensus 180 ~~eaveAI~~A----D~IviGPgSl~TS 203 (323)
T COG0391 180 APEAVEAIKEA----DLIVIGPGSLFTS 203 (323)
T ss_pred CHHHHHHHHhC----CEEEEcCCccHhh
Confidence 34566666654 5899999999884
No 26
>PRK11548 outer membrane biogenesis protein BamE; Provisional
Probab=31.39 E-value=53 Score=20.13 Aligned_cols=17 Identities=18% Similarity=0.415 Sum_probs=14.2
Q ss_pred CCeeEEEECCCCcEEec
Q 040548 51 CDRVRVFVNDHGIVTRV 67 (71)
Q Consensus 51 ~~RV~v~vD~~g~V~~v 67 (71)
..++.|+.|++|+|+++
T Consensus 88 ~~~l~V~Fd~~g~V~~i 104 (113)
T PRK11548 88 QQTLTLTFNSSGVLTNI 104 (113)
T ss_pred EEEEEEEECCCCeEEec
Confidence 45789999999999875
No 27
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=30.84 E-value=43 Score=20.12 Aligned_cols=42 Identities=21% Similarity=0.420 Sum_probs=23.0
Q ss_pred CCCCC------CCCcchhccCCCHHHHHHHHHHhCCCccEEEecCCceecCc
Q 040548 3 SSCPA------GKGSWPELVGMNGEAAAHIIMAENPKVGATTVDENAIVTAD 48 (71)
Q Consensus 3 ~~c~~------~k~~wpelVG~~~~~A~~~i~~~~p~~~vrvl~pg~~vTmD 48 (71)
+.||. +...|.+|...--..|... .+.. .+.|+..|.+|..+
T Consensus 24 tiCPSevARal~~~~WR~lm~~vR~~A~~L--~~~G--~i~I~qkG~~Vdp~ 71 (83)
T PF11625_consen 24 TICPSEVARALGPDDWRDLMPPVRAAARRL--ARAG--RIEITQKGKPVDPE 71 (83)
T ss_dssp -B-HHHHHHHH-TTS-GGGHHHHHHHHHHH--HHTT--SEEEEETTEE--TT
T ss_pred ccCHHHHHHHHCchhhHHHHHHHHHHHHHH--HHCC--cEEEEECCEecCcc
Confidence 45775 4556999988655544432 2222 58899999988654
No 28
>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=27.17 E-value=94 Score=17.85 Aligned_cols=28 Identities=11% Similarity=0.071 Sum_probs=15.3
Q ss_pred ecCCceecCcccCCeeEEEECCCCcEEe
Q 040548 39 VDENAIVTADFRCDRVRVFVNDHGIVTR 66 (71)
Q Consensus 39 l~pg~~vTmDy~~~RV~v~vD~~g~V~~ 66 (71)
|++|......+....+-|+-+++|.+..
T Consensus 10 l~~~~~~~~~~~g~~i~l~r~~~g~~~A 37 (98)
T cd03530 10 IPPRGARKVQTGGGEIAVFRTADDEVFA 37 (98)
T ss_pred CCCCCcEEEEECCEEEEEEEeCCCCEEE
Confidence 3445444444445566666666565544
No 29
>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=26.63 E-value=1.4e+02 Score=18.10 Aligned_cols=30 Identities=30% Similarity=0.350 Sum_probs=22.6
Q ss_pred hhccCCCHHH-HHHHHHHhCCCccEEEecCC
Q 040548 13 PELVGMNGEA-AAHIIMAENPKVGATTVDEN 42 (71)
Q Consensus 13 pelVG~~~~~-A~~~i~~~~p~~~vrvl~pg 42 (71)
++-+|++-.+ +++.+.+.+|+++++.++..
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 4578988555 57889999999888766543
No 30
>COG1264 PtsG Phosphotransferase system IIB components [Carbohydrate transport and metabolism]
Probab=26.06 E-value=43 Score=19.91 Aligned_cols=21 Identities=43% Similarity=0.561 Sum_probs=17.1
Q ss_pred eecCcccCCeeEEEECCCCcE
Q 040548 44 IVTADFRCDRVRVFVNDHGIV 64 (71)
Q Consensus 44 ~vTmDy~~~RV~v~vD~~g~V 64 (71)
....+.+..|||+.+.+...|
T Consensus 17 I~~~~~C~TRLR~~v~D~s~V 37 (88)
T COG1264 17 IVSVDHCATRLRVTVKDESKV 37 (88)
T ss_pred HhhhhcCcceEEEEEcChhhc
Confidence 456799999999998877655
No 31
>PHA02087 hypothetical protein
Probab=25.87 E-value=83 Score=18.65 Aligned_cols=22 Identities=18% Similarity=0.507 Sum_probs=15.6
Q ss_pred cccCCeeEE--EECCCCcEEeccc
Q 040548 48 DFRCDRVRV--FVNDHGIVTRVPR 69 (71)
Q Consensus 48 Dy~~~RV~v--~vD~~g~V~~vP~ 69 (71)
.|.++.+.= .||.+|++...|-
T Consensus 38 ~~d~nk~v~y~lvdsdg~~ielpe 61 (83)
T PHA02087 38 KFDPNKLVQYMLVDSDGVKIELPE 61 (83)
T ss_pred cCCCccceeEEEEcCCCcEEECCc
Confidence 456666544 3899999988873
No 32
>COG1614 CdhC CO dehydrogenase/acetyl-CoA synthase beta subunit [Energy production and conversion]
Probab=25.72 E-value=17 Score=27.72 Aligned_cols=40 Identities=18% Similarity=0.308 Sum_probs=28.4
Q ss_pred CCCCCCCCCCcchhccCCCHHH--HHHHHHHhCCCccEEEecC
Q 040548 1 MSSSCPAGKGSWPELVGMNGEA--AAHIIMAENPKVGATTVDE 41 (71)
Q Consensus 1 m~~~c~~~k~~wpelVG~~~~~--A~~~i~~~~p~~~vrvl~p 41 (71)
|+++|+ |-.+-|.++|..... ..++|..+-.+-++.++|.
T Consensus 315 mAGq~s-GGkQv~GF~Gisi~Ym~SpKFlQ~DGGw~RvvW~Pk 356 (470)
T COG1614 315 MAGQCS-GGKQVPGFVGISISYMRSPKFLQADGGWERVVWLPK 356 (470)
T ss_pred hccccC-CCccccceeeeeeeeecCccceecCCCeeEEEEchH
Confidence 789998 555678899887655 3466777766656777653
No 33
>COG1430 Uncharacterized conserved protein [Function unknown]
Probab=25.62 E-value=59 Score=20.86 Aligned_cols=13 Identities=23% Similarity=0.623 Sum_probs=10.9
Q ss_pred EEEECCCCcEEec
Q 040548 55 RVFVNDHGIVTRV 67 (71)
Q Consensus 55 ~v~vD~~g~V~~v 67 (71)
-+|+|++|+|+.+
T Consensus 66 iiFid~dg~i~~i 78 (126)
T COG1430 66 IIFIDSDGRVVDI 78 (126)
T ss_pred EEEEcCCCCEEEE
Confidence 5689999999875
No 34
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=25.59 E-value=80 Score=21.02 Aligned_cols=19 Identities=16% Similarity=0.352 Sum_probs=15.6
Q ss_pred ccCCeeEEEECCCCcEEec
Q 040548 49 FRCDRVRVFVNDHGIVTRV 67 (71)
Q Consensus 49 y~~~RV~v~vD~~g~V~~v 67 (71)
=.+..+.|+.|++|.|..+
T Consensus 119 r~~kiltVh~De~G~Ii~V 137 (153)
T PRK14584 119 KSGSCLTLYNDEHGHIIDV 137 (153)
T ss_pred HhCCeEEEEECCCCCEEEe
Confidence 3467788999999999876
No 35
>PRK11251 DNA-binding transcriptional activator OsmE; Provisional
Probab=25.52 E-value=79 Score=19.72 Aligned_cols=17 Identities=24% Similarity=0.210 Sum_probs=14.4
Q ss_pred CCeeEEEECCCCcEEec
Q 040548 51 CDRVRVFVNDHGIVTRV 67 (71)
Q Consensus 51 ~~RV~v~vD~~g~V~~v 67 (71)
..++.|+.|++|+|++.
T Consensus 77 ~~~~tV~Fd~~G~V~~~ 93 (109)
T PRK11251 77 AQTYFVSFDDTGHVDNK 93 (109)
T ss_pred eEEEEEEECCCCCEEec
Confidence 46789999999999874
No 36
>KOG2819 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.48 E-value=1.7e+02 Score=22.32 Aligned_cols=53 Identities=17% Similarity=0.320 Sum_probs=35.0
Q ss_pred CCCcchhccCCCHHHHHHHHHHhCCCcc-EEEecCC-ceec----CcccCCeeEEEECC
Q 040548 8 GKGSWPELVGMNGEAAAHIIMAENPKVG-ATTVDEN-AIVT----ADFRCDRVRVFVND 60 (71)
Q Consensus 8 ~k~~wpelVG~~~~~A~~~i~~~~p~~~-vrvl~pg-~~vT----mDy~~~RV~v~vD~ 60 (71)
|-..|+-.+|.+..+|.++|++.-.-.+ |.|+--. ++.. ..+-.+=++++.|+
T Consensus 13 g~~~~eF~lGMpi~qaiAiiqqh~riik~VqvlYsd~~Pl~~DiIinl~qdGirL~FD~ 71 (413)
T KOG2819|consen 13 GSSQWEFVLGMPIAQAIAIIQQHPRIIKNVQVLYSDQDPLSHDIIINLPQDGIRLMFDP 71 (413)
T ss_pred CCccceeEecChHHHHHHHHHhCccceeeEEEEEecCCCcceeEEEecCCCceEEEech
Confidence 6689999999999999988887733333 6665332 3433 33455556666653
No 37
>PRK03760 hypothetical protein; Provisional
Probab=25.47 E-value=58 Score=20.33 Aligned_cols=13 Identities=15% Similarity=0.350 Sum_probs=11.3
Q ss_pred EEEECCCCcEEec
Q 040548 55 RVFVNDHGIVTRV 67 (71)
Q Consensus 55 ~v~vD~~g~V~~v 67 (71)
-||+|++|+|+.+
T Consensus 63 iiFld~~g~Vv~i 75 (117)
T PRK03760 63 VIFLDSNRRVVDF 75 (117)
T ss_pred EEEECCCCeEEEE
Confidence 6799999999876
No 38
>PF13994 PgaD: PgaD-like protein
Probab=25.39 E-value=53 Score=20.82 Aligned_cols=16 Identities=25% Similarity=0.480 Sum_probs=13.0
Q ss_pred cCCeeEEEECCCCcEE
Q 040548 50 RCDRVRVFVNDHGIVT 65 (71)
Q Consensus 50 ~~~RV~v~vD~~g~V~ 65 (71)
++..+.|+.|++|.|+
T Consensus 122 ~~k~~~V~~d~~G~I~ 137 (138)
T PF13994_consen 122 QAKVLTVHHDDHGRII 137 (138)
T ss_pred hCCeEEEEeCCCCCcC
Confidence 4677888999999876
No 39
>COG1596 Wza Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]
Probab=25.37 E-value=88 Score=21.61 Aligned_cols=41 Identities=20% Similarity=0.148 Sum_probs=29.5
Q ss_pred hccCCCHHHHHHHHHHhCCCccEEEecCCceecC-cccCCeeEEE
Q 040548 14 ELVGMNGEAAAHIIMAENPKVGATTVDENAIVTA-DFRCDRVRVF 57 (71)
Q Consensus 14 elVG~~~~~A~~~i~~~~p~~~vrvl~pg~~vTm-Dy~~~RV~v~ 57 (71)
...|++..+....|...... ....|...|++ .||+.++.|-
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 46788999988888877554 44567766666 7888876664
No 40
>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=25.19 E-value=82 Score=21.98 Aligned_cols=21 Identities=29% Similarity=0.544 Sum_probs=15.8
Q ss_pred CcchhccCCCHHHHHHHHHHhCCCc
Q 040548 10 GSWPELVGMNGEAAAHIIMAENPKV 34 (71)
Q Consensus 10 ~~wpelVG~~~~~A~~~i~~~~p~~ 34 (71)
.+||+|-|..+.+. ....|++
T Consensus 97 ~~~P~L~Gm~y~dv----r~~Fpda 117 (206)
T PF06241_consen 97 KRWPQLDGMKYRDV----RRSFPDA 117 (206)
T ss_pred ecCcccCCcCHHHH----HhcCCcc
Confidence 47999999999873 4555664
No 41
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=24.56 E-value=63 Score=19.61 Aligned_cols=13 Identities=23% Similarity=0.590 Sum_probs=10.1
Q ss_pred EEEECCCCcEEec
Q 040548 55 RVFVNDHGIVTRV 67 (71)
Q Consensus 55 ~v~vD~~g~V~~v 67 (71)
-+|+|.+|+|+.+
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 6789999999875
No 42
>COG2815 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.74 E-value=1.2e+02 Score=22.04 Aligned_cols=22 Identities=27% Similarity=0.292 Sum_probs=18.9
Q ss_pred CCCcchhccCCCHHHHHHHHHH
Q 040548 8 GKGSWPELVGMNGEAAAHIIMA 29 (71)
Q Consensus 8 ~k~~wpelVG~~~~~A~~~i~~ 29 (71)
.+..-|+++|.+.++|.+.++.
T Consensus 91 ~~~~vpdv~Gl~~~eA~~~L~~ 112 (303)
T COG2815 91 QYITVPDVVGLTIEEAVAKLKA 112 (303)
T ss_pred cceecCcccCCcHHHHHHHHHH
Confidence 3458899999999999988877
No 43
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=23.67 E-value=89 Score=17.57 Aligned_cols=26 Identities=23% Similarity=0.495 Sum_probs=10.3
Q ss_pred ceecCcccCCeeEEEECCCCcEEecc
Q 040548 43 AIVTADFRCDRVRVFVNDHGIVTRVP 68 (71)
Q Consensus 43 ~~vTmDy~~~RV~v~vD~~g~V~~vP 68 (71)
++++.+|+..+|+|.=++-+.-+.+|
T Consensus 18 ~pmP~~Y~~~~v~IlCNDC~~~s~v~ 43 (61)
T PF14599_consen 18 TPMPEEYRNKKVWILCNDCNAKSEVP 43 (61)
T ss_dssp ----------EEEEEESSS--EEEEE
T ss_pred CCCCHHHhCCEEEEECCCCCCcccee
Confidence 56899999999999988766555544
No 44
>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=23.57 E-value=89 Score=19.40 Aligned_cols=16 Identities=19% Similarity=0.366 Sum_probs=13.2
Q ss_pred CeeEEEECCCCcEEec
Q 040548 52 DRVRVFVNDHGIVTRV 67 (71)
Q Consensus 52 ~RV~v~vD~~g~V~~v 67 (71)
+|-.+++|.+|+|+..
T Consensus 123 ~~ttflId~~G~i~~~ 138 (152)
T cd00340 123 NFTKFLVDRDGEVVKR 138 (152)
T ss_pred ccEEEEECCCCcEEEE
Confidence 4568999999999863
No 45
>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=23.53 E-value=72 Score=19.27 Aligned_cols=17 Identities=35% Similarity=0.440 Sum_probs=13.4
Q ss_pred CCeeEEEECCCCcEEec
Q 040548 51 CDRVRVFVNDHGIVTRV 67 (71)
Q Consensus 51 ~~RV~v~vD~~g~V~~v 67 (71)
.-+|+|.+..+|.|..+
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 45788899999998875
No 46
>TIGR02480 fliN flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.
Probab=23.50 E-value=1e+02 Score=17.49 Aligned_cols=24 Identities=17% Similarity=0.351 Sum_probs=18.1
Q ss_pred EEecCCceecCcc-cCCeeEEEECC
Q 040548 37 TTVDENAIVTADF-RCDRVRVFVND 60 (71)
Q Consensus 37 rvl~pg~~vTmDy-~~~RV~v~vD~ 60 (71)
.=|.+|+.+++|- -.+.|.+++++
T Consensus 27 l~L~~Gdvi~L~~~~~~~v~l~v~g 51 (77)
T TIGR02480 27 LKLGEGSVIELDKLAGEPLDILVNG 51 (77)
T ss_pred hcCCCCCEEEcCCCCCCcEEEEECC
Confidence 3468899999873 45678988884
No 47
>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=23.28 E-value=1.3e+02 Score=15.72 Aligned_cols=43 Identities=12% Similarity=0.076 Sum_probs=28.7
Q ss_pred HHHHHHHhCCCccEE---Eec----CCceecCcccCCeeEEEECCCCcEE
Q 040548 23 AAHIIMAENPKVGAT---TVD----ENAIVTADFRCDRVRVFVNDHGIVT 65 (71)
Q Consensus 23 A~~~i~~~~p~~~vr---vl~----pg~~vTmDy~~~RV~v~vD~~g~V~ 65 (71)
++..|....|+.++. ... ..--+-+.-+.+...|++|.+|.+.
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 567889999998532 222 2234555566788999999998763
No 48
>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=23.00 E-value=41 Score=17.74 Aligned_cols=18 Identities=22% Similarity=0.331 Sum_probs=9.3
Q ss_pred cCCceecCcccCCeeEEE
Q 040548 40 DENAIVTADFRCDRVRVF 57 (71)
Q Consensus 40 ~pg~~vTmDy~~~RV~v~ 57 (71)
.+|+.+..-+.++++.+|
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 455555555555555443
No 49
>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=22.87 E-value=69 Score=18.30 Aligned_cols=19 Identities=32% Similarity=0.440 Sum_probs=14.4
Q ss_pred cCcccCCeeEEEECCCCcE
Q 040548 46 TADFRCDRVRVFVNDHGIV 64 (71)
Q Consensus 46 TmDy~~~RV~v~vD~~g~V 64 (71)
+.+.+..||++.+++...|
T Consensus 19 ~v~~c~TRLRv~l~d~~~v 37 (78)
T cd00212 19 SLDHCATRLRLTVKDESKV 37 (78)
T ss_pred cccccccEEEEEEeCchhc
Confidence 4577889999998876544
No 50
>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=22.55 E-value=79 Score=23.13 Aligned_cols=24 Identities=13% Similarity=0.126 Sum_probs=17.1
Q ss_pred HHHHHHHHHHhCCCccEEEecCCceecC
Q 040548 20 GEAAAHIIMAENPKVGATTVDENAIVTA 47 (71)
Q Consensus 20 ~~~A~~~i~~~~p~~~vrvl~pg~~vTm 47 (71)
..+|.++|++. .+.+|.||+++|-
T Consensus 173 ~peal~AI~~A----D~IIlGPgsp~TS 196 (297)
T TIGR01819 173 APKVLEAIRKE----DNILIGPSNPITS 196 (297)
T ss_pred CHHHHHHHHhC----CEEEECCCccHHH
Confidence 34556666654 4899999998874
No 51
>COG5428 Uncharacterized conserved small protein [Function unknown]
Probab=21.97 E-value=1.8e+02 Score=16.96 Aligned_cols=28 Identities=7% Similarity=0.159 Sum_probs=21.7
Q ss_pred cCCceecCcccCCeeEEEECCCCcEEec
Q 040548 40 DENAIVTADFRCDRVRVFVNDHGIVTRV 67 (71)
Q Consensus 40 ~pg~~vTmDy~~~RV~v~vD~~g~V~~v 67 (71)
++++...+.=-.+-+.|.+|.+|.|.-+
T Consensus 18 ~~~~~~dt~e~~edi~Idide~GkV~Gi 45 (69)
T COG5428 18 EGKVVEDTIELGEDILIDIDENGKVIGI 45 (69)
T ss_pred cCcceeehhhcCCcEEEEecCCCcEEEE
Confidence 3446777777778899999999988754
No 52
>PF09363 XFP_C: XFP C-terminal domain; InterPro: IPR018969 Phosphoketolases (PK) are key enzymes of the pentose phosphate pathway of heterofermentative and facultative homofermentative lactic acid bacteria and of the D-fructose 6-phosphate shunt of bifidobacteria. PK activity has been sporadically reported in other microorganisms including eukaryotic yeasts. Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase is a thiamine diphosphate (ThdP)-dependent enzyme found in bacteria such as Bifidobacterium sp [, ]. This enzyme has dual-specificity with the following catalytic activities: 4.1.2.9 from EC: xylose 5-P + Pi = acetyl-P + glyeraldehyde-3-P 4.1.2.22 from EC: fructose-6-P + Pi = acetyl-P + erythrose-4-P Phosphoketolases are distantly related to transketolases, e.g. IPR005475 from INTERPRO.; GO: 0016832 aldehyde-lyase activity, 0005975 carbohydrate metabolic process; PDB: 3AI7_B 3AHC_A 3AHJ_A 3AHG_A 3AHE_A 3AHI_A 3AHD_A 3AHF_A 3AHH_A.
Probab=21.49 E-value=1e+02 Score=21.39 Aligned_cols=24 Identities=21% Similarity=0.311 Sum_probs=14.0
Q ss_pred HHHHHHHHhCCCccEEEecCCcee
Q 040548 22 AAAHIIMAENPKVGATTVDENAIV 45 (71)
Q Consensus 22 ~A~~~i~~~~p~~~vrvl~pg~~v 45 (71)
.|...+.+..|++++||+-.=+-+
T Consensus 52 AA~~lLr~~~P~lkiRvVNVvDLm 75 (203)
T PF09363_consen 52 AAASLLREHFPELKIRVVNVVDLM 75 (203)
T ss_dssp HHHHHHHHT--T--EEEEEESBGG
T ss_pred HHHHHHHHhccCceEEEEEEeEcc
Confidence 466778888999999987554433
No 53
>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=21.08 E-value=27 Score=18.28 Aligned_cols=14 Identities=29% Similarity=0.313 Sum_probs=10.5
Q ss_pred cCC--ceecCcccCCe
Q 040548 40 DEN--AIVTADFRCDR 53 (71)
Q Consensus 40 ~pg--~~vTmDy~~~R 53 (71)
.|| -+.||||+.+-
T Consensus 20 ~pg~wfa~t~df~k~~ 35 (42)
T PF06633_consen 20 EPGTWFADTMDFRKKH 35 (42)
T ss_pred CCCchhhhhhhhhhhh
Confidence 466 38999998764
No 54
>KOG4442 consensus Clathrin coat binding protein/Huntingtin interacting protein HIP1, involved in regulation of endocytosis [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.05 E-value=42 Score=27.51 Aligned_cols=18 Identities=22% Similarity=0.440 Sum_probs=16.5
Q ss_pred EEEecCCceecCcccCCe
Q 040548 36 ATTVDENAIVTADFRCDR 53 (71)
Q Consensus 36 vrvl~pg~~vTmDy~~~R 53 (71)
.++++||.-+|-||+-+|
T Consensus 223 kk~I~~GEEITFDYqf~r 240 (729)
T KOG4442|consen 223 KKVIKPGEEITFDYQFDR 240 (729)
T ss_pred ecccCCCceeeEeccccc
Confidence 578999999999999887
No 55
>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=21.04 E-value=43 Score=21.29 Aligned_cols=18 Identities=17% Similarity=0.056 Sum_probs=14.3
Q ss_pred cEEEecCCceecCcccCC
Q 040548 35 GATTVDENAIVTADFRCD 52 (71)
Q Consensus 35 ~vrvl~pg~~vTmDy~~~ 52 (71)
.+..++||.+++-||-+|
T Consensus 85 evE~~~Pg~P~~hD~epD 102 (112)
T PF08882_consen 85 EVEAPPPGYPPIHDFEPD 102 (112)
T ss_pred EEccCCCCCCceEecccC
Confidence 366788899999888765
No 56
>cd05744 Ig_Myotilin_C_like Immunoglobulin (Ig)-like domain of myotilin, palladin, and myopalladin. Ig_Myotilin_like_C: immunoglobulin (Ig)-like domain in myotilin, palladin, and myopalladin. Myotilin, palladin, and myopalladin function as scaffolds that regulate actin organization. Myotilin and myopalladin are most abundant in skeletal and cardiac muscle; palladin is ubiquitously expressed in the organs of developing vertebrates and plays a key role in cellular morphogenesis. The three family members each interact with specific molecular partners: all three bind to alpha-actinin; in addition, palladin also binds to vasodilator-stimulated phosphoprotein (VASP) and ezrin, myotilin binds to filamin and actin, and myopalladin also binds to nebulin and cardiac ankyrin repeat protein (CARP).
Probab=21.02 E-value=1.6e+02 Score=15.99 Aligned_cols=29 Identities=21% Similarity=0.402 Sum_probs=20.4
Q ss_pred CCccEEEecCCceecCcccCCeeEEEECCCC
Q 040548 32 PKVGATTVDENAIVTADFRCDRVRVFVNDHG 62 (71)
Q Consensus 32 p~~~vrvl~pg~~vTmDy~~~RV~v~vD~~g 62 (71)
|.-++.+.+.|.++..+ .+|+.++.+..+
T Consensus 11 P~P~v~W~k~~~~i~~~--~~r~~~~~~~~~ 39 (75)
T cd05744 11 PPPQIFWKKNNEMLTYN--TDRISLYQDNCG 39 (75)
T ss_pred CCCeEEEEECCEECCCC--CCcEEEEEcCCC
Confidence 44468899999877643 567777766544
No 57
>PRK09510 tolA cell envelope integrity inner membrane protein TolA; Provisional
Probab=20.53 E-value=90 Score=23.66 Aligned_cols=17 Identities=12% Similarity=0.255 Sum_probs=14.4
Q ss_pred CCeeEEEECCCCcEEec
Q 040548 51 CDRVRVFVNDHGIVTRV 67 (71)
Q Consensus 51 ~~RV~v~vD~~g~V~~v 67 (71)
.-+|+|.++++|.|+.+
T Consensus 327 tc~VrI~LapDG~V~sV 343 (387)
T PRK09510 327 TCTLRIKLAPDGTLLDI 343 (387)
T ss_pred eEEEEEEEcCCCcEEee
Confidence 35789999999999876
No 58
>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=20.42 E-value=1.1e+02 Score=13.92 Aligned_cols=21 Identities=33% Similarity=0.411 Sum_probs=15.3
Q ss_pred EEecCCceecCcccCCeeEEE
Q 040548 37 TTVDENAIVTADFRCDRVRVF 57 (71)
Q Consensus 37 rvl~pg~~vTmDy~~~RV~v~ 57 (71)
-+-+.|...-.|+...||.+|
T Consensus 8 av~~~g~i~VaD~~n~rV~vf 28 (28)
T PF01436_consen 8 AVDSDGNIYVADSGNHRVQVF 28 (28)
T ss_dssp EEETTSEEEEEECCCTEEEEE
T ss_pred EEeCCCCEEEEECCCCEEEEC
Confidence 344667777788888888775
No 59
>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=20.11 E-value=94 Score=17.88 Aligned_cols=16 Identities=38% Similarity=0.436 Sum_probs=10.7
Q ss_pred CeeEEEECCCCcEEec
Q 040548 52 DRVRVFVNDHGIVTRV 67 (71)
Q Consensus 52 ~RV~v~vD~~g~V~~v 67 (71)
+-|.|.+|.+|.|+.+
T Consensus 30 g~V~V~v~g~g~v~~i 45 (93)
T PF02575_consen 30 GLVTVTVNGNGEVVDI 45 (93)
T ss_dssp CTEEEEEETTS-EEEE
T ss_pred CEEEEEEecCceEEEE
Confidence 3577778888877764
No 60
>PRK13320 pantothenate kinase; Reviewed
Probab=20.08 E-value=1.3e+02 Score=20.85 Aligned_cols=39 Identities=21% Similarity=0.147 Sum_probs=26.6
Q ss_pred chhccCCCHHHHHHHHHHhCCCccEEEecCCceecCccc
Q 040548 12 WPELVGMNGEAAAHIIMAENPKVGATTVDENAIVTADFR 50 (71)
Q Consensus 12 wpelVG~~~~~A~~~i~~~~p~~~vrvl~pg~~vTmDy~ 50 (71)
=|+-+|.+--.+.....+..++-.+.|+--|++.|.|+-
T Consensus 92 ~p~~lG~DR~~~~~aa~~~~~~~~~lVID~GTA~Tid~v 130 (244)
T PRK13320 92 TPETLGADRLALCAGARYLFPGKNVLAIDAGTAITYDVL 130 (244)
T ss_pred ChhhcchhHHHHHHHHHHhcCCCCEEEEEcCCceEEEEE
Confidence 356788886554433344444545889999999999964
Done!