Query 033055
Match_columns 128
No_of_seqs 137 out of 328
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 09:15:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033055.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033055hhsearch_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 5E-29 1.1E-33 167.2 5.5 63 66-128 1-63 (63)
2 PF11720 Inhibitor_I78: Peptid 99.6 6.1E-17 1.3E-21 106.7 2.7 57 63-124 1-57 (60)
3 PF15284 PAGK: Phage-encoded v 62.5 6.8 0.00015 26.6 2.1 22 7-28 8-29 (61)
4 PF02533 PsbK: Photosystem II 51.8 8.8 0.00019 24.3 1.2 18 5-22 21-38 (42)
5 PRK02553 psbK photosystem II r 43.0 17 0.00037 23.3 1.5 18 5-22 24-41 (45)
6 PF03793 PASTA: PASTA domain; 42.6 22 0.00048 22.0 2.0 19 69-87 3-21 (63)
7 cd06573 PASTA PASTA domain. Th 36.3 67 0.0014 18.2 3.3 18 69-86 2-19 (53)
8 PLN00075 Photosystem II reacti 32.6 30 0.00065 22.8 1.4 18 5-22 31-48 (52)
9 CHL00047 psbK photosystem II p 31.3 32 0.0007 23.1 1.4 18 5-22 37-54 (58)
10 PF13103 TonB_2: TonB C termin 30.5 50 0.0011 21.5 2.3 18 107-124 26-43 (85)
11 PF03413 PepSY: Peptidase prop 28.2 1.1E+02 0.0024 18.3 3.5 48 76-123 3-62 (64)
12 cd06577 PASTA_pknB PASTA domai 27.9 54 0.0012 18.9 2.0 19 69-87 2-20 (62)
13 cd06576 PASTA_Pbp2x-like_1 PAS 26.4 1.3E+02 0.0029 17.2 3.5 18 70-87 3-20 (55)
14 PF08482 HrpB_C: ATP-dependent 25.7 69 0.0015 24.5 2.6 44 65-110 8-60 (133)
15 cd06575 PASTA_Pbp2x-like_2 PAS 24.5 1.3E+02 0.0028 17.0 3.1 19 69-87 2-20 (54)
16 PRK13328 pantothenate kinase; 24.1 1.3E+02 0.0027 24.6 4.0 56 52-107 76-134 (255)
17 cd03477 Rieske_YhfW_C YhfW fam 22.5 1E+02 0.0022 21.1 2.8 28 96-123 8-35 (91)
18 PF06241 DUF1012: Protein of u 22.1 88 0.0019 25.8 2.7 29 67-99 97-126 (206)
19 PF14326 DUF4384: Domain of un 21.9 78 0.0017 21.1 2.0 29 96-124 3-35 (83)
20 TIGR00638 Mop molybdenum-pteri 21.2 52 0.0011 20.4 1.0 21 96-116 49-69 (69)
21 PF02792 Mago_nashi: Mago nash 20.5 23 0.00051 27.6 -0.8 41 23-76 41-83 (143)
22 KOG0912 Thiol-disulfide isomer 20.3 1E+02 0.0022 27.4 2.9 18 93-110 76-93 (375)
23 TIGR01352 tonB_Cterm TonB fami 20.0 1.1E+02 0.0025 18.9 2.4 16 110-125 13-28 (74)
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=99.95 E-value=5e-29 Score=167.21 Aligned_cols=63 Identities=68% Similarity=1.113 Sum_probs=59.4
Q ss_pred CCCCccccCcchHHHHHHHHHhCCCCeEEEecCCCccCCCCcCCeEEEEECCCCCEEecCcCC
Q 033055 66 KSSWPELVGKNGEVAAAIIEKENPCVHAIVLLEGTPVTRDYRIDRVRVWVNKKGKVIRVPRIG 128 (128)
Q Consensus 66 K~sWPELVG~~a~~A~~~I~~erP~v~vrVL~pGs~VTmDfr~dRVnV~VD~~g~VvrVP~VG 128 (128)
|++||||||+++++|+++|++|||++++.++++|+++|+||||||||||+|.+|+|+++|+||
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=99.65 E-value=6.1e-17 Score=106.68 Aligned_cols=57 Identities=33% Similarity=0.440 Sum_probs=47.9
Q ss_pred CCCCCCCccccCcchHHHHHHHHHhCCCCeEEEecCCCccCCCCcCCeEEEEECCCCCEEec
Q 033055 63 CPRKSSWPELVGKNGEVAAAIIEKENPCVHAIVLLEGTPVTRDYRIDRVRVWVNKKGKVIRV 124 (128)
Q Consensus 63 C~gK~sWPELVG~~a~~A~~~I~~erP~v~vrVL~pGs~VTmDfr~dRVnV~VD~~g~VvrV 124 (128)
|+ ++..+.|||++.+++..... ...+||++||+++|||||+||+||++|++|+|+++
T Consensus 1 C~-A~~~q~lvGq~~~~~~~~~~----~~~~Rvi~Pg~~vTmDyr~dRLnv~~D~~g~I~~v 57 (60)
T PF11720_consen 1 CG-AAAAQSLVGQPASAAEREEL----AETVRVIRPGDAVTMDYRPDRLNVEVDDDGVITRV 57 (60)
T ss_pred CC-HHHHHHhhCCCccccccccc----ccceEEeCCCCcCcccCCCCcEEEEECCCCcEEEE
Confidence 64 67888999999886543322 33689999999999999999999999999999986
No 3
>PF15284 PAGK: Phage-encoded virulence factor
Probab=62.47 E-value=6.8 Score=26.57 Aligned_cols=22 Identities=36% Similarity=0.297 Sum_probs=20.0
Q ss_pred hHHHHHHHHHHhcCchhhcccC
Q 033055 7 ALALFFFLLAFAAKPSLAARHE 28 (128)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~ 28 (128)
.++++|.|+|+.|..|-||+..
T Consensus 8 fL~l~~~LsA~~FSasamAa~~ 29 (61)
T PF15284_consen 8 FLALVFILSAAGFSASAMAADS 29 (61)
T ss_pred HHHHHHHHHHhhhhHHHHHHhh
Confidence 5788999999999999999987
No 4
>PF02533 PsbK: Photosystem II 4 kDa reaction centre component; InterPro: IPR003687 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbK found in PSII, where it is tightly associated with the antenna protein CP43 (PsbC). PsbK is required for accumulation of the PSII complex, and may participate in the assembly and stability of the PSII complex. In particular, PsbK may be involved in the binding of plastoquinone and in maintaining the dimeric organisation of PSII [, ].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center; PDB: 4FBY_K 3PRQ_K 1IZL_W 3BZ1_K 2AXT_K 1S5L_K 3PRR_K 3BZ2_K 3KZI_K 3A0B_k ....
Probab=51.81 E-value=8.8 Score=24.29 Aligned_cols=18 Identities=39% Similarity=0.875 Sum_probs=14.7
Q ss_pred chhHHHHHHHHHHhcCch
Q 033055 5 LPALALFFFLLAFAAKPS 22 (128)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~ 22 (128)
+|..-++||||||..+.+
T Consensus 21 mPiIPvlf~LLAfVWQAa 38 (42)
T PF02533_consen 21 MPIIPVLFFLLAFVWQAA 38 (42)
T ss_dssp CCCHHHHHHHHHHHHHHH
T ss_pred cccHHHHHHHHHHHHHHh
Confidence 677778999999987654
No 5
>PRK02553 psbK photosystem II reaction center protein K; Provisional
Probab=42.97 E-value=17 Score=23.31 Aligned_cols=18 Identities=50% Similarity=0.931 Sum_probs=14.4
Q ss_pred chhHHHHHHHHHHhcCch
Q 033055 5 LPALALFFFLLAFAAKPS 22 (128)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~ 22 (128)
+|..=++||||||-.+.+
T Consensus 24 mPiIP~~f~lLafVWQAa 41 (45)
T PRK02553 24 LPLIPLFFLLLAFVWQAA 41 (45)
T ss_pred hchHHHHHHHHHHHHHHh
Confidence 577778999999987654
No 6
>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=42.56 E-value=22 Score=22.03 Aligned_cols=19 Identities=37% Similarity=0.539 Sum_probs=15.7
Q ss_pred CccccCcchHHHHHHHHHh
Q 033055 69 WPELVGKNGEVAAAIIEKE 87 (128)
Q Consensus 69 WPELVG~~a~~A~~~I~~e 87 (128)
-|+++|++..+|...++..
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 4899999999999888774
No 7
>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=36.32 E-value=67 Score=18.24 Aligned_cols=18 Identities=22% Similarity=0.283 Sum_probs=15.0
Q ss_pred CccccCcchHHHHHHHHH
Q 033055 69 WPELVGKNGEVAAAIIEK 86 (128)
Q Consensus 69 WPELVG~~a~~A~~~I~~ 86 (128)
-|.++|++..+|...++.
T Consensus 2 ~p~~~g~~~~~a~~~l~~ 19 (53)
T cd06573 2 VPDLVGISKKDLEEQLYD 19 (53)
T ss_pred CCcccCCcHHHHHHHHHc
Confidence 378899999999888775
No 8
>PLN00075 Photosystem II reaction center protein K; Provisional
Probab=32.59 E-value=30 Score=22.79 Aligned_cols=18 Identities=50% Similarity=1.025 Sum_probs=14.5
Q ss_pred chhHHHHHHHHHHhcCch
Q 033055 5 LPALALFFFLLAFAAKPS 22 (128)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~ 22 (128)
+|..-++|||||+-.+.+
T Consensus 31 mPiIP~~f~lLafVwQAa 48 (52)
T PLN00075 31 MPVIPLFFFLLAFVWQAA 48 (52)
T ss_pred cccHHHHHHHHHHHHHHh
Confidence 577778999999987754
No 9
>CHL00047 psbK photosystem II protein K
Probab=31.29 E-value=32 Score=23.12 Aligned_cols=18 Identities=39% Similarity=0.892 Sum_probs=14.4
Q ss_pred chhHHHHHHHHHHhcCch
Q 033055 5 LPALALFFFLLAFAAKPS 22 (128)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~ 22 (128)
+|..-++||||||-.+.+
T Consensus 37 mPiIP~~f~LLAfVWQAa 54 (58)
T CHL00047 37 MPVIPVLFFLLAFVWQAA 54 (58)
T ss_pred cccHHHHHHHHHHHHHHh
Confidence 567778999999987754
No 10
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=30.49 E-value=50 Score=21.47 Aligned_cols=18 Identities=33% Similarity=0.477 Sum_probs=12.4
Q ss_pred cCCeEEEEECCCCCEEec
Q 033055 107 RIDRVRVWVNKKGKVIRV 124 (128)
Q Consensus 107 r~dRVnV~VD~~g~VvrV 124 (128)
..-.|+|.+|.+|.|+.+
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 345788999999999754
No 11
>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=28.16 E-value=1.1e+02 Score=18.27 Aligned_cols=48 Identities=23% Similarity=0.178 Sum_probs=25.2
Q ss_pred chHHHHHHHHHhCCCCeEE-EecCC-Cc-----cCCCC----cCCeEEEEECCC-CCEEe
Q 033055 76 NGEVAAAIIEKENPCVHAI-VLLEG-TP-----VTRDY----RIDRVRVWVNKK-GKVIR 123 (128)
Q Consensus 76 ~a~~A~~~I~~erP~v~vr-VL~pG-s~-----VTmDf----r~dRVnV~VD~~-g~Vvr 123 (128)
+.++|..+..+..|+.... .+.++ .. +.... ...+..+++|+. |.|.+
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 3467888888888887554 33333 11 22221 233456668864 77764
No 12
>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=27.91 E-value=54 Score=18.94 Aligned_cols=19 Identities=32% Similarity=0.433 Sum_probs=15.7
Q ss_pred CccccCcchHHHHHHHHHh
Q 033055 69 WPELVGKNGEVAAAIIEKE 87 (128)
Q Consensus 69 WPELVG~~a~~A~~~I~~e 87 (128)
-|.++|++..+|...+...
T Consensus 2 vp~~~g~~~~~a~~~l~~~ 20 (62)
T cd06577 2 VPDVVGMTLDEAKAALEAA 20 (62)
T ss_pred CCCcCCCCHHHHHHHHHHC
Confidence 3789999999998888654
No 13
>cd06576 PASTA_Pbp2x-like_1 PASTA domain of PBP2x-like proteins, first repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by acylating the active site serine. PBPs catalyze key steps in the synthesis of the peptidoglycan, such as the interconnecting of glycan chains (polymers of N-glucosamine and N-acetylmuramic acid residues) and the cross-linking (transpeptidation) of short stem peptides, which are connected to glycan chains. Peptidoglycan is essential in cell division and protects bacteria from osmotic shock and lysis. PBP2x is one of the two monofunctional high molecular mass PBPs in Streptococcus pneumoniae and has been seen as the primary PBP target in beta-lactam-resistant strains. The PASTA domain is found at the C-termini of several PBPs and bacterial serine/threonine kinases. The name PASTA is derived from PBP and Serine/Threonine
Probab=26.42 E-value=1.3e+02 Score=17.18 Aligned_cols=18 Identities=28% Similarity=0.470 Sum_probs=15.0
Q ss_pred ccccCcchHHHHHHHHHh
Q 033055 70 PELVGKNGEVAAAIIEKE 87 (128)
Q Consensus 70 PELVG~~a~~A~~~I~~e 87 (128)
|.++|++..+|.+.+...
T Consensus 3 p~~~g~~~~~a~~~l~~~ 20 (55)
T cd06576 3 PDVTGKSVEEAKKELKEA 20 (55)
T ss_pred CcccCCCHHHHHHHHHHC
Confidence 788999999998877655
No 14
>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=25.74 E-value=69 Score=24.45 Aligned_cols=44 Identities=23% Similarity=0.205 Sum_probs=27.6
Q ss_pred CCCCCccccCcchHHHH---------HHHHHhCCCCeEEEecCCCccCCCCcCCe
Q 033055 65 RKSSWPELVGKNGEVAA---------AIIEKENPCVHAIVLLEGTPVTRDYRIDR 110 (128)
Q Consensus 65 gK~sWPELVG~~a~~A~---------~~I~~erP~v~vrVL~pGs~VTmDfr~dR 110 (128)
|.+++.+|-..+..++. ..+.+.-|. ...+|-|+.+..||..+.
T Consensus 8 g~~s~~~l~~~~l~~~L~~~L~~~~~~~Ld~~aP~--~~~~PsG~~~~I~Y~~~~ 60 (133)
T PF08482_consen 8 GVTSLKDLKKLDLLEALRSLLSWEQQQWLDRLAPE--HITLPSGRRIRIDYSDDG 60 (133)
T ss_pred CCCCHHHHhcCCHHHHHHHHCCHHHHHHHHHhCCC--eEEcCCCCEEEEEECCCC
Confidence 44445555444444442 455666553 456788999999998887
No 15
>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=24.47 E-value=1.3e+02 Score=16.99 Aligned_cols=19 Identities=26% Similarity=0.331 Sum_probs=15.3
Q ss_pred CccccCcchHHHHHHHHHh
Q 033055 69 WPELVGKNGEVAAAIIEKE 87 (128)
Q Consensus 69 WPELVG~~a~~A~~~I~~e 87 (128)
-|.++|++..+|...+...
T Consensus 2 vp~~~g~~~~~a~~~l~~~ 20 (54)
T cd06575 2 MPDLTGWSKRDALKLLELL 20 (54)
T ss_pred CCCcCCCCHHHHHHHHHHC
Confidence 3788999999998877644
No 16
>PRK13328 pantothenate kinase; Reviewed
Probab=24.09 E-value=1.3e+02 Score=24.61 Aligned_cols=56 Identities=20% Similarity=0.173 Sum_probs=37.1
Q ss_pred cccccccccCC-CCCCCCC--ccccCcchHHHHHHHHHhCCCCeEEEecCCCccCCCCc
Q 033055 52 DGPNLVMSAFD-CPRKSSW--PELVGKNGEVAAAIIEKENPCVHAIVLLEGTPVTRDYR 107 (128)
Q Consensus 52 d~~~~~~~m~~-C~gK~sW--PELVG~~a~~A~~~I~~erP~v~vrVL~pGs~VTmDfr 107 (128)
-.|.++..... |+-+..+ |+=+|.+--.|.-...+..|+-...|+--|++.|.|+=
T Consensus 76 ~~~~~v~~~~~~~gl~~~Y~~p~~LG~DR~~a~vaA~~~~~~~~~lViD~GTA~TiD~v 134 (255)
T PRK13328 76 LPVTWVRSRAAQCGVRNGYREPAQLGSDRWAGLIGARAAFPGEHLLIATFGTATTLDAL 134 (255)
T ss_pred CCeEEEecCccCCCceeCCCChhhccHHHHHHHHHHHHhcCCCCEEEEEcCCceEEEEE
Confidence 34566663222 4433334 67799887776655555566656789999999999963
No 17
>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=22.52 E-value=1e+02 Score=21.15 Aligned_cols=28 Identities=18% Similarity=0.216 Sum_probs=19.9
Q ss_pred ecCCCccCCCCcCCeEEEEECCCCCEEe
Q 033055 96 LLEGTPVTRDYRIDRVRVWVNKKGKVIR 123 (128)
Q Consensus 96 L~pGs~VTmDfr~dRVnV~VD~~g~Vvr 123 (128)
|++|+..+..+...+|-|+.+.+|.+..
T Consensus 8 l~~g~~~~~~~~g~~v~v~r~~~g~~~A 35 (91)
T cd03477 8 LAPGEGGVVNIGGKRLAVYRDEDGVLHT 35 (91)
T ss_pred cCCCCeEEEEECCEEEEEEECCCCCEEE
Confidence 4777777777777777777776666654
No 18
>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=22.12 E-value=88 Score=25.75 Aligned_cols=29 Identities=24% Similarity=0.390 Sum_probs=21.5
Q ss_pred CCCccccCcchHHHHHHHHHhCCCCeE-EEecCC
Q 033055 67 SSWPELVGKNGEVAAAIIEKENPCVHA-IVLLEG 99 (128)
Q Consensus 67 ~sWPELVG~~a~~A~~~I~~erP~v~v-rVL~pG 99 (128)
.+||+|-|..+.+ .....|++.+ =+.+.|
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 3699999999986 6777788755 355555
No 19
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=21.91 E-value=78 Score=21.14 Aligned_cols=29 Identities=21% Similarity=0.323 Sum_probs=17.2
Q ss_pred ecCCCccCCCCcCCe---EEEE-ECCCCCEEec
Q 033055 96 LLEGTPVTRDYRIDR---VRVW-VNKKGKVIRV 124 (128)
Q Consensus 96 L~pGs~VTmDfr~dR---VnV~-VD~~g~VvrV 124 (128)
++.|+.+...++.+| |.|+ +|.+|.|+++
T Consensus 3 ~~~Ge~v~~~~~~~~~~Yl~l~~~~~~G~v~~L 35 (83)
T PF14326_consen 3 YRVGERVRFRVTSNRDGYLYLFYIDADGKVTLL 35 (83)
T ss_pred ccCCCEEEEEEEeCCCeEEEEEEECCCCCEEEE
Confidence 355666666655543 4443 6777877764
No 20
>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=21.18 E-value=52 Score=20.44 Aligned_cols=21 Identities=24% Similarity=0.150 Sum_probs=16.2
Q ss_pred ecCCCccCCCCcCCeEEEEEC
Q 033055 96 LLEGTPVTRDYRIDRVRVWVN 116 (128)
Q Consensus 96 L~pGs~VTmDfr~dRVnV~VD 116 (128)
|.+|+.+..-+++.++.++.|
T Consensus 49 l~~G~~v~~~ik~~~v~l~~~ 69 (69)
T TIGR00638 49 LKPGKEVYAVIKAPWVILAVD 69 (69)
T ss_pred CCCCCEEEEEEECcEEEEecC
Confidence 468888888888888887765
No 21
>PF02792 Mago_nashi: Mago nashi protein; InterPro: IPR004023 This family was originally identified in drosophila and called mago nashi, it is a strict maternal effect, grandchildless-like, gene []. The human homologue has been shown to interact with an RNA binding protein, ribonucleoprotein rbm8 (Q9Y5S9 from SWISSPROT) []. An RNAi knockout of the Caenorhabditis elegans homologue causes masculinization of the germ line (Mog phenotype) hermaphrodites, suggesting it is involved in hermaphrodite germ-line sex determination [] but the protein is also found in hermaphrodites and other organisms without a sexual differentiation.; GO: 0005634 nucleus; PDB: 2XB2_Y 2J0S_C 3EX7_A 2J0Q_F 1P27_C 2HYI_A 2X1G_B 1HL6_B 1RK8_B 1OO0_A ....
Probab=20.55 E-value=23 Score=27.58 Aligned_cols=41 Identities=27% Similarity=0.563 Sum_probs=24.9
Q ss_pred hhcccCCCccCCcccchHHHhhhhhcccccccccccccCCCCCCCCCc--cccCcc
Q 033055 23 LAARHEPCLTDGKELGSEVIVSALKGVVEDGPNLVMSAFDCPRKSSWP--ELVGKN 76 (128)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~m~~C~gK~sWP--ELVG~~ 76 (128)
-|-|||-|.+. ..+..++.|+.|. |.+++.+ ..|| .-+|+.
T Consensus 41 ~~IrKe~~vs~-------~vl~E~krII~~S-eI~kEdD-----~~WP~pd~~GrQ 83 (143)
T PF02792_consen 41 SMIRKEVYVSP-------AVLEELKRIIEDS-EIMKEDD-----SKWPEPDRVGRQ 83 (143)
T ss_dssp EEEEEEEEE-H-------HHHHHHHHHHHHH-TGGG--S-----TTS--SBTTBEE
T ss_pred ceeeeeeEecH-------HHHHHHHHHHHHh-hcccccc-----ccCCCCCCccce
Confidence 35678866655 5567788888776 7766643 6687 456654
No 22
>KOG0912 consensus Thiol-disulfide isomerase and thioredoxin [Posttranslational modification, protein turnover, chaperones; Energy production and conversion]
Probab=20.27 E-value=1e+02 Score=27.43 Aligned_cols=18 Identities=33% Similarity=0.512 Sum_probs=15.0
Q ss_pred EEEecCCCccCCCCcCCe
Q 033055 93 AIVLLEGTPVTRDYRIDR 110 (128)
Q Consensus 93 vrVL~pGs~VTmDfr~dR 110 (128)
..|.+.|.++|.+||..|
T Consensus 76 lKvfrnG~~~~rEYRg~R 93 (375)
T KOG0912|consen 76 LKVFRNGEMMKREYRGQR 93 (375)
T ss_pred eeeeeccchhhhhhccch
Confidence 457788999999999887
No 23
>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=20.04 E-value=1.1e+02 Score=18.86 Aligned_cols=16 Identities=38% Similarity=0.503 Sum_probs=12.4
Q ss_pred eEEEEECCCCCEEecC
Q 033055 110 RVRVWVNKKGKVIRVP 125 (128)
Q Consensus 110 RVnV~VD~~g~VvrVP 125 (128)
+|.+.+|.+|.|+.+.
T Consensus 13 ~v~~~i~~~G~v~~~~ 28 (74)
T TIGR01352 13 VVRFTVDADGRVTSVS 28 (74)
T ss_pred EEEEEECCCCCEEEEE
Confidence 4677899999988753
Done!