Query psy7408
Match_columns 66
No_of_seqs 12 out of 14
Neff 1.6
Searched_HMMs 46136
Date Fri Aug 16 17:29:11 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7408.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7408hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09790 hypothetical protein; 77.1 1.2 2.6E-05 29.7 1.0 26 7-32 63-89 (91)
2 PF02290 SRP14: Signal recogni 72.9 2.1 4.5E-05 26.9 1.2 18 18-35 74-91 (93)
3 PF00846 Hanta_nucleocap: Hant 57.9 3.4 7.3E-05 33.6 0.0 18 12-29 350-367 (428)
4 PF08589 DUF1770: Fungal prote 52.2 8.9 0.00019 25.6 1.3 19 16-34 72-90 (100)
5 cd00148 PROF Profilin binds ac 47.4 10 0.00023 24.1 1.0 11 23-33 2-13 (127)
6 PF00690 Cation_ATPase_N: Cati 46.5 18 0.00039 20.2 1.8 28 5-32 28-56 (69)
7 PF03909 BSD: BSD domain ; I 43.6 14 0.00031 21.0 1.1 14 18-31 40-53 (62)
8 TIGR03354 VI_FHA type VI secre 37.4 21 0.00046 27.3 1.5 16 15-30 353-368 (396)
9 PF00235 Profilin: Profilin; 36.9 22 0.00048 21.6 1.3 13 23-35 2-15 (121)
10 PF01806 Paramyxo_P: Paramyxov 35.9 25 0.00055 27.0 1.7 24 7-32 204-227 (248)
11 smart00831 Cation_ATPase_N Cat 35.2 27 0.00059 18.9 1.4 29 4-32 17-46 (64)
12 PF04959 ARS2: Arsenite-resist 33.1 29 0.00062 25.2 1.6 27 3-32 98-124 (214)
13 smart00751 BSD domain in trans 32.3 36 0.00079 18.7 1.6 13 19-31 36-48 (51)
14 PF09053 CagZ: CagZ; InterPro 29.9 33 0.00072 25.4 1.4 17 19-35 28-44 (199)
15 PTZ00316 profilin; Provisional 27.7 35 0.00076 23.9 1.2 12 23-34 3-15 (150)
16 KOG0750|consensus 27.5 39 0.00084 26.7 1.5 25 9-33 198-222 (304)
17 KOG1761|consensus 27.2 35 0.00076 23.5 1.1 15 21-35 79-93 (116)
18 smart00392 PROF Profilin. Bind 24.2 43 0.00093 21.2 1.0 11 23-33 3-14 (129)
19 PF01639 v110: Viral family 11 23.7 16 0.00034 24.9 -1.1 17 14-30 26-42 (110)
20 PF09628 YvfG: YvfG protein; 21.7 48 0.001 21.2 0.9 28 3-33 12-39 (68)
21 PF11393 IcmL: Macrophage kill 21.6 52 0.0011 20.6 1.1 17 21-37 53-69 (108)
22 PF03245 Phage_lysis: Bacterio 21.1 63 0.0014 21.0 1.4 24 7-30 100-123 (125)
23 PF10446 DUF2457: Protein of u 20.1 66 0.0014 26.5 1.6 13 17-29 401-413 (458)
No 1
>PRK09790 hypothetical protein; Reviewed
Probab=77.09 E-value=1.2 Score=29.68 Aligned_cols=26 Identities=42% Similarity=0.690 Sum_probs=21.3
Q ss_pred hhhhccCCchhhHHHHHHHHHH-hhcc
Q psy7408 7 LDMIGRNEPITRKAKFWQSYVR-ALKG 32 (66)
Q Consensus 7 LdMIGrNE~~skKAkFWqsYvr-aLKG 32 (66)
|--||.|-|..||+.||...+. .|||
T Consensus 63 lv~ig~nlpaekk~~f~atliamklkg 89 (91)
T PRK09790 63 LVHIGKNLPAEKKAEFLATLIAMKLKG 89 (91)
T ss_pred EEEecCCCCccccccHHHHHHHHHHcc
Confidence 4569999999999999999874 3555
No 2
>PF02290 SRP14: Signal recognition particle 14kD protein; InterPro: IPR003210 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the 14 kDa SRP14 component. Both SRP9 and SRP14 have the same (beta)-alpha-beta(3)-alpha fold. The heterodimer has pseudo two-fold symmetry and is saddle-like, consisting of a curved six-stranded beta-sheet that has four helices packed on the convex side and an exposed concave surface lined with positively charged residues. The SRP9/SRP14 heterodimer is essential for SRP RNA binding, mediating the pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP [].; GO: 0008312 7S RNA binding, 0030942 endoplasmic reticulum signal peptide binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0005786 signal recognition particle, endoplasmic reticulum targeting; PDB: 1914_A 1RY1_D 1E8O_B 2W9J_B.
Probab=72.89 E-value=2.1 Score=26.93 Aligned_cols=18 Identities=44% Similarity=0.780 Sum_probs=14.6
Q ss_pred hHHHHHHHHHHhhccccc
Q psy7408 18 RKAKFWQSYVRALKGSTA 35 (66)
Q Consensus 18 kKAkFWqsYvraLKGs~D 35 (66)
.=.+||++|...||++=|
T Consensus 74 ~l~~F~~~Y~~v~K~~M~ 91 (93)
T PF02290_consen 74 DLDKFWQSYANVLKAGMD 91 (93)
T ss_dssp CHHHHHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHHHhhCc
Confidence 347899999999998643
No 3
>PF00846 Hanta_nucleocap: Hantavirus nucleocapsid protein; InterPro: IPR002214 Hantaviruses are ssRNA negative-strand viruses. The nucleocapsid protein is an internal protein of the virus particle [, ].; GO: 0019013 viral nucleocapsid; PDB: 2IC9_A 2IC6_A 2K48_A 4FI5_A.
Probab=57.88 E-value=3.4 Score=33.64 Aligned_cols=18 Identities=39% Similarity=0.796 Sum_probs=0.0
Q ss_pred cCCchhhHHHHHHHHHHh
Q psy7408 12 RNEPITRKAKFWQSYVRA 29 (66)
Q Consensus 12 rNE~~skKAkFWqsYvra 29 (66)
..|-+-||..|.|||+|.
T Consensus 350 AEEKlkkkssfyqsylrr 367 (428)
T PF00846_consen 350 AEEKLKKKSSFYQSYLRR 367 (428)
T ss_dssp ------------------
T ss_pred HHHHHHhhhHHHHHHHHH
Confidence 357789999999999985
No 4
>PF08589 DUF1770: Fungal protein of unknown function (DUF1770); InterPro: IPR013898 The functions of these proteins are unknown. They are rather dissimilar except for a single strongly conserved motif (PDLRFEQ).
Probab=52.20 E-value=8.9 Score=25.58 Aligned_cols=19 Identities=21% Similarity=0.359 Sum_probs=15.2
Q ss_pred hhhHHHHHHHHHHhhcccc
Q psy7408 16 ITRKAKFWQSYVRALKGST 34 (66)
Q Consensus 16 ~skKAkFWqsYvraLKGs~ 34 (66)
+----+|=|||+.+++|.+
T Consensus 72 PlPDLRFEQSYL~SI~~A~ 90 (100)
T PF08589_consen 72 PLPDLRFEQSYLASIRKAD 90 (100)
T ss_pred CCCcchhHHHHHHHHhccc
Confidence 3334689999999999876
No 5
>cd00148 PROF Profilin binds actin monomers, membrane polyphosphoinositides such as PI(4,5)P2, and poly-L-proline. Profilin can inhibit actin polymerization into F-actin by binding to monomeric actin (G-actin) and terminal F-actin subunits, but - as a regulator of the cytoskeleton - it may also promote actin polymerization. It plays a role in the assembly of branched actin filament networks, by activating WASP via binding to WASP's proline rich domain. Profilin may link the cytoskeleton with major signalling pathways by interacting with components of the phosphatidylinositol cycle and Ras pathway.
Probab=47.37 E-value=10 Score=24.14 Aligned_cols=11 Identities=55% Similarity=1.168 Sum_probs=9.6
Q ss_pred HHHHHH-hhccc
Q psy7408 23 WQSYVR-ALKGS 33 (66)
Q Consensus 23 WqsYvr-aLKGs 33 (66)
||+||. .|-|+
T Consensus 2 Wq~yvd~~L~~~ 13 (127)
T cd00148 2 WQAYVDDNLLGT 13 (127)
T ss_pred hHHHHHHHHhhc
Confidence 999999 68776
No 6
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=46.53 E-value=18 Score=20.25 Aligned_cols=28 Identities=21% Similarity=0.515 Sum_probs=22.5
Q ss_pred hhhhhhccCCc-hhhHHHHHHHHHHhhcc
Q psy7408 5 QHLDMIGRNEP-ITRKAKFWQSYVRALKG 32 (66)
Q Consensus 5 ~HLdMIGrNE~-~skKAkFWqsYvraLKG 32 (66)
..++-+|.|+- ..++..+|+-+++.++.
T Consensus 28 ~r~~~~G~N~l~~~~~~s~~~~~~~~f~~ 56 (69)
T PF00690_consen 28 ERRKKYGPNELPEPKKKSLWRIFLKQFKN 56 (69)
T ss_dssp HHHHHHSSSSTTTTTSSSHHHHHHHHTTS
T ss_pred HHHHhcccccccccccCcHHHHHHHHHHh
Confidence 45778999998 67778899999888753
No 7
>PF03909 BSD: BSD domain ; InterPro: IPR005607 The BSD domain is an about 60-residue long domain named after the BTF2-like transcription factors, Synapse-associated proteins and DOS2-like proteins in which it is found. Additionally, it is also found in several hypothetical proteins. The BSD domain occurs in one or two copies in a variety of species ranging from primal protozoan to human. It can be found associated with other domains such as the BTB domain (see PDOC50097 from PROSITEDOC) or the U-box in multidomain proteins. The function of the BSD domain is yet unknown []. Secondary structure prediction indicates the presence of three predicted alpha helices, which probably form a three-helical bundle in small domains. The third predicted helix contains neighbouring phenylalanine and tryptophan residues - less common amino acids that are invariant in all the BSD domains identified and that are the most striking sequence features of the domain []. Some proteins known to contain one or two BSD domains are listed below: Mammalian TFIIH basal transcription factor complex p62 subunit (GTF2H1). Yeast RNA polymerase II transcription factor B 73 kDa subunit (TFB1), the homologue of BTF2. Yeast DOS2 protein. It is involved in single-copy DNA replication and ubiquitination. Drosophila synapse-associated protein SAP47. Mammalian SYAP1. Various Arabidopsis thaliana (Mouse-ear cress) hypothetical proteins.; PDB: 1X3A_A 1PFJ_A 2RNR_B 2DII_A.
Probab=43.60 E-value=14 Score=20.96 Aligned_cols=14 Identities=29% Similarity=0.828 Sum_probs=10.2
Q ss_pred hHHHHHHHHHHhhc
Q psy7408 18 RKAKFWQSYVRALK 31 (66)
Q Consensus 18 kKAkFWqsYvraLK 31 (66)
.-..||+.|...+.
T Consensus 40 ~e~~FW~rYf~~~~ 53 (62)
T PF03909_consen 40 SEEEFWKRYFYRLH 53 (62)
T ss_dssp -HHHHHHHHHCHHH
T ss_pred CHHHHHHHHHHHHH
Confidence 35789999987653
No 8
>TIGR03354 VI_FHA type VI secretion system FHA domain protein. Members of this protein family are FHA (forkhead-associated) domain-containing proteins that are part of type VI secretion loci in a considerable number of bacteria, most of which are known pathogens. Species include Pseudomonas aeruginosa PAO1, Aeromonas hydrophila, Yersinia pestis, Burkholderia mallei, etc.
Probab=37.40 E-value=21 Score=27.26 Aligned_cols=16 Identities=31% Similarity=0.381 Sum_probs=13.0
Q ss_pred chhhHHHHHHHHHHhh
Q psy7408 15 PITRKAKFWQSYVRAL 30 (66)
Q Consensus 15 ~~skKAkFWqsYvraL 30 (66)
..++|||.|+.|++--
T Consensus 353 ~~~~~a~~W~~Y~~~y 368 (396)
T TIGR03354 353 FGGRDAWAWDMYLRYY 368 (396)
T ss_pred ccchhHHHHHHHHHHH
Confidence 4479999999998754
No 9
>PF00235 Profilin: Profilin; InterPro: IPR002097 Profilin is a small eukaryotic protein that binds to monomeric actin (G-actin) in a 1:1 ratio thus preventing the polymerisation of actin into filaments (F-actin). It can also in certain circumstance promote actin polymerisation. Profilin also binds to polyphosphoinositides such as PIP2. Overall sequence similarity among profilin from organisms which belong to different phyla (ranging from fungi to mammals) is low, but the N-terminal region is relatively well conserved. That region is thought to be involved in the binding to actin. A protein structurally similar to profilin is present in the genome of Variola virus and Vaccinia virus (gene A42R). Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Ara t 8, Bet v 2, Cyn d 12, Hel a 2, Mer a 1 and Phl p 11.; GO: 0003779 actin binding, 0007010 cytoskeleton organization, 0015629 actin cytoskeleton; PDB: 1ACF_A 3NEC_C 2V8F_B 2V8C_A 2VK3_A 2JKF_A 2JKG_A 1F2K_B 2ACG_A 1YPR_B ....
Probab=36.94 E-value=22 Score=21.56 Aligned_cols=13 Identities=38% Similarity=0.933 Sum_probs=10.9
Q ss_pred HHHHHH-hhccccc
Q psy7408 23 WQSYVR-ALKGSTA 35 (66)
Q Consensus 23 WqsYvr-aLKGs~D 35 (66)
||+||. .|-++.-
T Consensus 2 W~~~i~~~L~~~~~ 15 (121)
T PF00235_consen 2 WQDYIDEQLIGTGN 15 (121)
T ss_dssp HHHHHHTHHHTTSS
T ss_pred hhHHHHHHhcccCc
Confidence 999999 8888753
No 10
>PF01806 Paramyxo_P: Paramyxovirinae P phosphoprotein C-terminal region; InterPro: IPR002693 Sendai virus is a member of the Paramyxovirinae family. Its negative-sense ssRNA genome is packaged by the viral nucleoprotein (N) within a helical nucleocapsid. Paramyxovirinae use this N-RNA (nucleoprotein-RNA) complex as a template for both transcription and replication. During viral genome replication, the synthesis of viral RNA and its encapsidation by N are concomitant. Viral transcription and replication are carried out by viral RNA-dependent RNA polymerase, which consists of two proteins: L polymerase and phosphoprotein P. The L polymerase carries the enzyme activity. Phosphoprotein P binds the viral nucleocapsid, and positions the L polymerase on the template for transcription and replication formed by nucleoprotein-RNA (N-RNA) []. This entry represents phosphoprotein P from Sendai virus as well as from close family members. Phosphoprotein P, an indispensable subunit of the viral polymerase complex, is a modular protein organised into two moieties that are both functionally and structurally distinct: a well-conserved C-terminal moiety that contains all the regions required for transcription, and a poorly conserved, intrinsically unstructured N-terminal moiety that provides several additional functions required for replication. The N-terminal moiety is responsible for binding to newly synthesized free N(0) (nucleoprotein that has not yet bound RNA), in order to prevent the binding of N(0) to cellular RNA. The C-terminal moiety consists of an oligomerisation domain, an N-RNA (nucleoprotein-RNA)-binding domain and an L polymerase-binding domain [, ]. ; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0019079 viral genome replication; PDB: 1R4G_A 1EZJ_A.
Probab=35.93 E-value=25 Score=26.98 Aligned_cols=24 Identities=42% Similarity=0.667 Sum_probs=17.7
Q ss_pred hhhhccCCchhhHHHHHHHHHHhhcc
Q psy7408 7 LDMIGRNEPITRKAKFWQSYVRALKG 32 (66)
Q Consensus 7 LdMIGrNE~~skKAkFWqsYvraLKG 32 (66)
|-+|=-|+|+|+.+| |+||..|+-
T Consensus 204 L~lvI~nS~LS~~~K--~sYI~~L~~ 227 (248)
T PF01806_consen 204 LILVINNSPLSRSEK--QSYINELKK 227 (248)
T ss_dssp HHHHHTTS---SHHH--HHHHHHHHT
T ss_pred eeeeeeCCCcchHHH--HHHHHHHHh
Confidence 556778999999999 999999974
No 11
>smart00831 Cation_ATPase_N Cation transporter/ATPase, N-terminus. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+, Na+, Ca2+, Na+/K+, and H+/K+. In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases PUBMED:12480547, PUBMED:12529322.
Probab=35.17 E-value=27 Score=18.94 Aligned_cols=29 Identities=21% Similarity=0.280 Sum_probs=21.6
Q ss_pred hhhhhhhccCCchhhH-HHHHHHHHHhhcc
Q psy7408 4 KQHLDMIGRNEPITRK-AKFWQSYVRALKG 32 (66)
Q Consensus 4 K~HLdMIGrNE~~skK-AkFWqsYvraLKG 32 (66)
.+.++-.|.|+-..++ -.||.-++++++.
T Consensus 17 ~~r~~~~G~N~l~~~~~~s~~~~~l~~~~~ 46 (64)
T smart00831 17 ARRLERYGPNELPPPKKRSPLLRFLRQFHN 46 (64)
T ss_pred HHHHHHhCCCCCCCCCCCCHHHHHHHHHHh
Confidence 3567789999966654 6788888888764
No 12
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=33.12 E-value=29 Score=25.15 Aligned_cols=27 Identities=15% Similarity=0.509 Sum_probs=15.9
Q ss_pred hhhhhhhhccCCchhhHHHHHHHHHHhhcc
Q psy7408 3 LKQHLDMIGRNEPITRKAKFWQSYVRALKG 32 (66)
Q Consensus 3 fK~HLdMIGrNE~~skKAkFWqsYvraLKG 32 (66)
++-|-|.| |.+.+++.|+++||.-.+-
T Consensus 98 ~nKH~e~v---e~~~~ev~~fnnY~~Dp~r 124 (214)
T PF04959_consen 98 FNKHPEKV---EEVKKEVEYFNNYLLDPKR 124 (214)
T ss_dssp HHH-HHHH---HHHHHHHHHHHHH------
T ss_pred hhcCHHHH---HHHHHHHHHHHHHhcCccc
Confidence 45677777 4577889999999975443
No 13
>smart00751 BSD domain in transcription factors and synapse-associated proteins.
Probab=32.32 E-value=36 Score=18.68 Aligned_cols=13 Identities=31% Similarity=0.769 Sum_probs=9.9
Q ss_pred HHHHHHHHHHhhc
Q psy7408 19 KAKFWQSYVRALK 31 (66)
Q Consensus 19 KAkFWqsYvraLK 31 (66)
-..||+.|...+.
T Consensus 36 e~~FW~ryF~~~~ 48 (51)
T smart00751 36 EEEFWARYFYLLY 48 (51)
T ss_pred HHHHHHHHHHHHH
Confidence 4689999987653
No 14
>PF09053 CagZ: CagZ; InterPro: IPR015139 Helicobacter pylori (Campylobacter pylori) clinical isolates can be classified into two types according to their degree of pathogenicity. Type I strains are associated with a severe disease pathology, express functional VacA (vacuolating cytotoxin A) and contain an insertion of 40 kb of foreign DNA: the cag (cytotoxin-associated gene) pathogenicity island (cagPAI). Type II strains lack the 40 kb insert, cagPAI. The cagPAI may be divided into two regions, cag I and cag II and contain approximately 16 and 15 genes, respectively. The cagPAI encodes a type IV secretion system (T4SS), which delivers CagA into the cytosol of gastric epithelial cells through a rigid needle structure covered by Cag7 or CagY, a VirB10-homologous protein, and CagT, a VirB7-homologous protein, at the base []. The CagA protein is the virulence factor that induces morphological changes in host cells, which may be associated with the development of peptic ulcer and gastric carcinoma []. CagZ is a 23 kDa protein consisting of a single compact L-shaped domain, composed of seven alpha-helices that run antiparallel to each other. 70% of the residues are in alpha-helix conformation and no beta-sheet is present. CagZ is essential for the translocation of the pathogenic protein CagA into host cells []. ; PDB: 1S2X_A.
Probab=29.89 E-value=33 Score=25.36 Aligned_cols=17 Identities=41% Similarity=0.645 Sum_probs=13.6
Q ss_pred HHHHHHHHHHhhccccc
Q psy7408 19 KAKFWQSYVRALKGSTA 35 (66)
Q Consensus 19 KAkFWqsYvraLKGs~D 35 (66)
..||-|+|..+||.|.|
T Consensus 28 rdkfiqnyatslkdsnd 44 (199)
T PF09053_consen 28 RDKFIQNYATSLKDSND 44 (199)
T ss_dssp HHHHHHHHTGGGGG--S
T ss_pred HHHHHHHHHhhcccCCC
Confidence 46899999999999977
No 15
>PTZ00316 profilin; Provisional
Probab=27.69 E-value=35 Score=23.89 Aligned_cols=12 Identities=58% Similarity=1.060 Sum_probs=9.8
Q ss_pred HHHHHHh-hcccc
Q psy7408 23 WQSYVRA-LKGST 34 (66)
Q Consensus 23 WqsYvra-LKGs~ 34 (66)
||+||.. |-||.
T Consensus 3 WQaYVD~~L~gsg 15 (150)
T PTZ00316 3 WQAYVDDSLIGSG 15 (150)
T ss_pred HHHHHHhhhhccC
Confidence 9999994 87764
No 16
>KOG0750|consensus
Probab=27.51 E-value=39 Score=26.65 Aligned_cols=25 Identities=24% Similarity=0.335 Sum_probs=18.9
Q ss_pred hhccCCchhhHHHHHHHHHHhhccc
Q psy7408 9 MIGRNEPITRKAKFWQSYVRALKGS 33 (66)
Q Consensus 9 MIGrNE~~skKAkFWqsYvraLKGs 33 (66)
++=|-..-|-+|-||||++..|-|.
T Consensus 198 lgpr~~D~Sg~avF~~sF~agl~~g 222 (304)
T KOG0750|consen 198 LGPRKKDGSGAAVFYQSFLAGLVAG 222 (304)
T ss_pred hccCCCCcccchhhHHHHHHHHHhh
Confidence 3445556788899999999988653
No 17
>KOG1761|consensus
Probab=27.23 E-value=35 Score=23.49 Aligned_cols=15 Identities=47% Similarity=0.572 Sum_probs=12.7
Q ss_pred HHHHHHHHhhccccc
Q psy7408 21 KFWQSYVRALKGSTA 35 (66)
Q Consensus 21 kFWqsYvraLKGs~D 35 (66)
+|||+|-..|||--|
T Consensus 79 ~F~~~YS~vlk~~M~ 93 (116)
T KOG1761|consen 79 KFQQSYSAVLKAQMD 93 (116)
T ss_pred HHHHHHHHHHHHHhh
Confidence 899999999987544
No 18
>smart00392 PROF Profilin. Binds actin monomers, membrane polyphosphoinositides and poly-L-proline.
Probab=24.16 E-value=43 Score=21.22 Aligned_cols=11 Identities=64% Similarity=1.202 Sum_probs=8.4
Q ss_pred HHHHHHh-hccc
Q psy7408 23 WQSYVRA-LKGS 33 (66)
Q Consensus 23 WqsYvra-LKGs 33 (66)
||+||.. |-||
T Consensus 3 Wq~yvd~~l~~~ 14 (129)
T smart00392 3 WQAYVDNLLVGS 14 (129)
T ss_pred hHHHHHHHhhcc
Confidence 9999996 4443
No 19
>PF01639 v110: Viral family 110; InterPro: IPR004848 This entry represents a family of viral proteins of unknown function known as the 110 family []. They contain a central cysteine rich region with eight conserved cysteines. Some proteins in this entry contain two copies of the cysteine rich region eg P18560 from SWISSPROT.
Probab=23.65 E-value=16 Score=24.86 Aligned_cols=17 Identities=18% Similarity=0.669 Sum_probs=14.3
Q ss_pred CchhhHHHHHHHHHHhh
Q psy7408 14 EPITRKAKFWQSYVRAL 30 (66)
Q Consensus 14 E~~skKAkFWqsYvraL 30 (66)
-||.+.-.||++|+..-
T Consensus 26 ~PP~~EL~YWCTY~~~C 42 (110)
T PF01639_consen 26 NPPEEELEYWCTYAKHC 42 (110)
T ss_pred CCChHHhceeccccccC
Confidence 47889999999998753
No 20
>PF09628 YvfG: YvfG protein; InterPro: IPR018590 Yvfg is a hypothetical protein of 71 residues expressed in some bacteria. The monomer consists of two parallel alpha helices, and the protein crystallises as a homo-dimer. ; PDB: 2GSV_A 2JS1_B.
Probab=21.75 E-value=48 Score=21.24 Aligned_cols=28 Identities=29% Similarity=0.494 Sum_probs=16.8
Q ss_pred hhhhhhhhccCCchhhHHHHHHHHHHhhccc
Q psy7408 3 LKQHLDMIGRNEPITRKAKFWQSYVRALKGS 33 (66)
Q Consensus 3 fK~HLdMIGrNE~~skKAkFWqsYvraLKGs 33 (66)
||+|++| |+.--.|-.=-++|-|+.-||
T Consensus 12 ~~q~i~~---N~~~~~ki~AmNaYYr~Vv~t 39 (68)
T PF09628_consen 12 FKQHIQM---NQNYEDKIHAMNAYYRSVVST 39 (68)
T ss_dssp HHHHHHC----SS-S-CCHHHHHHHHHHHHH
T ss_pred HHHHHHh---CccHHHHHHHHHHHHHHHHHH
Confidence 7888776 565445555567777776665
No 21
>PF11393 IcmL: Macrophage killing protein with similarity to conjugation protein; InterPro: IPR021055 IcmL contains two amphipathic beta-sheet regions, required for the pore-forming ability which may be related to the transfer of this protein into a host cell membrane []. The icmL gene shows significant similarity to plasmid genes involved in conjugation however IcmL is thought to be required for macrophage killing. It is unknown whether conjugation plays a role in macrophage killing [].
Probab=21.65 E-value=52 Score=20.64 Aligned_cols=17 Identities=29% Similarity=0.497 Sum_probs=14.3
Q ss_pred HHHHHHHHhhccccccc
Q psy7408 21 KFWQSYVRALKGSTAIL 37 (66)
Q Consensus 21 kFWqsYvraLKGs~Dir 37 (66)
+.|.+|..+|+.|.-|.
T Consensus 53 ~g~~~f~~aL~~Sg~l~ 69 (108)
T PF11393_consen 53 EGWNSFQKALQKSGILD 69 (108)
T ss_pred HHHHHHHHHHHHCCCHH
Confidence 67999999999887664
No 22
>PF03245 Phage_lysis: Bacteriophage Rz lysis protein; InterPro: IPR004929 Many bacteriophages with Gram-negative hosts contain two auxiliary lysis genes Rz and Rz1. These genes are nested, with Rz1 occupying the last third of Rz in a +1 reading frame. Both of these genes are required for host cell lysis if the outer membrane is stabilised by millimolar concentrations of divalent cations, but are otherwise uneccessary []. The Rz protein is believed to posses endopeptidase activity, while Rz1 encodes a prolipoprotein which, after cleavage by a signal peptidase, is located in the outer membrane. It has been suggested that these two proteins may form a complex which cleaves the oligopeptide crosslinks between glycosidic strands in the peptidoglycan and the Lpp lipoproteins of the outer bacterial membrane. For more information see []. This entry represents the Rz protein and related sequences. This family is not considered to be a peptidase according to the MEROPs database.; GO: 0019835 cytolysis
Probab=21.07 E-value=63 Score=21.00 Aligned_cols=24 Identities=21% Similarity=0.338 Sum_probs=17.1
Q ss_pred hhhhccCCchhhHHHHHHHHHHhh
Q psy7408 7 LDMIGRNEPITRKAKFWQSYVRAL 30 (66)
Q Consensus 7 LdMIGrNE~~skKAkFWqsYvraL 30 (66)
+++-.+-+...++-++.|.|||+.
T Consensus 100 ~~lr~~i~~~~~ql~~LQ~YIr~~ 123 (125)
T PF03245_consen 100 FRLRERIDRAIRQLNALQDYIRTQ 123 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444455678899999999974
No 23
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=20.06 E-value=66 Score=26.48 Aligned_cols=13 Identities=46% Similarity=0.912 Sum_probs=10.8
Q ss_pred hhHHHHHHHHHHh
Q psy7408 17 TRKAKFWQSYVRA 29 (66)
Q Consensus 17 skKAkFWqsYvra 29 (66)
-+|-||||-|-+-
T Consensus 401 rRKEKf~rk~C~r 413 (458)
T PF10446_consen 401 RRKEKFWRKHCRR 413 (458)
T ss_pred hhhHHHHHHHHHH
Confidence 4789999999864
Done!