Query psy511
Match_columns 67
No_of_seqs 103 out of 325
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 17:30:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy511.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/511hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2189|consensus 100.0 1.2E-29 2.5E-34 191.5 7.8 65 2-66 186-250 (829)
2 PF01496 V_ATPase_I: V-type AT 99.3 9.9E-13 2.1E-17 99.7 3.1 63 2-66 156-218 (759)
3 PF08793 2C_adapt: 2-cysteine 87.8 0.61 1.3E-05 23.4 2.2 28 25-60 9-36 (37)
4 COG1269 NtpI Archaeal/vacuolar 79.4 1.2 2.6E-05 34.4 1.6 55 8-66 164-218 (660)
5 PF11430 EGL-1: Programmed cel 74.8 0.83 1.8E-05 20.4 -0.2 16 49-64 2-17 (21)
6 PF14202 TnpW: Transposon-enco 68.7 6.6 0.00014 19.5 2.3 26 35-60 6-36 (37)
7 PF09827 CRISPR_Cas2: CRISPR a 58.4 19 0.00041 19.8 3.2 23 40-62 3-27 (78)
8 TIGR01573 cas2 CRISPR-associat 46.0 31 0.00068 20.0 2.9 29 32-60 28-61 (95)
9 PF04807 Gemini_AC4_5: Geminiv 45.9 11 0.00024 18.5 0.8 14 2-15 17-30 (33)
10 PF13443 HTH_26: Cro/C1-type H 45.8 11 0.00024 19.6 0.8 15 51-65 40-54 (63)
11 PRK05771 V-type ATP synthase s 43.1 37 0.0008 26.0 3.6 31 36-66 175-205 (646)
12 PF10369 ALS_ss_C: Small subun 42.2 25 0.00054 19.7 2.0 19 47-65 12-30 (75)
13 PF13014 KH_3: KH domain 37.3 25 0.00054 17.1 1.3 17 51-67 10-26 (43)
14 PF04914 DltD_C: DltD C-termin 34.1 44 0.00096 20.8 2.4 19 48-66 75-93 (130)
15 PF09353 DUF1995: Domain of un 31.1 1E+02 0.0022 20.1 3.8 25 39-63 99-123 (209)
16 PF03937 Sdh5: Flavinator of s 30.8 36 0.00078 19.0 1.4 12 4-15 2-14 (74)
17 PF07401 Lenti_VIF_2: Bovine L 29.2 29 0.00063 23.2 1.0 19 8-26 170-189 (198)
18 PF07830 PP2C_C: Protein serin 27.8 97 0.0021 17.9 2.9 22 39-60 1-38 (81)
19 PF08142 AARP2CN: AARP2CN (NUC 27.2 67 0.0015 18.4 2.2 25 3-27 13-37 (85)
20 smart00785 AARP2CN AARP2CN (NU 26.9 71 0.0015 18.3 2.2 24 3-26 13-36 (83)
21 PF04086 SRP-alpha_N: Signal r 26.9 94 0.002 21.0 3.2 20 38-57 38-64 (279)
22 cd00231 ZipA ZipA C-terminal d 26.7 1.6E+02 0.0036 18.2 4.6 62 5-66 39-111 (130)
23 TIGR00789 flhB_rel flhB C-term 26.2 1.2E+02 0.0026 17.4 3.1 25 42-66 19-44 (82)
24 PF04312 DUF460: Protein of un 26.1 40 0.00087 21.5 1.2 19 49-67 87-105 (138)
25 PF03479 DUF296: Domain of unk 25.6 93 0.002 18.6 2.7 25 40-64 4-28 (120)
26 COG4062 MtrB Tetrahydromethano 24.9 91 0.002 19.1 2.5 31 27-57 13-43 (108)
27 PF12153 CAP18_C: LPS binding 24.6 59 0.0013 15.4 1.3 13 47-59 8-20 (28)
28 PF08889 WbqC: WbqC-like prote 24.4 55 0.0012 21.9 1.6 22 46-67 138-159 (219)
29 PF12844 HTH_19: Helix-turn-he 23.7 57 0.0012 16.8 1.3 14 51-64 41-54 (64)
30 smart00530 HTH_XRE Helix-turn- 23.7 68 0.0015 14.5 1.5 15 50-64 38-52 (56)
31 PF00356 LacI: Bacterial regul 23.6 82 0.0018 16.0 1.9 16 47-62 27-42 (46)
32 cd02394 vigilin_like_KH K homo 22.9 72 0.0016 16.4 1.6 17 51-67 19-35 (62)
33 cd02393 PNPase_KH Polynucleoti 22.8 67 0.0014 17.0 1.5 17 51-67 21-37 (61)
34 COG2102 Predicted ATPases of P 22.4 95 0.0021 21.4 2.5 19 48-66 98-116 (223)
35 PF00013 KH_1: KH domain syndr 22.3 61 0.0013 16.5 1.3 17 51-67 19-35 (60)
36 COG3655 Predicted transcriptio 22.3 64 0.0014 18.4 1.4 14 51-64 45-58 (73)
37 TIGR02684 dnstrm_HI1420 probab 22.1 71 0.0015 18.5 1.6 15 51-65 72-86 (89)
38 cd02979 PHOX_C FAD-dependent P 22.0 1E+02 0.0022 19.6 2.5 22 42-63 32-57 (167)
39 COG2938 Uncharacterized conser 21.9 68 0.0015 19.2 1.5 12 3-14 14-25 (94)
40 PF05184 SapB_1: Saposin-like 21.5 1E+02 0.0022 14.3 1.9 14 48-61 25-38 (39)
41 PF12682 Flavodoxin_4: Flavodo 21.0 1.7E+02 0.0037 18.3 3.3 26 41-66 3-29 (156)
42 PRK04017 hypothetical protein; 20.5 89 0.0019 19.7 1.9 20 46-65 77-96 (132)
No 1
>KOG2189|consensus
Probab=99.96 E-value=1.2e-29 Score=191.48 Aligned_cols=65 Identities=62% Similarity=1.128 Sum_probs=64.1
Q ss_pred hhHHHHHHHhhCCcEEEEeeecCCcccCCCCCCceeeEEEEEEEecHHHHHHHHHhhhhcCCeee
Q psy511 2 PAFERMLWRACRGNVFLRQAEIETPLEDINSGDPVYKSVFIIFFQGDQLKTRVMKICEGKKLSSV 66 (67)
Q Consensus 2 ~~fer~lwR~~RGN~~~~~~~i~~~~~d~~~~~~~~k~vFiv~~~G~~l~~Ki~KIc~~f~a~~~ 66 (67)
++|||+|||+||||+|+++.++|+++.||+|||+++|+|||||||||++++||+||||||||++|
T Consensus 186 ~~fER~LWRa~Rgn~f~r~~~ie~~l~dp~Tge~~~K~vFivF~~Geql~~kIkKIcd~f~a~~y 250 (829)
T KOG2189|consen 186 FAFERMLWRACRGNLFIRQSDIEEPLEDPKTGEPVEKNVFIVFFQGEQLKQKIKKICDGFGATLY 250 (829)
T ss_pred HHHHHHHHHHhccceEEEeecccccccCCccCCcceeEEEEEEeecHHHHHHHHHHHhccCcEee
Confidence 68999999999999999999999999999999999999999999999999999999999999998
No 2
>PF01496 V_ATPase_I: V-type ATPase 116kDa subunit family ; InterPro: IPR002490 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. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents the 116kDa subunit (or subunit a) and subunit I found in the V0 or A0 complex of V- or A-ATPases, respectively. The 116kDa subunit is a transmembrane glycoprotein required for the assembly and proton transport activity of the ATPase complex. Several isoforms of the 116kDa subunit exist, providing a potential role in the differential targeting and regulation of the V-ATPase for specific organelles []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015991 ATP hydrolysis coupled proton transport, 0033177 proton-transporting two-sector ATPase complex, proton-transporting domain; PDB: 2RPW_X 2NVJ_A 2JTW_A 3RRK_A.
Probab=99.31 E-value=9.9e-13 Score=99.67 Aligned_cols=63 Identities=46% Similarity=0.805 Sum_probs=44.4
Q ss_pred hhHHHHHHHhhCCcEEEEeeecCCcccCCCCCCceeeEEEEEEEecHHHHHHHHHhhhhcCCeee
Q psy511 2 PAFERMLWRACRGNVFLRQAEIETPLEDINSGDPVYKSVFIIFFQGDQLKTRVMKICEGKKLSSV 66 (67)
Q Consensus 2 ~~fer~lwR~~RGN~~~~~~~i~~~~~d~~~~~~~~k~vFiv~~~G~~l~~Ki~KIc~~f~a~~~ 66 (67)
++|+|+|||+++||+|+++.+++++..|+. +.++|.+|+++++|++..+|++|||+++|++.|
T Consensus 156 ~~f~~~l~r~~~~N~fi~~~~Ie~~~~d~~--e~~~k~v~vv~~~~~~~~~kv~~il~~~~f~~~ 218 (759)
T PF01496_consen 156 ESFERILWRATRGNIFIRFSEIEEILEDPK--EEVEKEVFVVFFSGKELEEKVKKILRSFGFERY 218 (759)
T ss_dssp HHHHHHHHHHHTT-----S------EEEE---EE-SSSEEEEEEEEGGGHHHHHHHHHTTT--B-
T ss_pred HHHHHHHHHhccCCeEEEEEeeeccccccc--ceeeeeeEEEEEEchhhHHHHHHHhhccCceec
Confidence 579999999999999999999999988877 778899999999999999999999999999876
No 3
>PF08793 2C_adapt: 2-cysteine adaptor domain; InterPro: IPR014901 The virus-specific 2-cysteine adaptor is found fused to OTU/A20-like peptidases and S/T protein kinases. The associations to these proteins indicate that they might function as viral adaptors connecting the kinases and OTU/A20 peptidases to specific targets [].
Probab=87.83 E-value=0.61 Score=23.40 Aligned_cols=28 Identities=21% Similarity=0.434 Sum_probs=23.1
Q ss_pred CcccCCCCCCceeeEEEEEEEecHHHHHHHHHhhhh
Q psy511 25 TPLEDINSGDPVYKSVFIIFFQGDQLKTRVMKICEG 60 (67)
Q Consensus 25 ~~~~d~~~~~~~~k~vFiv~~~G~~l~~Ki~KIc~~ 60 (67)
++..+|.||.++.. |..+.+++.|.|++
T Consensus 9 np~~NP~Tgr~Ik~--------~gp~y~~l~~~C~~ 36 (37)
T PF08793_consen 9 NPTVNPITGRKIKP--------GGPTYKKLVKECGG 36 (37)
T ss_pred CCCCCCCCCCcCCC--------CChHHHHHHHHcCC
Confidence 44578899988765 88999999999986
No 4
>COG1269 NtpI Archaeal/vacuolar-type H+-ATPase subunit I [Energy production and conversion]
Probab=79.45 E-value=1.2 Score=34.37 Aligned_cols=55 Identities=25% Similarity=0.225 Sum_probs=38.9
Q ss_pred HHHhhCCcEEEEeeecCCcccCCCCCCceeeEEEEEEEecHHHHHHHHHhhhhcCCeee
Q psy511 8 LWRACRGNVFLRQAEIETPLEDINSGDPVYKSVFIIFFQGDQLKTRVMKICEGKKLSSV 66 (67)
Q Consensus 8 lwR~~RGN~~~~~~~i~~~~~d~~~~~~~~k~vFiv~~~G~~l~~Ki~KIc~~f~a~~~ 66 (67)
+|+..++++.....+..... -++...+.+++++.+++....++.+++++.+.+.+
T Consensus 164 ~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~v~~~~~~~~~~v~~~~~~~~~~~~ 218 (660)
T COG1269 164 LVRREKLEALVGVIEDEVAL----YGENVEASVVIVVAHGAEDLDKVSKILNELGFELY 218 (660)
T ss_pred eehhhhhhHHHhhcccccch----hhhccccceEEEEEecccchHHHHHHHHhCCcEEe
Confidence 45555555555444333321 11456789999999999999999999999988765
No 5
>PF11430 EGL-1: Programmed cell death activator EGL-1; InterPro: IPR021543 Initiation of programmed cell death in C.elegans occurs by the binding of EGL-1 to CED-9 which disrupts a complex involving CED-4/CED-9 and allows CED-4 to activate CED-3, a caspase. It is the C-terminal domain of EGL-1 which is involved in the formation of the complex with CED-9. The formation of the complex induces structural rearrangements in CED-9 and EGL-1 adopts an extended alpha-helical conformation []. ; PDB: 1TY4_D.
Probab=74.83 E-value=0.83 Score=20.35 Aligned_cols=16 Identities=13% Similarity=0.466 Sum_probs=13.6
Q ss_pred HHHHHHHHhhhhcCCe
Q psy511 49 QLKTRVMKICEGKKLS 64 (67)
Q Consensus 49 ~l~~Ki~KIc~~f~a~ 64 (67)
.|+.|+-+.||.|++.
T Consensus 2 ~IG~kla~MCDdFD~e 17 (21)
T PF11430_consen 2 EIGTKLAAMCDDFDAE 17 (21)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHH
Confidence 4789999999999765
No 6
>PF14202 TnpW: Transposon-encoded protein TnpW
Probab=68.75 E-value=6.6 Score=19.52 Aligned_cols=26 Identities=4% Similarity=0.335 Sum_probs=19.0
Q ss_pred ceeeEEEEEEEe-----cHHHHHHHHHhhhh
Q psy511 35 PVYKSVFIIFFQ-----GDQLKTRVMKICEG 60 (67)
Q Consensus 35 ~~~k~vFiv~~~-----G~~l~~Ki~KIc~~ 60 (67)
.+.+++|+|-.+ .|.+..|++|++..
T Consensus 6 kIG~Tty~V~~~F~~~s~et~~DKi~rli~~ 36 (37)
T PF14202_consen 6 KIGKTTYVVEVHFSETSKETMQDKIKRLIRR 36 (37)
T ss_pred EECCEEEEEEEEECCCccccHHHHHHHHHhc
Confidence 356778886542 37899999999863
No 7
>PF09827 CRISPR_Cas2: CRISPR associated protein Cas2; InterPro: IPR019199 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. Members of this family of bacterial proteins comprise various hypothetical proteins, as well as CRISPR (clustered regularly interspaced short palindromic repeats) associated proteins, conferring resistance to infection by certain bacteriophages. ; PDB: 3EXC_X 2I0X_A 3OQ2_B 3UI3_A 1ZPW_X 2I8E_A 2IVY_A.
Probab=58.39 E-value=19 Score=19.79 Aligned_cols=23 Identities=13% Similarity=0.423 Sum_probs=18.3
Q ss_pred EEEEEE--ecHHHHHHHHHhhhhcC
Q psy511 40 VFIIFF--QGDQLKTRVMKICEGKK 62 (67)
Q Consensus 40 vFiv~~--~G~~l~~Ki~KIc~~f~ 62 (67)
-++|.| ..+..++|+.|+++++|
T Consensus 3 ~~lv~YDi~~~k~~~kv~k~L~~~g 27 (78)
T PF09827_consen 3 LYLVAYDISDNKRRNKVRKILKSYG 27 (78)
T ss_dssp EEEEEEEEHSHHHHHHHHHHHHHTT
T ss_pred EEEEEEECCCcHHHHHHHHHHHHhC
Confidence 356666 45788999999999998
No 8
>TIGR01573 cas2 CRISPR-associated endoribonuclease Cas2. This model describes most members of the family of Cas2, one of the first four protein families found to mark prokaryotic genomes that contain multiple CRISPR elements. It is an endoribonuclease, capable of cleaving single-stranded RNA. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. The cas genes are found near the repeats. A distinct branch of the Cas2 family shows a very low level of sequence identity and is modeled by TIGR01873 instead.
Probab=46.01 E-value=31 Score=19.97 Aligned_cols=29 Identities=28% Similarity=0.330 Sum_probs=21.2
Q ss_pred CC-CceeeEEEEEEEecH----HHHHHHHHhhhh
Q psy511 32 SG-DPVYKSVFIIFFQGD----QLKTRVMKICEG 60 (67)
Q Consensus 32 ~~-~~~~k~vFiv~~~G~----~l~~Ki~KIc~~ 60 (67)
.| ..+++|||....... .+.+++.++.+.
T Consensus 28 ~G~~rvQ~SVf~~~~~~~~~~~~l~~~l~~~i~~ 61 (95)
T TIGR01573 28 YGLQRVQYSVFEGILEPNQLARKLIERLKRIIPD 61 (95)
T ss_pred cchhheeccEEEEEcCHHHHHHHHHHHHHHhCCC
Confidence 46 678999999988653 466777777654
No 9
>PF04807 Gemini_AC4_5: Geminivirus AC4/5 conserved region; InterPro: IPR006892 This entry represents a conserved domain found in Gemini virus AC4 and AC5 proteins [].
Probab=45.88 E-value=11 Score=18.53 Aligned_cols=14 Identities=29% Similarity=0.880 Sum_probs=11.0
Q ss_pred hhHHHHHHHhhCCc
Q psy511 2 PAFERMLWRACRGN 15 (67)
Q Consensus 2 ~~fer~lwR~~RGN 15 (67)
..|.+++|+++|-.
T Consensus 17 k~l~KIl~~~~rst 30 (33)
T PF04807_consen 17 KHLTKILWFICRST 30 (33)
T ss_pred HHHHHHhhhcccCc
Confidence 46889999998753
No 10
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=45.83 E-value=11 Score=19.57 Aligned_cols=15 Identities=20% Similarity=0.151 Sum_probs=10.6
Q ss_pred HHHHHHhhhhcCCee
Q psy511 51 KTRVMKICEGKKLSS 65 (67)
Q Consensus 51 ~~Ki~KIc~~f~a~~ 65 (67)
.+.+.+||+.||+++
T Consensus 40 ~~~l~~ia~~l~~~~ 54 (63)
T PF13443_consen 40 LDTLEKIAKALNCSP 54 (63)
T ss_dssp HHHHHHHHHHHT--H
T ss_pred HHHHHHHHHHcCCCH
Confidence 467889999998763
No 11
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=43.08 E-value=37 Score=25.97 Aligned_cols=31 Identities=10% Similarity=0.075 Sum_probs=25.1
Q ss_pred eeeEEEEEEEecHHHHHHHHHhhhhcCCeee
Q psy511 36 VYKSVFIIFFQGDQLKTRVMKICEGKKLSSV 66 (67)
Q Consensus 36 ~~k~vFiv~~~G~~l~~Ki~KIc~~f~a~~~ 66 (67)
....++++++......+++.++|++++++.+
T Consensus 175 ~~~~~~~vvv~~~~~~~~~~~~l~~~~f~~~ 205 (646)
T PRK05771 175 DKGYVYVVVVVLKELSDEVEEELKKLGFERL 205 (646)
T ss_pred cCCcEEEEEEEEhhhHHHHHHHHHHCCCEEe
Confidence 3557778877777888999999999988764
No 12
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=42.21 E-value=25 Score=19.65 Aligned_cols=19 Identities=5% Similarity=0.134 Sum_probs=15.5
Q ss_pred cHHHHHHHHHhhhhcCCee
Q psy511 47 GDQLKTRVMKICEGKKLSS 65 (67)
Q Consensus 47 G~~l~~Ki~KIc~~f~a~~ 65 (67)
...-+..|.+||+.|+|++
T Consensus 12 ~~~~r~ei~~l~~~f~a~i 30 (75)
T PF10369_consen 12 TPENRSEILQLAEIFRARI 30 (75)
T ss_dssp SCHHHHHHHHHHHHTT-EE
T ss_pred CccCHHHHHHHHHHhCCEE
Confidence 4577899999999999986
No 13
>PF13014 KH_3: KH domain
Probab=37.25 E-value=25 Score=17.15 Aligned_cols=17 Identities=12% Similarity=0.108 Sum_probs=13.6
Q ss_pred HHHHHHhhhhcCCeeeC
Q psy511 51 KTRVMKICEGKKLSSVV 67 (67)
Q Consensus 51 ~~Ki~KIc~~f~a~~~~ 67 (67)
+..|++|.+..+|++.+
T Consensus 10 G~~I~~I~~~tg~~I~i 26 (43)
T PF13014_consen 10 GSTIKEIREETGAKIQI 26 (43)
T ss_pred ChHHHHHHHHhCcEEEE
Confidence 45688999999998764
No 14
>PF04914 DltD_C: DltD C-terminal region; InterPro: IPR006998 The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation []. These sequences contain the C-terminal region of DltD.; PDB: 3BMA_C.
Probab=34.08 E-value=44 Score=20.79 Aligned_cols=19 Identities=0% Similarity=0.064 Sum_probs=14.3
Q ss_pred HHHHHHHHHhhhhcCCeee
Q psy511 48 DQLKTRVMKICEGKKLSSV 66 (67)
Q Consensus 48 ~~l~~Ki~KIc~~f~a~~~ 66 (67)
+...+||+++|++.|.++.
T Consensus 75 ~~~y~kI~~~~~~~gf~v~ 93 (130)
T PF04914_consen 75 QEYYKKIKYQLKSQGFNVA 93 (130)
T ss_dssp HHHHHHHHHHHHTTT--EE
T ss_pred HHHHHHHHHHHHHCCCEEE
Confidence 4678999999999998653
No 15
>PF09353 DUF1995: Domain of unknown function (DUF1995); InterPro: IPR018962 This family of proteins are functionally uncharacterised.
Probab=31.14 E-value=1e+02 Score=20.11 Aligned_cols=25 Identities=20% Similarity=0.317 Sum_probs=21.0
Q ss_pred EEEEEEEecHHHHHHHHHhhhhcCC
Q psy511 39 SVFIIFFQGDQLKTRVMKICEGKKL 63 (67)
Q Consensus 39 ~vFiv~~~G~~l~~Ki~KIc~~f~a 63 (67)
.+++++.++..-...+.++|+..+.
T Consensus 99 ~~~vvv~p~~~~l~~~e~~~~~~~~ 123 (209)
T PF09353_consen 99 DILVVVAPSPQELDDVEKLCEAAGG 123 (209)
T ss_pred CEEEEEECChhhHHHHHHHHHhcCC
Confidence 6778888777679999999999876
No 16
>PF03937 Sdh5: Flavinator of succinate dehydrogenase; InterPro: IPR005631 This entry represents a group of uncharacterised small proteins found in both eukaryotes and prokaryotes, including NMA1147 from Neisseria meningitidis [] and YgfY from Escherichia coli []. YgfY may be involved in transcriptional regulation. The structure of these proteins consists of a complex bundle of five alpha-helices, which is composed of an up-down 3-helix bundle plus an orthogonal 2-helix bundle. ; PDB: 2LM4_A 1PUZ_A 2JR5_A 1X6I_A 1X6J_A.
Probab=30.85 E-value=36 Score=18.98 Aligned_cols=12 Identities=42% Similarity=0.822 Sum_probs=8.8
Q ss_pred HHHHHHHh-hCCc
Q psy511 4 FERMLWRA-CRGN 15 (67)
Q Consensus 4 fer~lwR~-~RGN 15 (67)
-+|+.||+ -||.
T Consensus 2 ~kRl~~r~~rRG~ 14 (74)
T PF03937_consen 2 RKRLRWRCKRRGM 14 (74)
T ss_dssp HHHHHHHHSS-SS
T ss_pred cHHHHHHhhcccH
Confidence 47899999 7774
No 17
>PF07401 Lenti_VIF_2: Bovine Lentivirus VIF protein; InterPro: IPR009979 This family consists of several Lentivirus viral infectivity factor (VIF) proteins. VIF is known to be essential for ability of cell-free virus preparation to infect cells []. Members of this family are specific to Bovine immunodeficiency virus (BIV) and Jembrana disease virus (JDV) which also infects cattle.
Probab=29.24 E-value=29 Score=23.21 Aligned_cols=19 Identities=32% Similarity=0.639 Sum_probs=14.4
Q ss_pred HHHhhCCc-EEEEeeecCCc
Q psy511 8 LWRACRGN-VFLRQAEIETP 26 (67)
Q Consensus 8 lwR~~RGN-~~~~~~~i~~~ 26 (67)
|||+.||+ ++++|..=.+|
T Consensus 170 LwRarR~Ttlw~~f~~gkep 189 (198)
T PF07401_consen 170 LWRARRVTTLWMNFSSGKEP 189 (198)
T ss_pred eeeeccCceEEEEecCCCCc
Confidence 78999996 78887765554
No 18
>PF07830 PP2C_C: Protein serine/threonine phosphatase 2C, C-terminal domain; InterPro: IPR012911 Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain []. ; GO: 0000287 magnesium ion binding, 0004721 phosphoprotein phosphatase activity, 0030145 manganese ion binding; PDB: 2P8E_A 3FXL_A 3FXO_A 1A6Q_A 3FXK_A 3FXM_A 3FXJ_A.
Probab=27.76 E-value=97 Score=17.95 Aligned_cols=22 Identities=36% Similarity=0.629 Sum_probs=14.2
Q ss_pred EEEEEEEec----------------HHHHHHHHHhhhh
Q psy511 39 SVFIIFFQG----------------DQLKTRVMKICEG 60 (67)
Q Consensus 39 ~vFiv~~~G----------------~~l~~Ki~KIc~~ 60 (67)
++-+|.|+| ..|.+|++.|++.
T Consensus 1 SiILV~FPgAPkvs~EAv~~E~eLd~~l~~rv~ei~~~ 38 (81)
T PF07830_consen 1 SIILVCFPGAPKVSEEAVKKEAELDKYLEQRVEEIIEK 38 (81)
T ss_dssp EEEEEE-TTS----HHHHHHHHHHHHHHHHHHHHHT--
T ss_pred CEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456788887 2578888888865
No 19
>PF08142 AARP2CN: AARP2CN (NUC121) domain; InterPro: IPR012948 This domain is the central domain of AARP2 (asparagine and aspartate rich protein 2). It is weakly similar to the GTP-binding domain of elongation factor TU []. PfAARP2 is an antigen from Plasmodium falciparum of 150 kDa, which is encoded by a unique gene on chromosome 1 []. The central region of Pfaarp2 contains blocks of repetitions encoding asparagine and aspartate residues. ; GO: 0042254 ribosome biogenesis, 0005634 nucleus
Probab=27.25 E-value=67 Score=18.42 Aligned_cols=25 Identities=16% Similarity=0.230 Sum_probs=19.4
Q ss_pred hHHHHHHHhhCCcEEEEeeecCCcc
Q psy511 3 AFERMLWRACRGNVFLRQAEIETPL 27 (67)
Q Consensus 3 ~fer~lwR~~RGN~~~~~~~i~~~~ 27 (67)
.++.+-||-.|+.++..-.+....-
T Consensus 13 k~~~i~WR~~r~y~lad~~e~~~~~ 37 (85)
T PF08142_consen 13 KPRPISWRDQRPYMLADRVEFVPDP 37 (85)
T ss_pred ccCCCccccCCCeEEEEEEEecCCc
Confidence 3456789999999999887776543
No 20
>smart00785 AARP2CN AARP2CN (NUC121) domain. This domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU PUBMED:15112237.
Probab=26.94 E-value=71 Score=18.29 Aligned_cols=24 Identities=17% Similarity=0.174 Sum_probs=18.2
Q ss_pred hHHHHHHHhhCCcEEEEeeecCCc
Q psy511 3 AFERMLWRACRGNVFLRQAEIETP 26 (67)
Q Consensus 3 ~fer~lwR~~RGN~~~~~~~i~~~ 26 (67)
.++.+-||-.|+.+...-.+..+.
T Consensus 13 k~~~l~WR~~rpY~lad~~e~~~~ 36 (83)
T smart00785 13 KPRPLSWRDQHPYMLADRVEDITD 36 (83)
T ss_pred cCCCCcccCCCCeEEEEEeEecCC
Confidence 356678999999999877665543
No 21
>PF04086 SRP-alpha_N: Signal recognition particle, alpha subunit, N-terminal; InterPro: IPR007222 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 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. This entry represents the alpha subunit of the SR receptor.; GO: 0003924 GTPase activity, 0005047 signal recognition particle binding, 0005525 GTP binding, 0006184 GTP catabolic process, 0006886 intracellular protein transport, 0005785 signal recognition particle receptor complex; PDB: 2FH5_A 2GO5_1.
Probab=26.86 E-value=94 Score=21.01 Aligned_cols=20 Identities=35% Similarity=0.509 Sum_probs=13.1
Q ss_pred eEEEEEEEec-------HHHHHHHHHh
Q psy511 38 KSVFIIFFQG-------DQLKTRVMKI 57 (67)
Q Consensus 38 k~vFiv~~~G-------~~l~~Ki~KI 57 (67)
-.||||.||+ +.|...|+++
T Consensus 38 ~LvfVvvYq~il~l~yvd~LL~~v~~~ 64 (279)
T PF04086_consen 38 GLVFVVVYQKILQLTYVDKLLDDVKKE 64 (279)
T ss_dssp TEEEEEEES-GGGHHHHHHHHHHHHHH
T ss_pred CEEEeeeecccccchHHHHHHHHHHHH
Confidence 3899999998 4555555543
No 22
>cd00231 ZipA ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic tubulins, at the prospective division site, followed by the sequential addition of FtsK, FtsQ, FtsL, FtsW, FtsI, and FtsN. ZipA contains three domains: a short N-terminal membrane-anchored domain, a central P/Q domain that is rich in proline and glutamine and a C-terminal domain, which comprises almost half the protein.
Probab=26.67 E-value=1.6e+02 Score=18.17 Aligned_cols=62 Identities=15% Similarity=0.110 Sum_probs=39.3
Q ss_pred HHHHHHhhCCcEEEEeeecCCc-ccCCCCC--CceeeEEEEEEEec--------HHHHHHHHHhhhhcCCeee
Q psy511 5 ERMLWRACRGNVFLRQAEIETP-LEDINSG--DPVYKSVFIIFFQG--------DQLKTRVMKICEGKKLSSV 66 (67)
Q Consensus 5 er~lwR~~RGN~~~~~~~i~~~-~~d~~~~--~~~~k~vFiv~~~G--------~~l~~Ki~KIc~~f~a~~~ 66 (67)
.|..=....|++.+..+.+.+| ..|+.+- ....-.+|.+--++ +.+-+--+++++.+++.+.
T Consensus 39 Hr~~~~~~~g~vlFSlan~~~PG~F~~~~m~~~~t~Gvtlfm~lP~~~~~~~~F~~Ml~~A~~lA~~LgG~ll 111 (130)
T cd00231 39 HRHLSLSGSGPVLFSVANMVKPGTFDPDNMADFSTPGISFFMQLPSPGDALQNFKLMLQAAQRIADDLGGVVL 111 (130)
T ss_pred EeccccCCCCceEEEEeeccCCCCCChhhhhccccCeEEEEEECCCCCcHHHHHHHHHHHHHHHHHHcCCEEE
Confidence 3433345678888888887765 3455432 23344555555554 4677888899999998764
No 23
>TIGR00789 flhB_rel flhB C-terminus-related protein. This model describes a short protein (80-93 residues) homologous to the C-terminus of the flagellar biosynthetic protein FlhB. It is found so far only in species that also have FlhB. In a phylogenetic tree based on alignment of both this family and the homologous region of FlhB and its homologs, the members of this family form a monophyletic set.
Probab=26.25 E-value=1.2e+02 Score=17.38 Aligned_cols=25 Identities=16% Similarity=0.389 Sum_probs=19.5
Q ss_pred EEEEec-HHHHHHHHHhhhhcCCeee
Q psy511 42 IIFFQG-DQLKTRVMKICEGKKLSSV 66 (67)
Q Consensus 42 iv~~~G-~~l~~Ki~KIc~~f~a~~~ 66 (67)
+|...| +.+.++|+++++..+..++
T Consensus 19 ~VvAKG~g~~A~~I~~~A~e~~VPi~ 44 (82)
T TIGR00789 19 KVVASGVGEVAERIIEIAKKHGIPIV 44 (82)
T ss_pred EEEEEeCCHHHHHHHHHHHHcCCCEE
Confidence 355556 7999999999998887654
No 24
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=26.06 E-value=40 Score=21.55 Aligned_cols=19 Identities=16% Similarity=-0.011 Sum_probs=15.0
Q ss_pred HHHHHHHHhhhhcCCeeeC
Q psy511 49 QLKTRVMKICEGKKLSSVV 67 (67)
Q Consensus 49 ~l~~Ki~KIc~~f~a~~~~ 67 (67)
..=.-++||..+|+|..|+
T Consensus 87 p~P~~V~Kia~~f~A~ly~ 105 (138)
T PF04312_consen 87 PPPETVKKIARSFNAVLYT 105 (138)
T ss_pred CCcHHHHHHHHHhCCcccC
Confidence 3456788999999998885
No 25
>PF03479 DUF296: Domain of unknown function (DUF296); InterPro: IPR005175 This putative conserved domain is found in proteins that contain AT-hook motifs IPR000637 from INTERPRO, suggesting a DNA-binding function for the proteins as a whole, however, the function of this domain is unknown. Overexpression of a protein containing this domain, Q9S7C9 from SWISSPROT, in Arabidopsis thaliana causes late flowering and modified leaf development []. ; PDB: 2DT4_A 2P6Y_A 3HWU_A 3HTN_A 2NMU_A 2H6L_A 2HX0_A.
Probab=25.60 E-value=93 Score=18.58 Aligned_cols=25 Identities=12% Similarity=0.182 Sum_probs=19.1
Q ss_pred EEEEEEecHHHHHHHHHhhhhcCCe
Q psy511 40 VFIIFFQGDQLKTRVMKICEGKKLS 64 (67)
Q Consensus 40 vFiv~~~G~~l~~Ki~KIc~~f~a~ 64 (67)
..+-+-+|+.+.+.|.++|+..+.+
T Consensus 4 ~~~rl~~Gedl~~~l~~~~~~~~i~ 28 (120)
T PF03479_consen 4 FVIRLDPGEDLLESLEAFAREHGIR 28 (120)
T ss_dssp EEEEEETTSBHHHHHHHHHHHHT-S
T ss_pred EEEEECCCCHHHHHHHHHHHHCCCc
Confidence 3455558999999999999987653
No 26
>COG4062 MtrB Tetrahydromethanopterin S-methyltransferase, subunit B [Coenzyme metabolism]
Probab=24.93 E-value=91 Score=19.12 Aligned_cols=31 Identities=19% Similarity=0.266 Sum_probs=20.9
Q ss_pred ccCCCCCCceeeEEEEEEEecHHHHHHHHHh
Q psy511 27 LEDINSGDPVYKSVFIIFFQGDQLKTRVMKI 57 (67)
Q Consensus 27 ~~d~~~~~~~~k~vFiv~~~G~~l~~Ki~KI 57 (67)
..||+||--..+.==+|++.=+.+.++|+|.
T Consensus 13 vmd~~Tgvvae~~edvi~ldv~pi~Eqi~kL 43 (108)
T COG4062 13 VMDPETGVVAEGFEDVIFLDVDPIEEQIKKL 43 (108)
T ss_pred eEccchhhHhhccCceEEEeccHHHHHHHHH
Confidence 4799987544444345666668888888874
No 27
>PF12153 CAP18_C: LPS binding domain of CAP18 (C terminal); InterPro: IPR022746 This entry represents the cathlecidin antimicrobial C-terminal peptides. The C terminus is cleaved from the cathlecidin precursor, and is approximately 30 amino acids in length with a helical structure. This entry is found in association with PF00666 from PFAM. The C terminus peptides possess antimicrobial activity by virtue of their binding to bacterial lipopolysaccharides [][].; GO: 0042742 defense response to bacterium; PDB: 1LYP_A 2LMF_A 2FBU_H 2FBS_N 2K6O_A 2FCG_F.
Probab=24.65 E-value=59 Score=15.37 Aligned_cols=13 Identities=23% Similarity=0.575 Sum_probs=7.8
Q ss_pred cHHHHHHHHHhhh
Q psy511 47 GDQLKTRVMKICE 59 (67)
Q Consensus 47 G~~l~~Ki~KIc~ 59 (67)
|+.+.+|++||-+
T Consensus 8 ~eKigeklkkIGQ 20 (28)
T PF12153_consen 8 GEKIGEKLKKIGQ 20 (28)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 3566667766643
No 28
>PF08889 WbqC: WbqC-like protein family; InterPro: IPR014985 This family of proteins are functionally uncharacterised. However, it is found in an O-antigen gene cluster in Escherichia coli [] and other bacteria [] suggesting a role in O-antigen production. It has been suggested that wbnG may code for a glycine transferase [].
Probab=24.37 E-value=55 Score=21.86 Aligned_cols=22 Identities=18% Similarity=0.401 Sum_probs=17.9
Q ss_pred ecHHHHHHHHHhhhhcCCeeeC
Q psy511 46 QGDQLKTRVMKICEGKKLSSVV 67 (67)
Q Consensus 46 ~G~~l~~Ki~KIc~~f~a~~~~ 67 (67)
++..-.+++..||..+||+.|+
T Consensus 138 ~~~~~~~~vi~i~~~~ga~~Yi 159 (219)
T PF08889_consen 138 PEGKKSERVIDICKALGADTYI 159 (219)
T ss_pred CCCCchHHHHHHHHHcCCCeee
Confidence 3455678999999999999885
No 29
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=23.71 E-value=57 Score=16.77 Aligned_cols=14 Identities=29% Similarity=0.301 Sum_probs=10.6
Q ss_pred HHHHHHhhhhcCCe
Q psy511 51 KTRVMKICEGKKLS 64 (67)
Q Consensus 51 ~~Ki~KIc~~f~a~ 64 (67)
...+++||+.|+++
T Consensus 41 ~~~l~~i~~~~~v~ 54 (64)
T PF12844_consen 41 VSTLKKIAEALGVS 54 (64)
T ss_dssp HHHHHHHHHHHTS-
T ss_pred HHHHHHHHHHhCCC
Confidence 46678999998875
No 30
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=23.70 E-value=68 Score=14.52 Aligned_cols=15 Identities=13% Similarity=0.111 Sum_probs=11.0
Q ss_pred HHHHHHHhhhhcCCe
Q psy511 50 LKTRVMKICEGKKLS 64 (67)
Q Consensus 50 l~~Ki~KIc~~f~a~ 64 (67)
-...+.+||+.||.+
T Consensus 38 ~~~~~~~i~~~~~~~ 52 (56)
T smart00530 38 SLETLKKLAKALGVS 52 (56)
T ss_pred CHHHHHHHHHHhCCC
Confidence 356678888888765
No 31
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=23.58 E-value=82 Score=16.04 Aligned_cols=16 Identities=13% Similarity=0.360 Sum_probs=13.3
Q ss_pred cHHHHHHHHHhhhhcC
Q psy511 47 GDQLKTRVMKICEGKK 62 (67)
Q Consensus 47 G~~l~~Ki~KIc~~f~ 62 (67)
++..++||.++++.+|
T Consensus 27 s~~tr~rI~~~a~~lg 42 (46)
T PF00356_consen 27 SEETRERILEAAEELG 42 (46)
T ss_dssp THHHHHHHHHHHHHHT
T ss_pred CHHHHHHHHHHHHHHC
Confidence 4788999999998765
No 32
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=22.86 E-value=72 Score=16.37 Aligned_cols=17 Identities=18% Similarity=0.167 Sum_probs=12.4
Q ss_pred HHHHHHhhhhcCCeeeC
Q psy511 51 KTRVMKICEGKKLSSVV 67 (67)
Q Consensus 51 ~~Ki~KIc~~f~a~~~~ 67 (67)
+..+++|.+..++++.+
T Consensus 19 G~~i~~i~~~~g~~I~i 35 (62)
T cd02394 19 GSNIRKIMEETGVKIRF 35 (62)
T ss_pred CCcHHHHHHHhCCEEEc
Confidence 34577888888888764
No 33
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=22.81 E-value=67 Score=16.98 Aligned_cols=17 Identities=18% Similarity=0.173 Sum_probs=13.2
Q ss_pred HHHHHHhhhhcCCeeeC
Q psy511 51 KTRVMKICEGKKLSSVV 67 (67)
Q Consensus 51 ~~Ki~KIc~~f~a~~~~ 67 (67)
+.-+++|.+.++|++.+
T Consensus 21 G~~ik~I~~~tg~~I~i 37 (61)
T cd02393 21 GKTIKKIIEETGVKIDI 37 (61)
T ss_pred chHHHHHHHHHCCEEEe
Confidence 45678899999998753
No 34
>COG2102 Predicted ATPases of PP-loop superfamily [General function prediction only]
Probab=22.45 E-value=95 Score=21.35 Aligned_cols=19 Identities=32% Similarity=0.478 Sum_probs=16.4
Q ss_pred HHHHHHHHHhhhhcCCeee
Q psy511 48 DQLKTRVMKICEGKKLSSV 66 (67)
Q Consensus 48 ~~l~~Ki~KIc~~f~a~~~ 66 (67)
+.-++++.++|+.+|+..|
T Consensus 98 ~yqk~rve~lc~~lGl~~~ 116 (223)
T COG2102 98 EYQKERVERLCEELGLKVY 116 (223)
T ss_pred HHHHHHHHHHHHHhCCEEe
Confidence 5678999999999998876
No 35
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=22.25 E-value=61 Score=16.54 Aligned_cols=17 Identities=12% Similarity=0.161 Sum_probs=13.7
Q ss_pred HHHHHHhhhhcCCeeeC
Q psy511 51 KTRVMKICEGKKLSSVV 67 (67)
Q Consensus 51 ~~Ki~KIc~~f~a~~~~ 67 (67)
+..|++|.+.++|++.+
T Consensus 19 G~~i~~I~~~t~~~I~i 35 (60)
T PF00013_consen 19 GSNIKEIEEETGVKIQI 35 (60)
T ss_dssp GHHHHHHHHHHTSEEEE
T ss_pred CCcHHHhhhhcCeEEEE
Confidence 56788999999998753
No 36
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=22.25 E-value=64 Score=18.43 Aligned_cols=14 Identities=21% Similarity=0.411 Sum_probs=11.1
Q ss_pred HHHHHHhhhhcCCe
Q psy511 51 KTRVMKICEGKKLS 64 (67)
Q Consensus 51 ~~Ki~KIc~~f~a~ 64 (67)
-+-+.|||+++.|+
T Consensus 45 ~~tL~~iC~~LeCq 58 (73)
T COG3655 45 LSTLEKICKALECQ 58 (73)
T ss_pred HHHHHHHHHHcCCC
Confidence 35678999999875
No 37
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=22.08 E-value=71 Score=18.50 Aligned_cols=15 Identities=13% Similarity=0.195 Sum_probs=11.2
Q ss_pred HHHHHHhhhhcCCee
Q psy511 51 KTRVMKICEGKKLSS 65 (67)
Q Consensus 51 ~~Ki~KIc~~f~a~~ 65 (67)
...+.|||++||.++
T Consensus 72 ~~tL~kI~~aLgi~l 86 (89)
T TIGR02684 72 FDTILKVTKALGLKL 86 (89)
T ss_pred HHHHHHHHHHcCCce
Confidence 466788888888765
No 38
>cd02979 PHOX_C FAD-dependent Phenol hydoxylase (PHOX) family, C-terminal TRX-fold domain; composed of proteins similar to PHOX from the aerobic topsoil yeast Trichosporon cutaneum. PHOX is a flavoprotein monooxygenase that catalyzes the hydroxylation of phenol and simple phenol derivatives in the ortho position with the consumption of NADPH and oxygen. This is the first step in the biodegradation and detoxification of phenolic compounds. PHOX contains three domains. The substrate and FAD/NAD(P) binding sites are contained in the first two domains, which adopt a complicated folding pattern. The third or C-terminal domain contains a TRX fold and is involved in dimerization. The functional unit of PHOX is a dimer, although active tetramers of the recombinant enzyme can be isolated when overproduced in bacteria.
Probab=22.00 E-value=1e+02 Score=19.58 Aligned_cols=22 Identities=36% Similarity=0.735 Sum_probs=16.7
Q ss_pred EEEEecH----HHHHHHHHhhhhcCC
Q psy511 42 IIFFQGD----QLKTRVMKICEGKKL 63 (67)
Q Consensus 42 iv~~~G~----~l~~Ki~KIc~~f~a 63 (67)
|++|.|+ .-.+++.+.|+.+..
T Consensus 32 I~vFagd~~~~~~~~~l~~~~~~L~~ 57 (167)
T cd02979 32 IYVFAGDIAPAQQKSRLTQLCDALDS 57 (167)
T ss_pred EEEEcCCCCchhHHHHHHHHHHHHcC
Confidence 5667775 557899999998854
No 39
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=21.92 E-value=68 Score=19.16 Aligned_cols=12 Identities=42% Similarity=0.847 Sum_probs=10.2
Q ss_pred hHHHHHHHhhCC
Q psy511 3 AFERMLWRACRG 14 (67)
Q Consensus 3 ~fer~lwR~~RG 14 (67)
.-.|+.||+=||
T Consensus 14 ~~~RL~~rsrRG 25 (94)
T COG2938 14 RKARLRWRSRRG 25 (94)
T ss_pred HHHHHHHHHHhc
Confidence 457999999999
No 40
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=21.45 E-value=1e+02 Score=14.31 Aligned_cols=14 Identities=21% Similarity=0.508 Sum_probs=11.1
Q ss_pred HHHHHHHHHhhhhc
Q psy511 48 DQLKTRVMKICEGK 61 (67)
Q Consensus 48 ~~l~~Ki~KIc~~f 61 (67)
+.+.+.+.++|+.+
T Consensus 25 ~~I~~~l~~~C~~l 38 (39)
T PF05184_consen 25 EEIKKALEKACNKL 38 (39)
T ss_dssp HHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHHhhC
Confidence 57888888898765
No 41
>PF12682 Flavodoxin_4: Flavodoxin; PDB: 3EDO_B 3KLB_A.
Probab=20.98 E-value=1.7e+02 Score=18.34 Aligned_cols=26 Identities=15% Similarity=0.299 Sum_probs=15.9
Q ss_pred EEEEEe-cHHHHHHHHHhhhhcCCeee
Q psy511 41 FIIFFQ-GDQLKTRVMKICEGKKLSSV 66 (67)
Q Consensus 41 Fiv~~~-G~~l~~Ki~KIc~~f~a~~~ 66 (67)
-||+|+ ....+.=-++|++..+|.++
T Consensus 3 LVvYyS~tGnT~~vA~~Ia~~~gadi~ 29 (156)
T PF12682_consen 3 LVVYYSRTGNTKKVAEKIAEKTGADIF 29 (156)
T ss_dssp EEEE--SSSHHHHHHHHHHHCCT-EEE
T ss_pred EEEEECCCchHHHHHHHHHHHHCCCEE
Confidence 467774 45666666678888888775
No 42
>PRK04017 hypothetical protein; Provisional
Probab=20.52 E-value=89 Score=19.69 Aligned_cols=20 Identities=15% Similarity=0.423 Sum_probs=15.5
Q ss_pred ecHHHHHHHHHhhhhcCCee
Q psy511 46 QGDQLKTRVMKICEGKKLSS 65 (67)
Q Consensus 46 ~G~~l~~Ki~KIc~~f~a~~ 65 (67)
+|+.++.++.+.-.+.|+.+
T Consensus 77 ~GekIr~~l~~~l~~~G~~v 96 (132)
T PRK04017 77 KGEELAKKLSEYLQGYGIKV 96 (132)
T ss_pred chHHHHHHHHHHHHhCCCCc
Confidence 47899999988887777653
Done!