Query psy2115
Match_columns 77
No_of_seqs 108 out of 410
Neff 4.6
Searched_HMMs 46136
Date Sat Aug 17 00:38:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2115.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2115hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01130 CD36: CD36 family; I 99.9 3E-22 6.6E-27 155.1 7.0 55 1-55 44-98 (467)
2 KOG3776|consensus 99.8 9.1E-20 2E-24 145.7 6.5 56 1-56 55-110 (507)
3 cd08519 PBP2_NikA_DppA_OppA_li 40.0 31 0.00066 26.4 2.8 31 34-65 158-189 (469)
4 cd08518 PBP2_NikA_DppA_OppA_li 39.2 30 0.00065 26.4 2.6 33 33-65 148-181 (464)
5 cd08510 PBP2_Lactococcal_OppA_ 38.4 32 0.0007 26.7 2.7 34 33-66 182-216 (516)
6 cd08508 PBP2_NikA_DppA_OppA_li 36.0 34 0.00073 26.2 2.4 33 34-66 162-195 (470)
7 PF14498 Glyco_hyd_65N_2: Glyc 34.3 23 0.0005 25.2 1.3 23 44-66 29-51 (236)
8 PF01289 Thiol_cytolysin: Thio 33.4 48 0.001 27.2 3.0 55 15-71 349-416 (467)
9 PRK09755 putative ABC transpor 32.8 40 0.00087 26.6 2.4 35 32-66 206-242 (535)
10 cd08507 PBP2_SgrR_like The C-t 32.7 42 0.0009 25.7 2.5 32 34-66 157-189 (448)
11 PRK15104 oligopeptide ABC tran 32.7 41 0.0009 26.6 2.5 34 32-65 211-246 (543)
12 cd08513 PBP2_thermophilic_Hb8_ 32.3 48 0.001 25.2 2.7 33 33-65 159-192 (482)
13 cd08514 PBP2_AppA_like The sub 32.2 41 0.00089 25.6 2.4 33 33-65 160-193 (483)
14 cd08512 PBP2_NikA_DppA_OppA_li 31.5 47 0.001 25.2 2.6 33 34-66 171-204 (476)
15 KOG2577|consensus 31.2 37 0.00079 27.1 2.0 33 11-58 105-138 (354)
16 cd08494 PBP2_NikA_DppA_OppA_li 29.6 55 0.0012 24.5 2.6 32 34-65 153-185 (448)
17 cd08501 PBP2_Lpqw The substrat 29.2 62 0.0013 24.7 2.9 35 32-66 163-200 (486)
18 cd08516 PBP2_NikA_DppA_OppA_li 29.2 56 0.0012 24.6 2.6 34 33-66 151-186 (457)
19 cd08506 PBP2_clavulanate_OppA2 28.9 56 0.0012 24.8 2.6 27 33-59 143-169 (466)
20 cd08515 PBP2_NikA_DppA_OppA_li 28.5 55 0.0012 24.9 2.5 33 33-65 159-192 (460)
21 cd08520 PBP2_NikA_DppA_OppA_li 28.1 64 0.0014 24.6 2.8 35 32-66 157-193 (468)
22 cd08498 PBP2_NikA_DppA_OppA_li 28.0 59 0.0013 24.9 2.6 33 34-66 156-189 (481)
23 cd08505 PBP2_NikA_DppA_OppA_li 27.9 53 0.0011 26.0 2.4 26 34-59 168-193 (528)
24 cd08499 PBP2_Ylib_like The sub 27.2 55 0.0012 24.9 2.3 33 33-65 155-188 (474)
25 cd08496 PBP2_NikA_DppA_OppA_li 26.8 65 0.0014 24.4 2.6 32 34-65 153-186 (454)
26 cd08490 PBP2_NikA_DppA_OppA_li 26.4 62 0.0013 24.4 2.4 33 34-66 148-181 (470)
27 cd08495 PBP2_NikA_DppA_OppA_li 25.2 71 0.0015 24.4 2.6 33 34-66 168-202 (482)
28 smart00879 Brix Brix domain. T 24.9 1E+02 0.0022 20.3 3.1 10 28-37 167-176 (180)
29 TIGR02294 nickel_nikA nickel A 24.9 60 0.0013 25.1 2.2 33 33-65 162-195 (500)
30 cd08489 PBP2_NikA The substrat 24.3 76 0.0017 24.2 2.6 33 33-65 155-188 (488)
31 PF02056 Glyco_hydro_4: Family 24.2 49 0.0011 23.6 1.5 13 12-24 138-150 (183)
32 PF07565 Band_3_cyto: Band 3 c 24.1 27 0.00059 26.1 0.2 17 52-69 4-20 (257)
33 PF09200 Monellin: Monellin; 23.6 64 0.0014 18.5 1.6 11 31-41 4-14 (43)
34 PHA02757 hypothetical protein; 22.7 62 0.0013 20.4 1.5 20 22-41 4-28 (75)
35 cd00995 PBP2_NikA_DppA_OppA_li 22.6 77 0.0017 23.6 2.3 33 33-65 155-189 (466)
36 cd08493 PBP2_DppA_like The sub 22.6 83 0.0018 24.0 2.5 32 34-65 173-205 (482)
37 PF07619 DUF1581: Protein of u 22.5 42 0.00091 21.8 0.8 16 57-72 37-52 (84)
38 PRK15413 glutathione ABC trans 22.1 93 0.002 24.3 2.7 33 34-66 184-218 (512)
39 cd08517 PBP2_NikA_DppA_OppA_li 21.5 86 0.0019 23.7 2.4 33 33-65 158-192 (480)
40 cd08500 PBP2_NikA_DppA_OppA_li 21.1 89 0.0019 24.3 2.5 33 33-65 148-187 (499)
41 PF00496 SBP_bac_5: Bacterial 20.8 58 0.0013 23.5 1.3 39 30-68 114-154 (374)
42 cd08502 PBP2_NikA_DppA_OppA_li 20.1 98 0.0021 23.7 2.5 27 32-58 155-181 (472)
43 PRK15109 antimicrobial peptide 20.1 97 0.0021 24.7 2.5 31 34-64 214-245 (547)
No 1
>PF01130 CD36: CD36 family; InterPro: IPR002159 CD36 is a transmembrane, highly glycosylated, 88kDa glycoprotein expressed by monocytes, macrophages, platelets, microvascular endothelial cells and adipose tissues. Platelet glycoprotein IV (GP IV)(GPIIIb) (CD36 antigen) is also called GPIV, OKM5-antigen or PASIV. CD36 recognises oxidized low density lipoprotein, long chain fatty acids, anionic phospholipids, collagen types I, IV and V, thrombospondin (TSP) and Plasmodium falciparum infected erythrocytes. The recognition of apoptotic neutrophils is in co-operation with TSP and avb3. Other ligands may still be unknown. CD36 is a scavenger receptor for oxidized LDL and shed photoreceptor outer segments and in recognition and phagocytosis of apoptotic cells and is the cell adhesion molecule in platelet adhesion and aggregation, platelet-monocyte and platelet-tumor cell interaction []. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0007155 cell adhesion, 0016020 membrane
Probab=99.86 E-value=3e-22 Score=155.09 Aligned_cols=55 Identities=27% Similarity=0.345 Sum_probs=53.2
Q ss_pred CccCCCcceEEEEEEeccChhhhhCCCCCcceEEeCCeEEEEeeeeeceEEcCCc
Q psy2115 1 MEINTNPKKLRGHKFNWTNPEDIRNNETKPNFVEMGPYRFHYGDKYKSQKTSGPQ 55 (77)
Q Consensus 1 ~~~pP~p~~~~~y~FNvTNpeevl~G~~kP~v~EvGPYvY~E~~~K~nvtf~~~~ 55 (77)
|++||+|++++||+||||||+||++|++||+|+|+|||+|+|+++|.|++|++++
T Consensus 44 W~~~p~p~~~~~y~fNvTNp~ev~~~g~kP~~~EvGPY~y~e~~~k~nv~~~~~~ 98 (467)
T PF01130_consen 44 WKKPPVPIYFKFYFFNVTNPEEVLNGGAKPNVQEVGPYVYREYREKVNVTFNDNG 98 (467)
T ss_pred hhcCCCccEEEEEEEeccCHHHHhCcCCCceEEEeCCEEEEeeeeeeeeEEcCCC
Confidence 8999999999999999999999999668999999999999999999999999997
No 2
>KOG3776|consensus
Probab=99.79 E-value=9.1e-20 Score=145.74 Aligned_cols=56 Identities=25% Similarity=0.307 Sum_probs=54.2
Q ss_pred CccCCCcceEEEEEEeccChhhhhCCCCCcceEEeCCeEEEEeeeeeceEEcCCcc
Q psy2115 1 MEINTNPKKLRGHKFNWTNPEDIRNNETKPNFVEMGPYRFHYGDKYKSQKTSGPQK 56 (77)
Q Consensus 1 ~~~pP~p~~~~~y~FNvTNpeevl~G~~kP~v~EvGPYvY~E~~~K~nvtf~~~~~ 56 (77)
|.+||++++++||+|||||||||++|++||+|+|+|||+|+|..+|+|+.|++|++
T Consensus 55 W~~pp~~~~~~~yiFNvTNpde~~~~~~kp~v~EvGPyvy~E~~~K~~~~f~~n~t 110 (507)
T KOG3776|consen 55 WLNPPYPIYLNFYIFNVTNPDEFLSGGAKPNVQEVGPYVYREIEQKVNIDFNENNT 110 (507)
T ss_pred hhcCCCccEEEEEEEecCCHHHhhCcCCCCceEeeCCeEEEEEecccceeeccCCc
Confidence 89999999999999999999999998789999999999999999999999999977
No 3
>cd08519 PBP2_NikA_DppA_OppA_like_20 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=40.01 E-value=31 Score=26.39 Aligned_cols=31 Identities=19% Similarity=0.398 Sum_probs=24.7
Q ss_pred EeCCeEEEEeeeeeceEEcCCcc-cCCCCeeec
Q psy2115 34 EMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVAR 65 (77)
Q Consensus 34 EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~~ 65 (77)
=-|||...++.. ..+++..++. |.+.|++++
T Consensus 158 gsGPy~~~~~~~-~~~~l~~n~~y~~~~p~~~~ 189 (469)
T cd08519 158 GTGPYKLKSFRS-ESIRLEPNPDYWGEKPKNDG 189 (469)
T ss_pred ccCCEEEEEeec-cEEEEEeChhhcCCCCCcce
Confidence 479999999887 7888888887 666666664
No 4
>cd08518 PBP2_NikA_DppA_OppA_like_19 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=39.24 E-value=30 Score=26.37 Aligned_cols=33 Identities=21% Similarity=0.417 Sum_probs=24.7
Q ss_pred EEeCCeEEEEeeeeeceEEcCCcc-cCCCCeeec
Q psy2115 33 VEMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVAR 65 (77)
Q Consensus 33 ~EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~~ 65 (77)
.=-|||...+......+++..++. |.+.|++++
T Consensus 148 vGtGPy~l~~~~~~~~i~l~rn~~Yw~~~p~~d~ 181 (464)
T cd08518 148 IGTGPYKLVQWDKGQQVIFEANPDYYGGKPKFKK 181 (464)
T ss_pred cccCCeEEEEeccCceEEEEECccccCCCCCcCE
Confidence 357999999887767788888877 555566664
No 5
>cd08510 PBP2_Lactococcal_OppA_like The substrate binding component of an ABC-type lactococcal OppA-like transport system contains. This family represents the substrate binding domain of an ATP-binding cassette (ABC)-type oligopeptide import system from Lactococcus lactis and other gram-positive bacteria, as well as its closet homologs from gram-negative bacteria. Oligopeptide-binding protein (OppA) from Lactococcus lactis can bind peptides of length from 4 to at least 35 residues without sequence preference. The oligopeptide import system OppABCDEF is consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in sev
Probab=38.44 E-value=32 Score=26.72 Aligned_cols=34 Identities=21% Similarity=0.400 Sum_probs=25.3
Q ss_pred EEeCCeEEEEeeeeeceEEcCCcc-cCCCCeeecc
Q psy2115 33 VEMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVARR 66 (77)
Q Consensus 33 ~EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~~~ 66 (77)
.=-|||...+......+++..++. |.+.|++++.
T Consensus 182 vGtGPy~l~~~~~~~~~~l~rn~~yw~~~p~~d~I 216 (516)
T cd08510 182 LGFGPYKVKKIVPGESVEYVPNEYYWRGKPKLDKI 216 (516)
T ss_pred CccCCeEEEEeccCceEEEEeCccccCCCCcccEE
Confidence 357999999887666788887766 6677777744
No 6
>cd08508 PBP2_NikA_DppA_OppA_like_1 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=35.98 E-value=34 Score=26.23 Aligned_cols=33 Identities=15% Similarity=0.338 Sum_probs=23.8
Q ss_pred EeCCeEEEEeeeeeceEEcCCcc-cCCCCeeecc
Q psy2115 34 EMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVARR 66 (77)
Q Consensus 34 EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~~~ 66 (77)
=-|||...+......+++..++. |.+.|++++.
T Consensus 162 gsGPy~l~~~~~~~~~~l~rn~~Yw~~~~~~d~i 195 (470)
T cd08508 162 GTGPFEVEEHSPQQGVTLVANDGYFRGAPKLERI 195 (470)
T ss_pred cCCCcEEEEecCCCeEEEEeCccccCCCCCCCeE
Confidence 58999999877656677877777 5555666643
No 7
>PF14498 Glyco_hyd_65N_2: Glycosyl hydrolase family 65, N-terminal domain; PDB: 2EAE_A 2EAB_B 2EAC_A 2EAD_B 2RDY_A.
Probab=34.31 E-value=23 Score=25.22 Aligned_cols=23 Identities=22% Similarity=0.375 Sum_probs=17.7
Q ss_pred eeeeceEEcCCcccCCCCeeecc
Q psy2115 44 DKYKSQKTSGPQKWSGGPHVARR 66 (77)
Q Consensus 44 ~~K~nvtf~~~~~~~~~~~~~~~ 66 (77)
-.++-|.+|++.+||++|+-...
T Consensus 29 ~~~E~i~lNe~tlWsg~p~~~~~ 51 (236)
T PF14498_consen 29 PAKERIQLNEDTLWSGGPSDRTP 51 (236)
T ss_dssp SSEEEEEEEETT-BSSSTTSSSS
T ss_pred CCeEEEEEcchheECCCCccccC
Confidence 34778999999999999986643
No 8
>PF01289 Thiol_cytolysin: Thiol-activated cytolysin; InterPro: IPR001869 Thiol-activated cytolysins [] are toxins produced by a variety of Gram-positive bacteria and are characterised by their ability to lyse cholesterol-containing membranes, their reversible inactivation by oxidation and their capacity to bind to cholesterol. All these proteins contain a single cysteine residue, located in their C-terminal section, which has been shown [] to be essential for the binding to cholesterol.; GO: 0015485 cholesterol binding, 0009405 pathogenesis; PDB: 1S3R_A 1M3I_A 1PFO_A 1M3J_B 3CQF_A 3HVN_A.
Probab=33.41 E-value=48 Score=27.17 Aligned_cols=55 Identities=22% Similarity=0.399 Sum_probs=36.4
Q ss_pred EeccChhhhhCCCCCcceEEeCCeEEEEeeeeeceEEcCCcc-------cCCC-----Ceee-cccccCC
Q psy2115 15 FNWTNPEDIRNNETKPNFVEMGPYRFHYGDKYKSQKTSGPQK-------WSGG-----PHVA-RRPLVGN 71 (77)
Q Consensus 15 FNvTNpeevl~G~~kP~v~EvGPYvY~E~~~K~nvtf~~~~~-------~~~~-----~~~~-~~~~~~~ 71 (77)
|-.|...+..+| +..+.-.|-|+.+-...=+++++.++-+ |+++ +||. .+||-||
T Consensus 349 YieT~~t~y~~~--~i~l~h~g~yva~~~~~w~e~~yd~~g~~~~~~~~w~~~~~~~ta~~~~~i~~~~n 416 (467)
T PF01289_consen 349 YIETTSTEYTNG--KITLDHSGAYVAQFNVTWDEVSYDENGNEVITHKTWEGNGKDRTAHFSTVIPLPGN 416 (467)
T ss_dssp EEEEEEEEEE-E--EEEEEEECSSEEEEEEEEEEEEE-TTS-EEEEEEE-TTTT-EEESSEEEEEEE-TT
T ss_pred EEEEeeeeccCc--cEEEecCCcEEEEEEEEeeecccCCCCCEEeeeeccCCCCccccccceEEEecCCC
Confidence 346666666665 8899999999988666667777665443 8775 6765 7777776
No 9
>PRK09755 putative ABC transporter periplasmic-binding protein; Provisional
Probab=32.76 E-value=40 Score=26.64 Aligned_cols=35 Identities=9% Similarity=0.050 Sum_probs=26.7
Q ss_pred eEEeCCeEEEEeeeeeceEEcCCccc-CCC-Ceeecc
Q psy2115 32 FVEMGPYRFHYGDKYKSQKTSGPQKW-SGG-PHVARR 66 (77)
Q Consensus 32 v~EvGPYvY~E~~~K~nvtf~~~~~~-~~~-~~~~~~ 66 (77)
..--|||...++.....+++..++.| .++ |++++.
T Consensus 206 ~vGtGPy~l~~~~~~~~i~l~rn~~Yw~~~~p~~d~I 242 (535)
T PRK09755 206 MVYNGAFVLDQWVVNEKITARKNPKYRDAQHTVLQQV 242 (535)
T ss_pred eeecCCeEEeeeccCCeEEEeeCccccCCCCCCCCeE
Confidence 45689999999887778999998884 433 677754
No 10
>cd08507 PBP2_SgrR_like The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related to the ABC-type oligopeptide-binding proteins and contains the type 2 periplasmic-binding fold. A novel family of SgrR transcriptional regulator contains a two-domain structure with an N terminal DNA-binding domain of the winged helix family and a C-terminal solute-binding domain. The C-terminal domain shows strong homology with the ABC-type oligopeptide-binding protein family, a member of the type 2 periplasmic-binding fold protein (PBP2) superfamily that also includes the C-terminal substrate-binding domain of LysR-type transcriptional regulators. SgrR (SugaR transport-related Regulator) is negatively autoregulated and activates transcription of divergent operon SgrS, which encodes a small RNA required for recovery from glucose-phosphate stress. Hence, the small RNA SgrS and SgrR, the transcription factor that controls sgrS expression, are both required for recovery f
Probab=32.71 E-value=42 Score=25.68 Aligned_cols=32 Identities=16% Similarity=0.211 Sum_probs=23.4
Q ss_pred EeCCeEEEEeeeeeceEEcCCcc-cCCCCeeecc
Q psy2115 34 EMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVARR 66 (77)
Q Consensus 34 EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~~~ 66 (77)
=-|||...+.. +..+++..++. |.+.|++++.
T Consensus 157 gtGPy~l~~~~-~~~i~l~rn~~Yw~~~p~~~~v 189 (448)
T cd08507 157 GTGPFRVVENT-DKRLVLEAFDDYFGERPLLDEV 189 (448)
T ss_pred ccCCeEEEEcc-CCeEEEEECCCccCCCCCCCEE
Confidence 57999999875 56788888887 4445666643
No 11
>PRK15104 oligopeptide ABC transporter substrate-binding protein OppA; Provisional
Probab=32.69 E-value=41 Score=26.55 Aligned_cols=34 Identities=12% Similarity=0.214 Sum_probs=25.4
Q ss_pred eEEeCCeEEEEeeeeeceEEcCCcc-cCCC-Ceeec
Q psy2115 32 FVEMGPYRFHYGDKYKSQKTSGPQK-WSGG-PHVAR 65 (77)
Q Consensus 32 v~EvGPYvY~E~~~K~nvtf~~~~~-~~~~-~~~~~ 65 (77)
..--|||...++.....+++..++. |.++ |++++
T Consensus 211 pvGtGPy~~~~~~~~~~i~l~rn~~Yw~~~~p~~d~ 246 (543)
T PRK15104 211 IVTNGAYKLKDWVVNERIVLERNPTYWDNAKTVINQ 246 (543)
T ss_pred eeecCCeEEEEeccCCeEEEEeCccccCCCCccCCe
Confidence 3468999999888777788888887 5443 66664
No 12
>cd08513 PBP2_thermophilic_Hb8_like The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like import systems, contains the type 2 periplasmic binding fold. This family includes the substrate-binding domain of an ABC-type oligopeptide-binding protein Hb8 from Thermus thermophilius and its closest homologs from other bacteria. The structural topology of this substrate-binding domain is similar to those of DppA from Escherichia coli and OppA from Salmonella typhimurium, and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporter
Probab=32.26 E-value=48 Score=25.22 Aligned_cols=33 Identities=27% Similarity=0.457 Sum_probs=23.7
Q ss_pred EEeCCeEEEEeeeeeceEEcCCcc-cCCCCeeec
Q psy2115 33 VEMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVAR 65 (77)
Q Consensus 33 ~EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~~ 65 (77)
.=-|||...+......+++..+.. |.+.|+++.
T Consensus 159 vgtGPy~l~~~~~~~~~~l~~n~~Yw~~~p~~d~ 192 (482)
T cd08513 159 VGTGPYKLEEFVPGDSIELVRNPNYWGGKPYIDR 192 (482)
T ss_pred CccCCeEEEEEecCCeEEEEECCccccCCCCcCE
Confidence 357999999887656777777766 665666663
No 13
>cd08514 PBP2_AppA_like The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold. This family represents the substrate-binding domain of the oligopeptide-binding protein, AppA, from Bacillus subtilis and its closest homologs from other bacteria and archaea. Bacillus subtilis has three ABC-type peptide transport systems, a dipeptide-binding protein (DppA) and two oligopeptide-binding proteins (OppA and AppA) with overlapping specificity. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and also is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains correspondin
Probab=32.19 E-value=41 Score=25.59 Aligned_cols=33 Identities=18% Similarity=0.351 Sum_probs=24.3
Q ss_pred EEeCCeEEEEeeeeeceEEcCCcc-cCCCCeeec
Q psy2115 33 VEMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVAR 65 (77)
Q Consensus 33 ~EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~~ 65 (77)
.=-|||...++.....+++..++. |.+.+++++
T Consensus 160 vgtGPy~l~~~~~~~~i~l~rn~~Yw~~~~~~d~ 193 (483)
T cd08514 160 VGTGPYKLKEWKRGQYIVLEANPDYFLGRPYIDK 193 (483)
T ss_pred cccCCcEEEEecCCCeEEEEECccccCCCCCCcE
Confidence 468999999887666788888877 554566664
No 14
>cd08512 PBP2_NikA_DppA_OppA_like_7 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=31.54 E-value=47 Score=25.22 Aligned_cols=33 Identities=24% Similarity=0.505 Sum_probs=23.9
Q ss_pred EeCCeEEEEeeeeeceEEcCCcc-cCCCCeeecc
Q psy2115 34 EMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVARR 66 (77)
Q Consensus 34 EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~~~ 66 (77)
=-|||...+......+++..++. |.+.|++++.
T Consensus 171 gtGPy~l~~~~~~~~~~l~~n~~yw~~~p~~d~i 204 (476)
T cd08512 171 GSGPYKLKSWDPGEEVVLERNDDYWGGAPKLKRV 204 (476)
T ss_pred CCCCeEEEEEcCCCEEEEEecCcccCCCCCcCEE
Confidence 47999999877656777877776 5556776643
No 15
>KOG2577|consensus
Probab=31.23 E-value=37 Score=27.12 Aligned_cols=33 Identities=12% Similarity=0.054 Sum_probs=26.3
Q ss_pred EEEEEeccChhhhhCC-CCCcceEEeCCeEEEEeeeeeceEEcCCcccC
Q psy2115 11 RGHKFNWTNPEDIRNN-ETKPNFVEMGPYRFHYGDKYKSQKTSGPQKWS 58 (77)
Q Consensus 11 ~~y~FNvTNpeevl~G-~~kP~v~EvGPYvY~E~~~K~nvtf~~~~~~~ 58 (77)
+=.+|+||| ||.| + +.|.+.|.+|.|-+.+..+
T Consensus 105 KRRIYDITN---VLEGI~------------LIeKksKN~IqW~G~~~~~ 138 (354)
T KOG2577|consen 105 KRRIYDITN---VLEGIG------------LIEKKSKNNIQWIGGDFNS 138 (354)
T ss_pred cceeeehhh---hhhccc------------ceeeccccceeeecCCCcc
Confidence 346889999 6777 4 5688999999998887776
No 16
>cd08494 PBP2_NikA_DppA_OppA_like_6 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=29.60 E-value=55 Score=24.52 Aligned_cols=32 Identities=16% Similarity=0.348 Sum_probs=22.9
Q ss_pred EeCCeEEEEeeeeeceEEcCCcc-cCCCCeeec
Q psy2115 34 EMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVAR 65 (77)
Q Consensus 34 EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~~ 65 (77)
=-|||...+......+++..+.. |.+.|+++.
T Consensus 153 gtGPy~l~~~~~~~~i~l~~n~~Y~~~~~~~d~ 185 (448)
T cd08494 153 GTGPFTVAAWARGSSITLVRNDDYWGAKPKLDK 185 (448)
T ss_pred cCCCcEEEEEecCCeEEEEeCCcccCCcCCCCe
Confidence 47999999887766778887766 445555553
No 17
>cd08501 PBP2_Lpqw The substrate-binding domain of mycobacterial lipoprotein Lpqw contains type 2 periplasmic binding fold. LpqW is one of key players in synthesis and transport of the unique components of the mycobacterial cell wall which is a complex structure rich in two related lipoglycans, the phosphatidylinositol mannosides (PIMs) and lipoarabinomannans (LAMs). Lpqw is a highly conserved lipoprotein that transport intermediates from a pathway for mature PIMs production into a pathway for LAMs biosynthesis, thus controlling the relative abundance of these two essential components of cell wall. LpqW is thought to have been adapted by the cell-wall biosynthesis machinery of mycobacteria and other closely related pathogens, evolving to play an important role in PIMs/LAMs biosynthesis. Most of periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the LpqW protein. The structural topology of these domains is most similar to
Probab=29.19 E-value=62 Score=24.73 Aligned_cols=35 Identities=17% Similarity=0.351 Sum_probs=25.2
Q ss_pred eEEeCCeEEEEeeee-eceEEcCCcc-cCC-CCeeecc
Q psy2115 32 FVEMGPYRFHYGDKY-KSQKTSGPQK-WSG-GPHVARR 66 (77)
Q Consensus 32 v~EvGPYvY~E~~~K-~nvtf~~~~~-~~~-~~~~~~~ 66 (77)
..=-|||...+.... ..+++..+.. |.+ .|++++.
T Consensus 163 ~iGtGPy~l~~~~~~~~~~~l~~n~~Yw~~~~p~~d~i 200 (486)
T cd08501 163 PWSAGPYKVESVDRGRGEVTLVRNDRWWGDKPPKLDKI 200 (486)
T ss_pred cccCCCeEEEEEecCCCeEEeecCCcccCCCCCcccEE
Confidence 345799999988765 6788888777 544 4777643
No 18
>cd08516 PBP2_NikA_DppA_OppA_like_11 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=29.16 E-value=56 Score=24.57 Aligned_cols=34 Identities=21% Similarity=0.387 Sum_probs=23.4
Q ss_pred EEeCCeEEEEeeeeeceEEcCCcc-cC-CCCeeecc
Q psy2115 33 VEMGPYRFHYGDKYKSQKTSGPQK-WS-GGPHVARR 66 (77)
Q Consensus 33 ~EvGPYvY~E~~~K~nvtf~~~~~-~~-~~~~~~~~ 66 (77)
.=-|||...+......+++..++. |. +.|++++.
T Consensus 151 vgtGPy~l~~~~~~~~~~l~~n~~y~~~~~p~~d~i 186 (457)
T cd08516 151 IGTGPFKFASYEPGVSIVLEKNPDYWGKGLPKLDGI 186 (457)
T ss_pred cccCCeEEEEecCCCEEEEEeCCCccCCCCCCCCeE
Confidence 357999998876555677777666 55 56777643
No 19
>cd08506 PBP2_clavulanate_OppA2 The substrate-binding domain of an oligopeptide binding protein (OppA2) from the biosynthesis pathway of the beta-lactamase inhibitor clavulanic acid contains the type 2 periplasmic binding fold. Clavulanic acid (CA), a clinically important beta-lactamase inhibitor, is one of a family of clavams produced as secondary metabolites by fermentation of Streptomyces clavuligeru. The biosynthesis of CA proceeds via multiple steps from the precursors, glyceraldehyde-3-phosphate and arginine. CA possesses a characteristic (3R,5R) stereochemistry essential for reaction with penicillin-binding proteins and beta-lactamases. Two genes (oppA1 and oppA2) in the clavulanic acid gene cluster encode oligopeptide-binding proteins that are required for CA biosynthesis. OppA1/2 is involved in the binding and transport of peptides across the cell membrane of Streptomyces clavuligerus. Most of other periplasmic binding proteins are comprised of only two globular subdomains cor
Probab=28.89 E-value=56 Score=24.80 Aligned_cols=27 Identities=26% Similarity=0.423 Sum_probs=21.5
Q ss_pred EEeCCeEEEEeeeeeceEEcCCcccCC
Q psy2115 33 VEMGPYRFHYGDKYKSQKTSGPQKWSG 59 (77)
Q Consensus 33 ~EvGPYvY~E~~~K~nvtf~~~~~~~~ 59 (77)
.--|||...+......+++..++-|.+
T Consensus 143 igtGPy~l~~~~~~~~i~l~~n~~y~~ 169 (466)
T cd08506 143 VSSGPYKIESYDPGKGLVLVRNPHWDA 169 (466)
T ss_pred CCCCCeEEEEecCCCeEEEEeCCCCCC
Confidence 446999999888766788888887865
No 20
>cd08515 PBP2_NikA_DppA_OppA_like_10 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=28.52 E-value=55 Score=24.87 Aligned_cols=33 Identities=21% Similarity=0.388 Sum_probs=23.2
Q ss_pred EEeCCeEEEEeeeeeceEEcCCcc-cCCCCeeec
Q psy2115 33 VEMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVAR 65 (77)
Q Consensus 33 ~EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~~ 65 (77)
.--|||...+......+++..|.- |.+.|+++.
T Consensus 159 igsGPy~l~~~~~~~~~~l~~N~~yw~~~~~~d~ 192 (460)
T cd08515 159 VGTGPYKVTEFVPGERVVLEAFDDYWGGKPPIEK 192 (460)
T ss_pred CCCCCeEEeeeccCCEEEEEECccccCCCCCCCE
Confidence 358999999877656677777665 555666654
No 21
>cd08520 PBP2_NikA_DppA_OppA_like_21 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=28.15 E-value=64 Score=24.59 Aligned_cols=35 Identities=26% Similarity=0.474 Sum_probs=24.8
Q ss_pred eEEeCCeEEEEeeee-eceEEcCCcc-cCCCCeeecc
Q psy2115 32 FVEMGPYRFHYGDKY-KSQKTSGPQK-WSGGPHVARR 66 (77)
Q Consensus 32 v~EvGPYvY~E~~~K-~nvtf~~~~~-~~~~~~~~~~ 66 (77)
..--|||...+.... ..+++..++. |.+.|++++.
T Consensus 157 ~vGtGPy~~~~~~~~~~~i~L~rn~~Yw~~~p~~d~i 193 (468)
T cd08520 157 AIGSGPYKLVDYNKEQGTYLYEANEDYWGGKPKVKRL 193 (468)
T ss_pred ceeeCCeEEEEEecCceEEEEEeCcccccCCCCccEE
Confidence 456899999887664 4677777766 6666766643
No 22
>cd08498 PBP2_NikA_DppA_OppA_like_2 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=28.04 E-value=59 Score=24.88 Aligned_cols=33 Identities=21% Similarity=0.424 Sum_probs=23.7
Q ss_pred EeCCeEEEEeeeeeceEEcCCcc-cCCCCeeecc
Q psy2115 34 EMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVARR 66 (77)
Q Consensus 34 EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~~~ 66 (77)
=-|||...+......+++..+.- |.+.|+++..
T Consensus 156 gsGPy~l~~~~~~~~i~l~~n~~y~~~~p~~d~I 189 (481)
T cd08498 156 GTGPYKFVSWEPGDRTVLERNDDYWGGKPNWDEV 189 (481)
T ss_pred cCCCeEEEeeeCCCEEEEEECccccCCCCCcceE
Confidence 47999999887666677777766 5555666643
No 23
>cd08505 PBP2_NikA_DppA_OppA_like_18 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=27.92 E-value=53 Score=26.02 Aligned_cols=26 Identities=15% Similarity=0.291 Sum_probs=20.6
Q ss_pred EeCCeEEEEeeeeeceEEcCCcccCC
Q psy2115 34 EMGPYRFHYGDKYKSQKTSGPQKWSG 59 (77)
Q Consensus 34 EvGPYvY~E~~~K~nvtf~~~~~~~~ 59 (77)
=-|||...++.....+++..++.|-+
T Consensus 168 gtGPy~l~~~~~~~~~~l~~n~~Y~~ 193 (528)
T cd08505 168 GTGPYMLTENNPNSRMVLVRNPNYRG 193 (528)
T ss_pred cCCCeEEEeecCCCEEEEEecccccc
Confidence 46999999887666788888888654
No 24
>cd08499 PBP2_Ylib_like The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an uncharacterized ATP-binding cassette (ABC)-type peptide transport system YliB. Although the ligand specificity of Ylib protein is not known, it shares significant sequence similarity to the ABC-type dipeptide and oligopeptide binding proteins. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling
Probab=27.18 E-value=55 Score=24.90 Aligned_cols=33 Identities=24% Similarity=0.458 Sum_probs=23.7
Q ss_pred EEeCCeEEEEeeeeeceEEcCCcc-cCCCCeeec
Q psy2115 33 VEMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVAR 65 (77)
Q Consensus 33 ~EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~~ 65 (77)
.=-|||...+......+++..+.. |.+.|++++
T Consensus 155 vgsGPy~l~~~~~~~~~~l~~n~~Yw~~~~~~~~ 188 (474)
T cd08499 155 VGTGPFKFESWTPGDEVTLVKNDDYWGGLPKVDT 188 (474)
T ss_pred ccCCCceEEeecCCCEEEEEeCchhcCCCCCCCE
Confidence 358999999877666677777766 555566653
No 25
>cd08496 PBP2_NikA_DppA_OppA_like_9 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA can bind peptides of a wide range of lengths (2-35 amino-acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most
Probab=26.76 E-value=65 Score=24.44 Aligned_cols=32 Identities=19% Similarity=0.388 Sum_probs=23.7
Q ss_pred EeCCeEEEEeeeeeceEEcCCcc-cCC-CCeeec
Q psy2115 34 EMGPYRFHYGDKYKSQKTSGPQK-WSG-GPHVAR 65 (77)
Q Consensus 34 EvGPYvY~E~~~K~nvtf~~~~~-~~~-~~~~~~ 65 (77)
=-|||...+......+++..++. |.+ .+++++
T Consensus 153 gtGPy~l~~~~~~~~i~l~~n~~yw~~~~~~~d~ 186 (454)
T cd08496 153 GAGPYVLTEWVPNSKYVFERNEDYWDAANPHLDK 186 (454)
T ss_pred ccCCeEEEEeccCCEEEEEeCccccCCCCCcccE
Confidence 47999999887666788888888 554 366663
No 26
>cd08490 PBP2_NikA_DppA_OppA_like_3 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=26.42 E-value=62 Score=24.43 Aligned_cols=33 Identities=21% Similarity=0.477 Sum_probs=24.1
Q ss_pred EeCCeEEEEeeeeeceEEcCCcc-cCCCCeeecc
Q psy2115 34 EMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVARR 66 (77)
Q Consensus 34 EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~~~ 66 (77)
=.|||...+......+++..+.. |.+.++++..
T Consensus 148 gsGPy~l~~~~~~~~i~l~~n~~y~~~~~~~d~I 181 (470)
T cd08490 148 GTGPYKVESFEPDQSLTLERNDDYWGGKPKLDKV 181 (470)
T ss_pred ccCCcEEEEecCCceEEEEeCccccCCCCCCCEE
Confidence 46999999887656788888776 5555766643
No 27
>cd08495 PBP2_NikA_DppA_OppA_like_8 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=25.18 E-value=71 Score=24.44 Aligned_cols=33 Identities=12% Similarity=0.127 Sum_probs=23.0
Q ss_pred EeCCeEEEEeeeeeceEEcCCcccCC--CCeeecc
Q psy2115 34 EMGPYRFHYGDKYKSQKTSGPQKWSG--GPHVARR 66 (77)
Q Consensus 34 EvGPYvY~E~~~K~nvtf~~~~~~~~--~~~~~~~ 66 (77)
=-|||...+...-..+++..++.|-+ .|++++.
T Consensus 168 gsGPy~~~~~~~~~~i~l~rn~~y~~~~~~~~~~i 202 (482)
T cd08495 168 GTGPFRITRFVPRERIELVRNDGYWDKRPPKNDKL 202 (482)
T ss_pred ccCCeEEEEecCCCeEEEEECCCcCCCCCCCccEE
Confidence 47999998876545677888777644 3666643
No 28
>smart00879 Brix Brix domain. The Brix domain is found in a number of eukaryotic proteins including SSF proteins from yeast and humans, Arabidopsis thaliana Peter Pan-like protein and several hypothetical proteins.
Probab=24.90 E-value=1e+02 Score=20.29 Aligned_cols=10 Identities=30% Similarity=0.757 Sum_probs=8.0
Q ss_pred CCcceEEeCC
Q psy2115 28 TKPNFVEMGP 37 (77)
Q Consensus 28 ~kP~v~EvGP 37 (77)
.+-.++|+||
T Consensus 167 ~~v~l~eiGP 176 (180)
T smart00879 167 PRVELQEIGP 176 (180)
T ss_pred CceEEEEecC
Confidence 3578899999
No 29
>TIGR02294 nickel_nikA nickel ABC transporter, periplasmic nickel-binding protein. Members of this family are periplasmic nickel-binding proteins of nickel ABC transporters. Nickel is bound specifically, albeit weakly, through water molecules positioned in the binding site. The amino acids whose side chains line the binding site include Tyr-44, Met-49, Trp-122, Arg-159, Trp-420, and Tyr-424 (numbering based on the precursor sequence of E. coli NikA) with the Arg contributing a hydrogen bond indirectly through a water molecule. Sequences that exactly (or mostly) have the same binding site residues score above the trusted (or noise) cutoffs to this model. Most appear to be lipoproteins.
Probab=24.85 E-value=60 Score=25.07 Aligned_cols=33 Identities=9% Similarity=0.222 Sum_probs=23.3
Q ss_pred EEeCCeEEEEeeeeeceEEcCCcccC-CCCeeec
Q psy2115 33 VEMGPYRFHYGDKYKSQKTSGPQKWS-GGPHVAR 65 (77)
Q Consensus 33 ~EvGPYvY~E~~~K~nvtf~~~~~~~-~~~~~~~ 65 (77)
.=-|||...++.....+++..++.|- +.+++++
T Consensus 162 vgtGPy~l~~~~~~~~i~l~~n~~yw~~~~~~d~ 195 (500)
T TIGR02294 162 IGTGPWMLGESKQDEYAVFVRNENYWGEKPKLKK 195 (500)
T ss_pred cccCCcEEEeccCCceEEEeeCccccCCCCcccE
Confidence 45799999887655567888877754 3466663
No 30
>cd08489 PBP2_NikA The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel transport system, which functions in the import of nickel and in the control of chemotactic response away from nickel. The ATP-binding cassette (ABC) type nickel transport system is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, the initial nickel receptor. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides,
Probab=24.27 E-value=76 Score=24.24 Aligned_cols=33 Identities=15% Similarity=0.320 Sum_probs=23.6
Q ss_pred EEeCCeEEEEeeeeeceEEcCCcc-cCCCCeeec
Q psy2115 33 VEMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVAR 65 (77)
Q Consensus 33 ~EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~~ 65 (77)
.--|||...++....-+++..++. |.+-|++++
T Consensus 155 vgsGPy~l~~~~~~~~i~l~~n~~y~~~~~~~d~ 188 (488)
T cd08489 155 IGTGPWVLAEYKKGEYAVFVRNPNYWGEKPKIDK 188 (488)
T ss_pred cccCCeEEEEecCCceEEEEeCccccCCCCCcCE
Confidence 457999999887656677777766 555566553
No 31
>PF02056 Glyco_hydro_4: Family 4 glycosyl hydrolase; InterPro: IPR001088 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 4 GH4 from CAZY comprises enzymes with several known activities; 6-phospho-beta-glucosidase (3.2.1.86 from EC); 6-phospho-alpha-glucosidase (3.2.1.122 from EC); alpha-galactosidase (3.2.1.22 from EC). 6-phospho-alpha-glucosidase requires both NAD(H) and divalent metal (Mn2+, Fe2+, Co2+, or Ni2+) for activity [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 1U8X_X 1S6Y_A 3FEF_B 1VJT_A 1UP4_A 1UP6_C 1UP7_E 1OBB_A.
Probab=24.21 E-value=49 Score=23.64 Aligned_cols=13 Identities=38% Similarity=0.527 Sum_probs=10.0
Q ss_pred EEEEeccChhhhh
Q psy2115 12 GHKFNWTNPEDIR 24 (77)
Q Consensus 12 ~y~FNvTNpeevl 24 (77)
-|++|.|||...+
T Consensus 138 Aw~iNytNP~~~v 150 (183)
T PF02056_consen 138 AWLINYTNPMGIV 150 (183)
T ss_dssp SEEEE-SSSHHHH
T ss_pred cEEEeccChHHHH
Confidence 3899999998875
No 32
>PF07565 Band_3_cyto: Band 3 cytoplasmic domain; InterPro: IPR013769 Bicarbonate (HCO3 -) transport mechanisms are the principal regulators of pH in animal cells. Such transport also plays a vital role in acid-base movements in the stomach, pancreas, intestine, kidney, reproductive organs and the central nervous system. Functional studies have suggested four different HCO3 - transport modes. Anion exchanger proteins exchange HCO3 - for Cl- in a reversible, electroneutral manner []. Na+/HCO3 - co-transport proteins mediate the coupled movement of Na+ and HCO3 - across plasma membranes, often in an electrogenic manner []. Na- driven Cl-/HCO3 - exchange and K+/HCO3 - exchange activities have also been detected in certain cell types, although the molecular identities of the proteins responsible remain to be determined. Sequence analysis of the two families of HCO3 - transporters that have been cloned to date (the anion exchangers and Na+/HCO3 - co-transporters) reveals that they are homologous. This is not entirely unexpected, given that they both transport HCO3 - and are inhibited by a class of pharmacological agents called disulphonic stilbenes []. They share around ~25-30% sequence identity, which is distributed along their entire sequence length, and have similar predicted membrane topologies, suggesting they have ~10 transmembrane (TM) domains.; GO: 0008509 anion transmembrane transporter activity, 0006820 anion transport, 0016021 integral to membrane; PDB: 1HYN_Q.
Probab=24.15 E-value=27 Score=26.15 Aligned_cols=17 Identities=41% Similarity=0.829 Sum_probs=6.5
Q ss_pred cCCcccCCCCeeeccccc
Q psy2115 52 SGPQKWSGGPHVARRPLV 69 (77)
Q Consensus 52 ~~~~~~~~~~~~~~~~~~ 69 (77)
.+.+.||| ||||.+.||
T Consensus 4 eg~~RWsK-PHVatLSfh 20 (257)
T PF07565_consen 4 EGGERWSK-PHVATLSFH 20 (257)
T ss_dssp -TTS-B----B---BEHH
T ss_pred ccCCccCC-CcccccCHH
Confidence 35567888 999988774
No 33
>PF09200 Monellin: Monellin; InterPro: IPR015283 Monellin, a protein produced by the West African plant Dioscoreophyllum cumminsii (Serendipity berry), is approximately 70,000 times sweeter than sucrose on a molar basis. The protein adopts an alpha-beta structure, with a cystatin-like fold, where each helix packs against a coiled antiparallel beta-sheet []. ; PDB: 3PXM_A 1IV7_A 3PYJ_A 1KRL_D 4MON_B 2O9U_X 3Q2P_C 3MON_F 1MOL_B 1IV9_A ....
Probab=23.59 E-value=64 Score=18.47 Aligned_cols=11 Identities=18% Similarity=0.144 Sum_probs=9.4
Q ss_pred ceEEeCCeEEE
Q psy2115 31 NFVEMGPYRFH 41 (77)
Q Consensus 31 ~v~EvGPYvY~ 41 (77)
+.-|+|||+|.
T Consensus 4 ~~~e~~~~~~~ 14 (43)
T PF09200_consen 4 KGYEYQLYVYA 14 (43)
T ss_dssp EEEECCCCEEE
T ss_pred eEEEeeeeeeh
Confidence 46799999997
No 34
>PHA02757 hypothetical protein; Provisional
Probab=22.68 E-value=62 Score=20.44 Aligned_cols=20 Identities=25% Similarity=0.655 Sum_probs=15.6
Q ss_pred hhhCCCCCc-----ceEEeCCeEEE
Q psy2115 22 DIRNNETKP-----NFVEMGPYRFH 41 (77)
Q Consensus 22 evl~G~~kP-----~v~EvGPYvY~ 41 (77)
|+|.|+.|| .+.-.||+.|.
T Consensus 4 EflkGSskPprnvCViTPsgpfDFn 28 (75)
T PHA02757 4 EFLKGSSKPPRNVCVITPSGPFDFN 28 (75)
T ss_pred hhhcCCCCCCCCEEEEeCCCCccEE
Confidence 788997787 45677999886
No 35
>cd00995 PBP2_NikA_DppA_OppA_like The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is inv
Probab=22.64 E-value=77 Score=23.55 Aligned_cols=33 Identities=24% Similarity=0.485 Sum_probs=24.0
Q ss_pred EEeCCeEEEEeeeeeceEEcCCcc-cC-CCCeeec
Q psy2115 33 VEMGPYRFHYGDKYKSQKTSGPQK-WS-GGPHVAR 65 (77)
Q Consensus 33 ~EvGPYvY~E~~~K~nvtf~~~~~-~~-~~~~~~~ 65 (77)
.=-|||...+......+++..++- |. +.|++++
T Consensus 155 igtGPy~l~~~~~~~~~~l~~n~~Y~~~~~p~~d~ 189 (466)
T cd00995 155 VGTGPYKLVEWKPGESIVLERNDDYWGPGKPKIDK 189 (466)
T ss_pred ccCCCcEEEeeccCCeEEEEECchhhcCCCCCccE
Confidence 468999999877656677877777 44 4577764
No 36
>cd08493 PBP2_DppA_like The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of an ATP-binding cassette (ABC)-type dipeptide import system. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their li
Probab=22.61 E-value=83 Score=23.99 Aligned_cols=32 Identities=19% Similarity=0.465 Sum_probs=23.3
Q ss_pred EeCCeEEEEeeeeeceEEcCCcc-cCCCCeeec
Q psy2115 34 EMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVAR 65 (77)
Q Consensus 34 EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~~ 65 (77)
=.|||...+......+++..++. |.+.|++++
T Consensus 173 gsGPy~l~~~~~~~~~~l~~n~~y~~~~p~~d~ 205 (482)
T cd08493 173 GTGPFKFVSWQKDDRIRLEANPDYWGGKAKIDT 205 (482)
T ss_pred cCCCeEEEEecCCCEEEEEeCccccCCCCCCCe
Confidence 58999998877656677777766 566676663
No 37
>PF07619 DUF1581: Protein of unknown function (DUF1581); InterPro: IPR022660 Several Rhodopirellula baltica proteins share this domain. They also match PF07622 from PFAM
Probab=22.53 E-value=42 Score=21.77 Aligned_cols=16 Identities=19% Similarity=0.339 Sum_probs=14.2
Q ss_pred cCCCCeeecccccCCC
Q psy2115 57 WSGGPHVARRPLVGNP 72 (77)
Q Consensus 57 ~~~~~~~~~~~~~~~~ 72 (77)
|++.+||+++-|-|+|
T Consensus 37 ~~~~~~frNlrItG~P 52 (84)
T PF07619_consen 37 RRSHGHFRNLRITGSP 52 (84)
T ss_pred eeeccceeeeEEcCCC
Confidence 6778999999999998
No 38
>PRK15413 glutathione ABC transporter substrate-binding protein GsiB; Provisional
Probab=22.07 E-value=93 Score=24.28 Aligned_cols=33 Identities=21% Similarity=0.396 Sum_probs=24.0
Q ss_pred EeCCeEEEEeeeeeceEEcCCcc-cCCC-Ceeecc
Q psy2115 34 EMGPYRFHYGDKYKSQKTSGPQK-WSGG-PHVARR 66 (77)
Q Consensus 34 EvGPYvY~E~~~K~nvtf~~~~~-~~~~-~~~~~~ 66 (77)
=-|||...+......+++..++. |.++ |.++..
T Consensus 184 GtGPy~l~~~~~~~~i~l~rn~~Ywg~~~p~~d~i 218 (512)
T PRK15413 184 GTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSI 218 (512)
T ss_pred ccCCeEEEEeecCCEEEEEecccccCCCCCccceE
Confidence 46999999888777788887766 5533 666643
No 39
>cd08517 PBP2_NikA_DppA_OppA_like_13 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=21.49 E-value=86 Score=23.72 Aligned_cols=33 Identities=21% Similarity=0.433 Sum_probs=23.2
Q ss_pred EEeCCeEEEEeeeeeceEEcCCcc-cC-CCCeeec
Q psy2115 33 VEMGPYRFHYGDKYKSQKTSGPQK-WS-GGPHVAR 65 (77)
Q Consensus 33 ~EvGPYvY~E~~~K~nvtf~~~~~-~~-~~~~~~~ 65 (77)
.=-|||...+......+++..++. |. +.|++++
T Consensus 158 vgtGPy~l~~~~~~~~~~l~~n~~yw~~~~p~~~~ 192 (480)
T cd08517 158 IGTGPFKFVEWVRGSHIILERNPDYWDKGKPYLDR 192 (480)
T ss_pred cccCCeEEEEeccCCEEEEEECcccccCCCCCccE
Confidence 347999999877656677877776 54 4566663
No 40
>cd08500 PBP2_NikA_DppA_OppA_like_4 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=21.14 E-value=89 Score=24.30 Aligned_cols=33 Identities=12% Similarity=0.148 Sum_probs=23.4
Q ss_pred EEeCCeEEEEeeeeeceEEcCCcccCC-------CCeeec
Q psy2115 33 VEMGPYRFHYGDKYKSQKTSGPQKWSG-------GPHVAR 65 (77)
Q Consensus 33 ~EvGPYvY~E~~~K~nvtf~~~~~~~~-------~~~~~~ 65 (77)
.--|||...+......+++..+..|-+ .|+++.
T Consensus 148 vGsGPy~l~~~~~~~~~~l~~n~~yw~~~~~g~~~p~~d~ 187 (499)
T cd08500 148 PTLGPWKLESYTPGERVVLERNPYYWKVDTEGNQLPYIDR 187 (499)
T ss_pred cccCCeEEEeecCCceEEEEeCCcccccCCCCCcCCccce
Confidence 356999998877656788888877432 367763
No 41
>PF00496 SBP_bac_5: Bacterial extracellular solute-binding proteins, family 5 Middle; InterPro: IPR000914 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into Gram-positive bacteria which are surrounded by a single membrane and therefore have no periplasmic region the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families of clusters, which generally correlate with the nature of the solute bound. Family 5 currently includes periplasmic oligopeptide-binding proteins (oppA) of Gram-negative bacteria and homologous lipoproteins in Gram-positive bacteria (oppA, amiA or appA); periplasmic dipeptide-binding proteins of Escherichia coli (dppA) and Bacillus subtilis (dppE); periplasmic murein peptide-binding protein of E. coli (mppA); periplasmic peptide-binding proteins sapA of E. coli, Salmonella typhimurium and Haemophilus influenzae; periplasmic nickel-binding protein (nikA) of E. coli; haem-binding lipoprotein (hbpA or dppA) from H. influenzae; lipoprotein xP55 from Streptomyces lividans; and hypothetical proteins from H. influenzae (HI0213) and Rhizobium sp. (strain NGR234) symbiotic plasmid (y4tO and y4wM).; GO: 0005215 transporter activity, 0006810 transport; PDB: 1B51_A 1B0H_A 1QKA_A 1B9J_A 1B6H_A 1OLA_A 1B3L_C 1JEV_A 1B5H_A 1JET_A ....
Probab=20.81 E-value=58 Score=23.51 Aligned_cols=39 Identities=23% Similarity=0.432 Sum_probs=26.4
Q ss_pred cceEEeCCeEEEEeeeeeceEEcCCcc-c-CCCCeeecccc
Q psy2115 30 PNFVEMGPYRFHYGDKYKSQKTSGPQK-W-SGGPHVARRPL 68 (77)
Q Consensus 30 P~v~EvGPYvY~E~~~K~nvtf~~~~~-~-~~~~~~~~~~~ 68 (77)
....--|||...+......+++-.+.. | .+.+++++.-+
T Consensus 114 ~~~igtGPy~~~~~~~~~~~~l~~n~~Yw~~~~~~~~~i~~ 154 (374)
T PF00496_consen 114 KNPIGTGPYKLKSYSPGQRIVLERNPDYWGGGRPKIDRIEL 154 (374)
T ss_dssp TS-SBSSSEEEEEEETTTEEEEEE-TTSTTTGGGSCSEEEE
T ss_pred CCcccccceEEEEeccCcEEEEEeccccccccccccccccc
Confidence 345559999999988756788887777 6 55567775443
No 42
>cd08502 PBP2_NikA_DppA_OppA_like_16 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=20.13 E-value=98 Score=23.72 Aligned_cols=27 Identities=11% Similarity=0.234 Sum_probs=21.1
Q ss_pred eEEeCCeEEEEeeeeeceEEcCCcccC
Q psy2115 32 FVEMGPYRFHYGDKYKSQKTSGPQKWS 58 (77)
Q Consensus 32 v~EvGPYvY~E~~~K~nvtf~~~~~~~ 58 (77)
..=-|||...++.....+++..++.|-
T Consensus 155 ~vgtGPy~l~~~~~~~~i~l~rn~~Y~ 181 (472)
T cd08502 155 YIGSGPFKFVEWEPDQYVVYEKFADYV 181 (472)
T ss_pred eeecCCeEEEeecCCcEEEEEecCCcC
Confidence 345799999988766678888888753
No 43
>PRK15109 antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional
Probab=20.08 E-value=97 Score=24.68 Aligned_cols=31 Identities=16% Similarity=0.373 Sum_probs=22.7
Q ss_pred EeCCeEEEEeeeeeceEEcCCcc-cCCCCeee
Q psy2115 34 EMGPYRFHYGDKYKSQKTSGPQK-WSGGPHVA 64 (77)
Q Consensus 34 EvGPYvY~E~~~K~nvtf~~~~~-~~~~~~~~ 64 (77)
=-|||...+......+++..++. |.+.+.++
T Consensus 214 GtGPy~l~~~~~~~~i~l~rn~~Yw~~~~~~d 245 (547)
T PRK15109 214 GTGPFQLSEYRAGQFIRLQRHDDYWRGKPLMP 245 (547)
T ss_pred ccCCeEEEeecCCCEEEEEeCcccccCCCCCC
Confidence 57999999887666788888887 54444444
Done!