Query 009849
Match_columns 524
No_of_seqs 98 out of 105
Neff 2.8
Searched_HMMs 46136
Date Thu Mar 28 18:04:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009849.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009849hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14418 OHA: OST-HTH Associat 99.4 1E-13 2.2E-18 114.4 1.1 60 457-517 9-71 (75)
2 PF01936 NYN: NYN domain; Int 98.3 5.9E-07 1.3E-11 76.3 3.8 56 1-57 87-143 (146)
3 cd06167 LabA_like LabA_like pr 98.0 6E-06 1.3E-10 71.6 4.7 53 1-54 91-144 (149)
4 TIGR00288 conserved hypothetic 95.4 0.043 9.4E-07 51.9 6.6 49 9-57 104-153 (160)
5 COG1432 Uncharacterized conser 93.2 0.22 4.8E-06 46.8 6.3 58 6-63 106-164 (181)
6 KOG0260 RNA polymerase II, lar 79.9 1E+02 0.0022 38.2 17.8 14 15-28 1327-1340(1605)
7 KOG0260 RNA polymerase II, lar 72.3 1.4E+02 0.003 37.2 16.2 11 72-82 1365-1375(1605)
8 PRK08349 hypothetical protein; 53.5 16 0.00034 34.3 3.6 32 13-44 3-34 (198)
9 cd01712 ThiI ThiI is required 50.6 20 0.00044 32.6 3.8 28 14-41 3-30 (177)
10 cd08502 PBP2_NikA_DppA_OppA_li 49.9 18 0.00039 37.4 3.8 34 377-410 254-287 (472)
11 PRK14820 NADH dehydrogenase su 44.4 22 0.00048 34.8 3.2 31 337-370 136-166 (180)
12 PRK14814 NADH dehydrogenase su 42.3 26 0.00057 34.5 3.3 27 337-366 136-162 (186)
13 PRK14818 NADH dehydrogenase su 36.4 34 0.00074 33.5 3.1 30 337-369 134-163 (173)
14 PF07283 TrbH: Conjugal transf 34.2 68 0.0015 29.6 4.5 38 10-47 23-62 (121)
15 PRK14816 NADH dehydrogenase su 34.1 33 0.00072 33.7 2.6 28 337-367 145-172 (182)
16 PF10073 DUF2312: Uncharacteri 34.1 13 0.00027 32.1 -0.2 41 351-397 6-48 (74)
17 cd08519 PBP2_NikA_DppA_OppA_li 33.7 31 0.00068 35.6 2.5 34 376-409 247-280 (469)
18 PRK14815 NADH dehydrogenase su 33.1 37 0.0008 33.5 2.8 27 337-366 136-162 (183)
19 cd08496 PBP2_NikA_DppA_OppA_li 33.0 35 0.00076 35.0 2.7 30 380-409 243-272 (454)
20 cd08491 PBP2_NikA_DppA_OppA_li 32.7 32 0.0007 35.6 2.4 34 376-409 236-269 (473)
21 cd01994 Alpha_ANH_like_IV This 32.6 49 0.0011 31.6 3.5 28 14-41 3-30 (194)
22 PF00496 SBP_bac_5: Bacterial 32.5 34 0.00074 33.4 2.5 31 379-409 210-240 (374)
23 COG2267 PldB Lysophospholipase 31.6 59 0.0013 32.8 4.0 40 2-41 25-68 (298)
24 smart00645 Pept_C1 Papain fami 31.4 61 0.0013 29.9 3.8 54 346-399 26-79 (174)
25 KOG2236 Uncharacterized conser 30.1 3.4E+02 0.0074 30.6 9.6 16 50-65 233-248 (483)
26 cd01995 ExsB ExsB is a transcr 29.8 57 0.0012 29.3 3.2 28 14-41 3-30 (169)
27 cd00995 PBP2_NikA_DppA_OppA_li 29.7 40 0.00088 33.8 2.5 31 379-409 247-277 (466)
28 PF06508 QueC: Queuosine biosy 29.5 51 0.0011 31.9 3.1 28 14-41 3-30 (209)
29 PF10965 DUF2767: Protein of u 28.8 88 0.0019 26.8 3.9 54 346-399 10-66 (69)
30 cd08498 PBP2_NikA_DppA_OppA_li 28.7 50 0.0011 34.2 3.0 29 381-409 259-287 (481)
31 PRK06411 NADH dehydrogenase su 27.9 52 0.0011 32.3 2.8 29 337-368 138-166 (183)
32 cd08510 PBP2_Lactococcal_OppA_ 27.9 47 0.001 34.9 2.7 28 381-408 287-314 (516)
33 cd08512 PBP2_NikA_DppA_OppA_li 27.8 47 0.001 34.1 2.6 33 376-408 258-290 (476)
34 KOG1924 RhoA GTPase effector D 27.3 2.8E+02 0.006 33.5 8.6 37 355-395 626-664 (1102)
35 cd08489 PBP2_NikA The substrat 27.1 46 0.001 34.4 2.4 31 379-409 249-279 (488)
36 PF03033 Glyco_transf_28: Glyc 27.0 79 0.0017 26.7 3.5 29 23-51 15-43 (139)
37 cd08492 PBP2_NikA_DppA_OppA_li 27.0 60 0.0013 33.4 3.2 28 381-408 261-288 (484)
38 PRK14813 NADH dehydrogenase su 26.9 54 0.0012 32.5 2.8 28 337-367 132-159 (189)
39 PF03054 tRNA_Me_trans: tRNA m 26.9 60 0.0013 34.4 3.3 28 14-41 4-31 (356)
40 TIGR00364 exsB protein. This p 26.6 61 0.0013 30.3 2.9 28 14-41 2-29 (201)
41 cd08517 PBP2_NikA_DppA_OppA_li 26.4 50 0.0011 33.8 2.6 29 381-409 257-285 (480)
42 TIGR01957 nuoB_fam NADH-quinon 26.4 57 0.0012 30.8 2.7 25 337-364 121-145 (145)
43 PF11553 DUF3231: Protein of u 26.4 80 0.0017 29.0 3.6 71 426-499 87-159 (166)
44 TIGR00342 thiazole biosynthesi 26.2 76 0.0016 33.2 3.8 29 13-41 175-203 (371)
45 PF14258 DUF4350: Domain of un 25.7 1.1E+02 0.0023 24.1 3.8 32 9-40 33-69 (70)
46 PF04009 DUF356: Protein of un 25.3 69 0.0015 29.4 2.9 22 9-30 78-100 (107)
47 cd08493 PBP2_DppA_like The sub 25.0 53 0.0011 33.9 2.4 29 380-408 263-291 (482)
48 cd05014 SIS_Kpsf KpsF-like pro 24.9 2.1E+02 0.0046 24.1 5.7 49 11-60 48-99 (128)
49 PRK14971 DNA polymerase III su 24.4 1.8E+02 0.0038 32.9 6.4 59 430-488 130-193 (614)
50 cd08513 PBP2_thermophilic_Hb8_ 24.0 60 0.0013 33.4 2.6 27 382-408 255-281 (482)
51 PF10686 DUF2493: Protein of u 23.9 1.1E+02 0.0025 25.3 3.8 31 11-41 2-38 (71)
52 TIGR03679 arCOG00187 arCOG0018 23.4 69 0.0015 31.1 2.8 25 14-38 1-25 (218)
53 cd08508 PBP2_NikA_DppA_OppA_li 23.4 63 0.0014 33.5 2.6 31 379-409 253-283 (470)
54 cd04182 GT_2_like_f GT_2_like_ 23.1 1.5E+02 0.0033 25.9 4.6 77 347-446 73-151 (186)
55 PRK09755 putative ABC transpor 22.6 69 0.0015 34.2 2.8 30 379-408 298-327 (535)
56 KOG0258 Alanine aminotransfera 22.3 1.8E+02 0.0039 32.4 5.8 70 422-492 75-161 (475)
57 PRK13883 conjugal transfer pro 22.2 1.1E+02 0.0025 29.2 3.9 33 12-44 53-87 (151)
58 cd08506 PBP2_clavulanate_OppA2 22.0 71 0.0015 32.8 2.7 33 376-408 239-271 (466)
59 PF09832 DUF2059: Uncharacteri 21.8 51 0.0011 25.7 1.3 28 431-458 15-42 (64)
60 cd08516 PBP2_NikA_DppA_OppA_li 21.6 72 0.0016 32.5 2.6 28 381-408 245-272 (457)
61 PF12146 Hydrolase_4: Putative 21.5 1.9E+02 0.0041 23.9 4.6 38 3-40 8-49 (79)
62 CHL00023 ndhK NADH dehydrogena 21.5 91 0.002 31.8 3.2 45 337-385 136-180 (225)
63 cd08490 PBP2_NikA_DppA_OppA_li 21.5 71 0.0015 32.6 2.5 29 380-408 239-267 (470)
64 PRK08384 thiamine biosynthesis 21.3 1.1E+02 0.0023 32.9 3.8 31 13-43 183-213 (381)
65 cd08518 PBP2_NikA_DppA_OppA_li 21.1 69 0.0015 33.1 2.4 27 383-409 247-273 (464)
66 PRK14665 mnmA tRNA-specific 2- 20.9 1E+02 0.0022 32.6 3.6 29 13-41 8-36 (360)
67 cd08499 PBP2_Ylib_like The sub 20.9 79 0.0017 32.6 2.8 30 380-409 247-276 (474)
68 KOG2805 tRNA (5-methylaminomet 20.9 1E+02 0.0022 33.4 3.5 31 11-41 6-36 (377)
69 KOG1610 Corticosteroid 11-beta 20.9 1.5E+02 0.0031 31.8 4.6 45 9-53 26-73 (322)
70 TIGR00420 trmU tRNA (5-methyla 20.8 1.1E+02 0.0023 32.1 3.6 29 13-41 3-31 (352)
71 cd08515 PBP2_NikA_DppA_OppA_li 20.5 80 0.0017 32.5 2.7 31 379-409 250-280 (460)
72 cd08501 PBP2_Lpqw The substrat 20.4 73 0.0016 32.9 2.4 31 379-409 258-288 (486)
73 cd01986 Alpha_ANH_like Adenine 20.3 1.2E+02 0.0026 25.3 3.3 28 14-41 2-29 (103)
74 PRK15104 oligopeptide ABC tran 20.2 85 0.0019 33.6 2.9 29 381-409 307-335 (543)
75 cd08511 PBP2_NikA_DppA_OppA_li 20.1 85 0.0018 32.2 2.8 30 380-409 248-277 (467)
76 cd08495 PBP2_NikA_DppA_OppA_li 20.1 79 0.0017 32.7 2.6 29 380-408 259-287 (482)
77 PF05402 PqqD: Coenzyme PQQ sy 20.1 1.3E+02 0.0029 23.3 3.2 41 453-494 25-67 (68)
No 1
>PF14418 OHA: OST-HTH Associated domain
Probab=99.37 E-value=1e-13 Score=114.35 Aligned_cols=60 Identities=35% Similarity=0.434 Sum_probs=55.7
Q ss_pred cccHHHHHHHHHHh---cccchhhhHHHHHHHHhhccccceeeCCCCceeeEEEEeeeecCCCc
Q 009849 457 SQCRYEAALILKNS---CLPELALGEILKILNMVITPKKWIIHHQSGWQPVTITLAEYKSDSGS 517 (524)
Q Consensus 457 SqsRyeaA~~LKk~---CLk~LalgDVLQILnmlIs~KKWi~~hpSgwqPl~itl~~~~~~~~~ 517 (524)
+++||++|+.||+. |||+|+||+|++||+|.|++|||+ ++++.|+|+.+++.++++..+.
T Consensus 9 ~~gRY~~A~~Lk~~gp~~lr~l~Lg~i~~iVqlai~~k~l~-y~~~~l~P~~~~~~~a~s~~~~ 71 (75)
T PF14418_consen 9 SGGRYGMAQFLKKRGPPFLRSLSLGDICHIVQLAISKKKLI-YENSNLKPFCISQKVANSFLGI 71 (75)
T ss_pred CCcHHHHHHHHHhcCchhhcCCcHHHHHHHHHHHHhCCeee-eCCCccccHHHHHHHHHhhhcc
Confidence 38999999999998 999999999999999999999999 9999999999999888876544
No 2
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=98.29 E-value=5.9e-07 Score=76.30 Aligned_cols=56 Identities=32% Similarity=0.488 Sum_probs=41.0
Q ss_pred CceecccCCCCceEEEEeCCcchHHHHHHHhhcCceEEEEc-cCCCCHHHHhhcceEE
Q 009849 1 MLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ-PHKASAPLVAAAKSVW 57 (524)
Q Consensus 1 ML~WAlDNPpPAnIvLISGDrDFS~ALh~LRmR~YNILLA~-P~~ASasL~sAAS~vW 57 (524)
|+.|+.+++. .++||||||+||+.++..||.+|++|.++. +..++..|..+|...+
T Consensus 87 ~~~~~~~~~~-d~ivLvSgD~Df~~~v~~l~~~g~~V~v~~~~~~~s~~L~~~ad~f~ 143 (146)
T PF01936_consen 87 ILELAYENPP-DTIVLVSGDSDFAPLVRKLRERGKRVIVVGAEDSASEALRSAADEFI 143 (146)
T ss_dssp HHHHG--GG--SEEEEE---GGGHHHHHHHHHH--EEEEEE-GGGS-HHHHHHSSEEE
T ss_pred HHHHhhccCC-CEEEEEECcHHHHHHHHHHHHcCCEEEEEEeCCCCCHHHHHhcCEEE
Confidence 3567777766 999999999999999999999999999998 6789999999887554
No 3
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=98.03 E-value=6e-06 Score=71.61 Aligned_cols=53 Identities=28% Similarity=0.312 Sum_probs=47.4
Q ss_pred CceecccCCCCceEEEEeCCcchHHHHHHHhhcCceEEEEccC-CCCHHHHhhcc
Q 009849 1 MLFWAVDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPH-KASAPLVAAAK 54 (524)
Q Consensus 1 ML~WAlDNPpPAnIvLISGDrDFS~ALh~LRmR~YNILLA~P~-~ASasL~sAAS 54 (524)
|+.++.++ .+..|||+|||+||+.++..||.+|.+|+++.+. .++..|..++.
T Consensus 91 ~~~~~~~~-~~d~ivLvSgD~Df~~~i~~lr~~G~~V~v~~~~~~~s~~L~~~~d 144 (149)
T cd06167 91 ALELAYKR-RIDTIVLVSGDSDFVPLVERLRELGKRVIVVGFEAKTSRELRKAAD 144 (149)
T ss_pred HHHHhhhc-CCCEEEEEECCccHHHHHHHHHHcCCEEEEEccCccChHHHHHhCC
Confidence 35566777 7899999999999999999999999999999988 78999988876
No 4
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=95.36 E-value=0.043 Score=51.88 Aligned_cols=49 Identities=16% Similarity=0.201 Sum_probs=42.5
Q ss_pred CCCceEEEEeCCcchHHHHHHHhhcCceEEEEc-cCCCCHHHHhhcceEE
Q 009849 9 PAPSNYLLISGDRDFSNALHQLRMRRYNILLAQ-PHKASAPLVAAAKSVW 57 (524)
Q Consensus 9 PpPAnIvLISGDrDFS~ALh~LRmR~YNILLA~-P~~ASasL~sAAS~vW 57 (524)
+.-.+++|+|||+||...+.+||.+|-.|+.+. +...+..|..++..-.
T Consensus 104 ~~iD~~vLvSgD~DF~~Lv~~lre~G~~V~v~g~~~~ts~~L~~acd~FI 153 (160)
T TIGR00288 104 PNIDAVALVTRDADFLPVINKAKENGKETIVIGAEPGFSTALQNSADIAI 153 (160)
T ss_pred CCCCEEEEEeccHhHHHHHHHHHHCCCEEEEEeCCCCChHHHHHhcCeEE
Confidence 556899999999999999999999999999998 5568889998886543
No 5
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=93.20 E-value=0.22 Score=46.84 Aligned_cols=58 Identities=26% Similarity=0.223 Sum_probs=49.1
Q ss_pred ccCCCCceEEEEeCCcchHHHHHHHhhcCceEEEEccCC-CCHHHHhhcceEEEcchhc
Q 009849 6 VDNPAPSNYLLISGDRDFSNALHQLRMRRYNILLAQPHK-ASAPLVAAAKSVWLWTSLV 63 (524)
Q Consensus 6 lDNPpPAnIvLISGDrDFS~ALh~LRmR~YNILLA~P~~-ASasL~sAAS~vWlW~SLl 63 (524)
.+|+.=.+|+|.|||.||..++..++.+|-.|.++.-.. .|..|..+|.....=.++.
T Consensus 106 ~~~~~~D~ivl~SgD~DF~p~v~~~~~~G~rv~v~~~~~~~s~~L~~~aD~~i~L~~~~ 164 (181)
T COG1432 106 ADKKNVDTIVLFSGDGDFIPLVEAARDKGKRVEVAGIEPMTSSDLRNAADYYIDLKSLE 164 (181)
T ss_pred hcccCCCEEEEEcCCccHHHHHHHHHHcCCEEEEEecCCcCHHHHHHhhcceEEchhhh
Confidence 456677899999999999999999999999999998554 6788999988776665544
No 6
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=79.95 E-value=1e+02 Score=38.24 Aligned_cols=14 Identities=36% Similarity=0.323 Sum_probs=7.2
Q ss_pred EEEeCCcchHHHHH
Q 009849 15 LLISGDRDFSNALH 28 (524)
Q Consensus 15 vLISGDrDFS~ALh 28 (524)
++|+.|..+.+.+|
T Consensus 1327 ~vi~f~gsyVnyrh 1340 (1605)
T KOG0260|consen 1327 NVISFDGSYVNYRH 1340 (1605)
T ss_pred heEeecccchhHHH
Confidence 44555555555444
No 7
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=72.35 E-value=1.4e+02 Score=37.22 Aligned_cols=11 Identities=0% Similarity=-0.475 Sum_probs=4.6
Q ss_pred cccccccCCCC
Q 009849 72 GESLLHTNDFG 82 (524)
Q Consensus 72 ~e~~~L~~~~~ 82 (524)
.+.-+|--|++
T Consensus 1365 ~~tgaLmrcSf 1375 (1605)
T KOG0260|consen 1365 QDTGALMRCSF 1375 (1605)
T ss_pred hhccccccccH
Confidence 33344444443
No 8
>PRK08349 hypothetical protein; Validated
Probab=53.46 E-value=16 Score=34.30 Aligned_cols=32 Identities=16% Similarity=0.094 Sum_probs=28.0
Q ss_pred eEEEEeCCcchHHHHHHHhhcCceEEEEccCC
Q 009849 13 NYLLISGDRDFSNALHQLRMRRYNILLAQPHK 44 (524)
Q Consensus 13 nIvLISGDrDFS~ALh~LRmR~YNILLA~P~~ 44 (524)
-++++||..|=+.+++.|..+||+|..++=..
T Consensus 3 ~vvllSGG~DS~v~~~~l~~~g~~v~av~~d~ 34 (198)
T PRK08349 3 AVALLSSGIDSPVAIYLMLRRGVEVYPVHFRQ 34 (198)
T ss_pred EEEEccCChhHHHHHHHHHHcCCeEEEEEEeC
Confidence 47999999999999999999999999877443
No 9
>cd01712 ThiI ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide.
Probab=50.64 E-value=20 Score=32.55 Aligned_cols=28 Identities=25% Similarity=0.165 Sum_probs=25.8
Q ss_pred EEEEeCCcchHHHHHHHhhcCceEEEEc
Q 009849 14 YLLISGDRDFSNALHQLRMRRYNILLAQ 41 (524)
Q Consensus 14 IvLISGDrDFS~ALh~LRmR~YNILLA~ 41 (524)
+|++||-.|=+.++..|+.+||+|+.++
T Consensus 3 lv~~SGG~DS~~la~ll~~~g~~v~av~ 30 (177)
T cd01712 3 LALLSGGIDSPVAAWLLMKRGIEVDALH 30 (177)
T ss_pred EEEecCChhHHHHHHHHHHcCCeEEEEE
Confidence 7899999999999999999999998877
No 10
>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=49.91 E-value=18 Score=37.39 Aligned_cols=34 Identities=21% Similarity=0.375 Sum_probs=28.3
Q ss_pred hhcCCCCCCCchHHHHHHHHHHHhHHHHHhcCCc
Q 009849 377 IRYGEPKHRNTDVRKALNCAIEQHMVIKRSLGAL 410 (524)
Q Consensus 377 IryGd~k~~~~DVkKaLe~Ai~~q~vvk~~lg~m 410 (524)
+....+-+...+|||||..||-+++|+++.+|..
T Consensus 254 ~N~~~~~~~d~~vR~Ai~~aidr~~i~~~~~~g~ 287 (472)
T cd08502 254 FNHLQPPFDNPKIRRAVLAALDQEDLLAAAVGDP 287 (472)
T ss_pred EcCCCCCCcCHHHHHHHHHhcCHHHHHHHHhCCC
Confidence 3345667889999999999999999999987654
No 11
>PRK14820 NADH dehydrogenase subunit B; Provisional
Probab=44.40 E-value=22 Score=34.81 Aligned_cols=31 Identities=13% Similarity=0.107 Sum_probs=25.5
Q ss_pred CCCCCCCccchhhHHHHHHHHHhhhhcccccCCC
Q 009849 337 TQGRLTPSEYVQGLIGVILLALNTLKIERVVPSE 370 (524)
Q Consensus 337 ~~g~p~ps~~~qglI~viL~aL~~LK~Eki~PtE 370 (524)
-+|||+ .++.+++.|+++++.++.|++-+..
T Consensus 136 IPGCPP---~Pe~il~~l~~l~~~i~~~~~~~~~ 166 (180)
T PRK14820 136 VPGCPP---RPEQIIDGVMRVQELVKNESLRRRN 166 (180)
T ss_pred ecCCCC---CHHHHHHHHHHHHHHHhhccccccC
Confidence 599999 5667899999999999999775543
No 12
>PRK14814 NADH dehydrogenase subunit B; Provisional
Probab=42.25 E-value=26 Score=34.48 Aligned_cols=27 Identities=11% Similarity=0.208 Sum_probs=21.1
Q ss_pred CCCCCCCccchhhHHHHHHHHHhhhhcccc
Q 009849 337 TQGRLTPSEYVQGLIGVILLALNTLKIERV 366 (524)
Q Consensus 337 ~~g~p~ps~~~qglI~viL~aL~~LK~Eki 366 (524)
-+|||+. ++.+++.|+..+..+|.|.+
T Consensus 136 IPGCPP~---Pe~il~~l~~L~~~i~~~~~ 162 (186)
T PRK14814 136 VPGCPPR---PEAILDALVKLQTKLKTQGL 162 (186)
T ss_pred ecCCCCC---HHHHHHHHHHHHHHHhcccc
Confidence 5999995 55677888888888887755
No 13
>PRK14818 NADH dehydrogenase subunit B; Provisional
Probab=36.42 E-value=34 Score=33.47 Aligned_cols=30 Identities=13% Similarity=0.047 Sum_probs=25.1
Q ss_pred CCCCCCCccchhhHHHHHHHHHhhhhcccccCC
Q 009849 337 TQGRLTPSEYVQGLIGVILLALNTLKIERVVPS 369 (524)
Q Consensus 337 ~~g~p~ps~~~qglI~viL~aL~~LK~Eki~Pt 369 (524)
-||||+ .++.+|..|+..++.++.|+....
T Consensus 134 IPGCPP---~PeaIl~gil~L~~~i~~~~~~~~ 163 (173)
T PRK14818 134 VPGCPP---RPEALTEGLLRLQEIVRSEPWSTK 163 (173)
T ss_pred ccCCCC---CHHHHHHHHHHHHHHHhccccccc
Confidence 489999 567789999999999999987763
No 14
>PF07283 TrbH: Conjugal transfer protein TrbH; InterPro: IPR010837 This entry represents TrbH, a bacterial conjugal transfer protein approximately 150 residues long. TrbH contains a putative membrane lipoprotein lipid attachment site [].
Probab=34.24 E-value=68 Score=29.58 Aligned_cols=38 Identities=34% Similarity=0.549 Sum_probs=27.3
Q ss_pred CCceEEEEeCCcc-hHHHHH-HHhhcCceEEEEccCCCCH
Q 009849 10 APSNYLLISGDRD-FSNALH-QLRMRRYNILLAQPHKASA 47 (524)
Q Consensus 10 pPAnIvLISGDrD-FS~ALh-~LRmR~YNILLA~P~~ASa 47 (524)
+-++|.|--.|.| |..+|. .||.+||-|+=..+.....
T Consensus 23 A~Tt~~L~q~~~d~Fg~aL~~~LR~~GYaV~e~~~~~~~~ 62 (121)
T PF07283_consen 23 AKTTFELKQKDPDPFGQALENALRAKGYAVIEDDPPDNSA 62 (121)
T ss_pred CccEEEEEcCCCChHHHHHHHHHHhcCcEEEecCCccccc
Confidence 3345555355555 988776 8999999999988877543
No 15
>PRK14816 NADH dehydrogenase subunit B; Provisional
Probab=34.09 E-value=33 Score=33.73 Aligned_cols=28 Identities=14% Similarity=0.141 Sum_probs=22.4
Q ss_pred CCCCCCCccchhhHHHHHHHHHhhhhccccc
Q 009849 337 TQGRLTPSEYVQGLIGVILLALNTLKIERVV 367 (524)
Q Consensus 337 ~~g~p~ps~~~qglI~viL~aL~~LK~Eki~ 367 (524)
-+|||+. ++.+|..|+..++.+|.|+++
T Consensus 145 IPGCPP~---Pe~Il~~l~~L~~ki~~~~~~ 172 (182)
T PRK14816 145 IPGCPPR---PEAFYYGMMQLQRKVKIEKFF 172 (182)
T ss_pred eeCcCCC---HHHHHHHHHHHHHHhcccccc
Confidence 3899994 566788888888999988764
No 16
>PF10073 DUF2312: Uncharacterized protein conserved in bacteria (DUF2312); InterPro: IPR018753 This entry is represented by Azospirillum phage Cd, Gp10. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family of hypothetical bacterial proteins have no known function.
Probab=34.07 E-value=13 Score=32.05 Aligned_cols=41 Identities=29% Similarity=0.435 Sum_probs=30.7
Q ss_pred HHHHHHHHhhhhcccccCCCccccchhh--cCCCCCCCchHHHHHHHHH
Q 009849 351 IGVILLALNTLKIERVVPSEANITDCIR--YGEPKHRNTDVRKALNCAI 397 (524)
Q Consensus 351 I~viL~aL~~LK~Eki~PtE~nI~DCIr--yGd~k~~~~DVkKaLe~Ai 397 (524)
++.++.=++-|..|| +.|+|+|+ |.+.|..|||+| +|.-.|
T Consensus 6 Lr~~ieRiErLEeEk-----~~i~~dikdVyaEAK~~GfD~K-~lr~ii 48 (74)
T PF10073_consen 6 LRQFIERIERLEEEK-----KAISDDIKDVYAEAKGNGFDTK-ALRQII 48 (74)
T ss_pred HHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHhCCCCHH-HHHHHH
Confidence 445556667777777 67999997 999999999985 444443
No 17
>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=33.74 E-value=31 Score=35.58 Aligned_cols=34 Identities=24% Similarity=0.412 Sum_probs=27.8
Q ss_pred hhhcCCCCCCCchHHHHHHHHHHHhHHHHHhcCC
Q 009849 376 CIRYGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 409 (524)
Q Consensus 376 CIryGd~k~~~~DVkKaLe~Ai~~q~vvk~~lg~ 409 (524)
++..-.+-+...+|||||..||-++.|+++.++.
T Consensus 247 ~~N~~~~~~~d~~vRkAl~~aiDr~~i~~~~~~g 280 (469)
T cd08519 247 VFNVNQPPLDNLAVRQALAYLIDRDLIVNRVYYG 280 (469)
T ss_pred EEeCCCCCCCCHHHHHHHHHHcCHHHHHHHHHhc
Confidence 3445556778899999999999999999987543
No 18
>PRK14815 NADH dehydrogenase subunit B; Provisional
Probab=33.11 E-value=37 Score=33.45 Aligned_cols=27 Identities=11% Similarity=0.235 Sum_probs=22.6
Q ss_pred CCCCCCCccchhhHHHHHHHHHhhhhcccc
Q 009849 337 TQGRLTPSEYVQGLIGVILLALNTLKIERV 366 (524)
Q Consensus 337 ~~g~p~ps~~~qglI~viL~aL~~LK~Eki 366 (524)
-+|||+ .++.+|+.|+..++.++.|+.
T Consensus 136 IPGCPP---~Pe~il~~l~~l~~~i~~~~~ 162 (183)
T PRK14815 136 ISGCPP---RPEAILDALIKLQKKIDTERA 162 (183)
T ss_pred ecCCCC---CHHHHHHHHHHHHHHHhhccc
Confidence 599999 567788889999999998754
No 19
>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=33.02 E-value=35 Score=34.98 Aligned_cols=30 Identities=23% Similarity=0.325 Sum_probs=25.8
Q ss_pred CCCCCCCchHHHHHHHHHHHhHHHHHhcCC
Q 009849 380 GEPKHRNTDVRKALNCAIEQHMVIKRSLGA 409 (524)
Q Consensus 380 Gd~k~~~~DVkKaLe~Ai~~q~vvk~~lg~ 409 (524)
..+.+.+..|||||..||..+.++++.++.
T Consensus 243 ~~~~~~d~~vRkAl~~aidr~~i~~~~~~g 272 (454)
T cd08496 243 TGAPFDDPKVRQAINYAIDRKAFVDALLFG 272 (454)
T ss_pred CCCCCCCHHHHHHHHhhcCHHHHHHHHhcC
Confidence 456688999999999999999999988653
No 20
>cd08491 PBP2_NikA_DppA_OppA_like_12 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
Probab=32.69 E-value=32 Score=35.61 Aligned_cols=34 Identities=32% Similarity=0.406 Sum_probs=28.2
Q ss_pred hhhcCCCCCCCchHHHHHHHHHHHhHHHHHhcCC
Q 009849 376 CIRYGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 409 (524)
Q Consensus 376 CIryGd~k~~~~DVkKaLe~Ai~~q~vvk~~lg~ 409 (524)
++....+.+.+.+|||||..||-++.|++..++.
T Consensus 236 ~~N~~~~~~~d~~vR~Ai~~aidr~~i~~~~~~g 269 (473)
T cd08491 236 RIDAQIPPLDDVRVRKALNLAIDRDGIVGALFGG 269 (473)
T ss_pred EecCCCCcccCHHHHHHHHHhcCHHHHHHHHhcC
Confidence 3445567888999999999999999999987653
No 21
>cd01994 Alpha_ANH_like_IV This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily of proteins is predicted to bind ATP. This domainhas a strongly conserved motif SGGKD at the N terminus.
Probab=32.56 E-value=49 Score=31.62 Aligned_cols=28 Identities=25% Similarity=0.207 Sum_probs=24.8
Q ss_pred EEEEeCCcchHHHHHHHhhcCceEEEEc
Q 009849 14 YLLISGDRDFSNALHQLRMRRYNILLAQ 41 (524)
Q Consensus 14 IvLISGDrDFS~ALh~LRmR~YNILLA~ 41 (524)
++++||-.|=+.+|+.+...||.|+.+.
T Consensus 3 ~v~~SGGkDS~~al~~a~~~G~~v~~l~ 30 (194)
T cd01994 3 VALISGGKDSCYALYRALEEGHEVVALL 30 (194)
T ss_pred EEEecCCHHHHHHHHHHHHcCCEEEEEE
Confidence 6899999999999999999999987655
No 22
>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=32.49 E-value=34 Score=33.37 Aligned_cols=31 Identities=29% Similarity=0.545 Sum_probs=25.3
Q ss_pred cCCCCCCCchHHHHHHHHHHHhHHHHHhcCC
Q 009849 379 YGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 409 (524)
Q Consensus 379 yGd~k~~~~DVkKaLe~Ai~~q~vvk~~lg~ 409 (524)
...+=+.+.+|||||..||.++++++..++.
T Consensus 210 ~~~~~~~d~~vR~Al~~aidr~~i~~~~~~g 240 (374)
T PF00496_consen 210 TNNPPFSDKAVRQALAYAIDREAIVKNIFGG 240 (374)
T ss_dssp TTSTTTTSHHHHHHHHHHS-HHHHHHHTTTT
T ss_pred ccccccchhhhHHHHHhhhhHHHHHHHHHhh
Confidence 3456678899999999999999999998654
No 23
>COG2267 PldB Lysophospholipase [Lipid metabolism]
Probab=31.58 E-value=59 Score=32.78 Aligned_cols=40 Identities=18% Similarity=0.420 Sum_probs=32.9
Q ss_pred ceecccCCCCceEEEEeCCcc----hHHHHHHHhhcCceEEEEc
Q 009849 2 LFWAVDNPAPSNYLLISGDRD----FSNALHQLRMRRYNILLAQ 41 (524)
Q Consensus 2 L~WAlDNPpPAnIvLISGDrD----FS~ALh~LRmR~YNILLA~ 41 (524)
-.|..++++...|||+.|=.| |...+..|.++||.|+..=
T Consensus 25 ~~~~~~~~~~g~Vvl~HG~~Eh~~ry~~la~~l~~~G~~V~~~D 68 (298)
T COG2267 25 RTWAAPEPPKGVVVLVHGLGEHSGRYEELADDLAARGFDVYALD 68 (298)
T ss_pred EeecCCCCCCcEEEEecCchHHHHHHHHHHHHHHhCCCEEEEec
Confidence 358888887799999999988 5567788999999998643
No 24
>smart00645 Pept_C1 Papain family cysteine protease.
Probab=31.41 E-value=61 Score=29.95 Aligned_cols=54 Identities=15% Similarity=0.087 Sum_probs=40.8
Q ss_pred chhhHHHHHHHHHhhhhcccccCCCccccchhhcCCCCCCCchHHHHHHHHHHH
Q 009849 346 YVQGLIGVILLALNTLKIERVVPSEANITDCIRYGEPKHRNTDVRKALNCAIEQ 399 (524)
Q Consensus 346 ~~qglI~viL~aL~~LK~Eki~PtE~nI~DCIryGd~k~~~~DVkKaLe~Ai~~ 399 (524)
..-..+.+|-.++.+...+.+.-+|+.|.||.++++-.-.+=+..+||+-++++
T Consensus 26 wAfa~~~~ie~~~~i~~~~~~~lS~q~l~~C~~~~~~gC~GG~~~~a~~~~~~~ 79 (174)
T smart00645 26 WAFSATGALEGRYCIKTGKLVSLSEQQLVDCSTGGNNGCNGGLPDNAFEYIKKN 79 (174)
T ss_pred HHHHHHHHHHHHHHHhcCCccccCHHHHhhhcCCCCCCCCCcCHHHHHHHHHHc
Confidence 445566666666666666688999999999999844334577889999988877
No 25
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.13 E-value=3.4e+02 Score=30.59 Aligned_cols=16 Identities=13% Similarity=0.198 Sum_probs=10.2
Q ss_pred HhhcceEEEcchhccC
Q 009849 50 VAAAKSVWLWTSLVAG 65 (524)
Q Consensus 50 ~sAAS~vWlW~SLl~G 65 (524)
+.--|+.|+=..-++|
T Consensus 233 lde~Svlf~edR~~lG 248 (483)
T KOG2236|consen 233 LDEDSVLFLEDRTALG 248 (483)
T ss_pred ccccceEEeeccccch
Confidence 3446777776666667
No 26
>cd01995 ExsB ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown
Probab=29.76 E-value=57 Score=29.33 Aligned_cols=28 Identities=21% Similarity=0.315 Sum_probs=23.2
Q ss_pred EEEEeCCcchHHHHHHHhhcCceEEEEc
Q 009849 14 YLLISGDRDFSNALHQLRMRRYNILLAQ 41 (524)
Q Consensus 14 IvLISGDrDFS~ALh~LRmR~YNILLA~ 41 (524)
+|++||-.|=+.+++.|+.+++.|..++
T Consensus 3 lv~~SGG~DS~~~~~~~~~~~~~v~~~~ 30 (169)
T cd01995 3 VVLLSGGLDSTTCLAWAKKEGYEVHALS 30 (169)
T ss_pred EEEecCcHHHHHHHHHHHHcCCcEEEEE
Confidence 5788999998888888888888877765
No 27
>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=29.74 E-value=40 Score=33.84 Aligned_cols=31 Identities=29% Similarity=0.534 Sum_probs=26.0
Q ss_pred cCCCCCCCchHHHHHHHHHHHhHHHHHhcCC
Q 009849 379 YGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 409 (524)
Q Consensus 379 yGd~k~~~~DVkKaLe~Ai~~q~vvk~~lg~ 409 (524)
...+-+.+.+|||||..||-++.+++..++.
T Consensus 247 ~~~~~~~d~~vR~Al~~aidr~~i~~~~~~g 277 (466)
T cd00995 247 TNKPPFDDKRVRQAISYAIDREEIIDAVLGG 277 (466)
T ss_pred cCCCCCCCHHHHHHHHHhcCHHHHHHHHHhC
Confidence 3445678999999999999999999988653
No 28
>PF06508 QueC: Queuosine biosynthesis protein QueC; InterPro: IPR018317 This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In Rhizobium meliloti (Sinorhizobium meliloti), a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA [, ]. In Arthrobacter viscosus, the homologous gene is designated alu1 and is associated with an aluminum tolerance phenotype. When expressed in Escherichia coli, it conferred aliminium tolerance []. The entry also contains the gene queC, which is responsible for the conversion of GTP to 7-cyano-7-deazaguanine (preQ0). The biosynthesis of hypermodified tRNA nucleoside queuosine only occurs in eubacteria. It occupies the wobble position for all known tRNAs that are specific for Asp, Asn, His or Tyr [].; PDB: 3BL5_B 2PG3_A.
Probab=29.51 E-value=51 Score=31.95 Aligned_cols=28 Identities=21% Similarity=0.297 Sum_probs=21.4
Q ss_pred EEEEeCCcchHHHHHHHhhcCceEEEEc
Q 009849 14 YLLISGDRDFSNALHQLRMRRYNILLAQ 41 (524)
Q Consensus 14 IvLISGDrDFS~ALh~LRmR~YNILLA~ 41 (524)
|||.||.-|=..+|+.++.++|+|+.++
T Consensus 3 vvl~SGG~DSt~~l~~~~~~~~~v~al~ 30 (209)
T PF06508_consen 3 VVLFSGGLDSTTCLYWAKKEGYEVYALT 30 (209)
T ss_dssp EEE--SSHHHHHHHHHHHHH-SEEEEEE
T ss_pred EEEeCCCHHHHHHHHHHHHcCCeEEEEE
Confidence 6888999998888888888888887766
No 29
>PF10965 DUF2767: Protein of unknown function (DUF2767); InterPro: IPR024493 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=28.78 E-value=88 Score=26.79 Aligned_cols=54 Identities=20% Similarity=0.105 Sum_probs=41.3
Q ss_pred chhhHHHHHHHHHhhhhcccccCCCccccchhhcCC---CCCCCchHHHHHHHHHHH
Q 009849 346 YVQGLIGVILLALNTLKIERVVPSEANITDCIRYGE---PKHRNTDVRKALNCAIEQ 399 (524)
Q Consensus 346 ~~qglI~viL~aL~~LK~Eki~PtE~nI~DCIryGd---~k~~~~DVkKaLe~Ai~~ 399 (524)
..|..-|||=.|.=.|-.+-.-|+-.+|+|-+|--- .-.+.-+..+|+|.||+.
T Consensus 10 ~Y~EmCRVVGd~Vl~L~~~G~etk~~~Ia~~LrT~l~~~~~kr~~~~~~~me~aI~~ 66 (69)
T PF10965_consen 10 LYQEMCRVVGDAVLELADLGHETKRIVIADVLRTELANGRSKRSELQQQAMELAIDL 66 (69)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHhccccccCHHHHHHHHHHHHH
Confidence 456666666666667777888899999999999733 344566889999999975
No 30
>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=28.67 E-value=50 Score=34.18 Aligned_cols=29 Identities=24% Similarity=0.471 Sum_probs=24.8
Q ss_pred CCCCCCchHHHHHHHHHHHhHHHHHhcCC
Q 009849 381 EPKHRNTDVRKALNCAIEQHMVIKRSLGA 409 (524)
Q Consensus 381 d~k~~~~DVkKaLe~Ai~~q~vvk~~lg~ 409 (524)
.+-+.+.+|||||..||-.+.++++.++.
T Consensus 259 ~~~~~d~~vR~Ai~~aidr~~i~~~~~~g 287 (481)
T cd08498 259 KNPLKDPRVRQALSLAIDREAIVDRVMRG 287 (481)
T ss_pred CCCCCCHHHHHHHHHhcCHHHHHHHHhcC
Confidence 45678899999999999999999987553
No 31
>PRK06411 NADH dehydrogenase subunit B; Validated
Probab=27.93 E-value=52 Score=32.31 Aligned_cols=29 Identities=14% Similarity=0.053 Sum_probs=22.9
Q ss_pred CCCCCCCccchhhHHHHHHHHHhhhhcccccC
Q 009849 337 TQGRLTPSEYVQGLIGVILLALNTLKIERVVP 368 (524)
Q Consensus 337 ~~g~p~ps~~~qglI~viL~aL~~LK~Eki~P 368 (524)
-+|||+. ++.+++.|+..++.++.|+..-
T Consensus 138 IPGCPP~---Pe~il~~l~~l~~~i~~~~~~~ 166 (183)
T PRK06411 138 VPGCPPR---PEALLYGILKLQKKIRQSERER 166 (183)
T ss_pred eCCCCCC---HHHHHHHHHHHHHHHhcccccc
Confidence 4999995 5667888888899999886653
No 32
>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=27.90 E-value=47 Score=34.94 Aligned_cols=28 Identities=25% Similarity=0.374 Sum_probs=24.7
Q ss_pred CCCCCCchHHHHHHHHHHHhHHHHHhcC
Q 009849 381 EPKHRNTDVRKALNCAIEQHMVIKRSLG 408 (524)
Q Consensus 381 d~k~~~~DVkKaLe~Ai~~q~vvk~~lg 408 (524)
.+.+.+.+|||||-.||.++.+++..++
T Consensus 287 ~~~~~d~~vR~Ai~~aiDr~~i~~~~~~ 314 (516)
T cd08510 287 NAKMADKNLRQAMAYAIDNDAVGKKFYN 314 (516)
T ss_pred ccccccHHHHHHHHHhhCHHHHHHHHhC
Confidence 4668889999999999999999998755
No 33
>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=27.76 E-value=47 Score=34.11 Aligned_cols=33 Identities=24% Similarity=0.353 Sum_probs=27.4
Q ss_pred hhhcCCCCCCCchHHHHHHHHHHHhHHHHHhcC
Q 009849 376 CIRYGEPKHRNTDVRKALNCAIEQHMVIKRSLG 408 (524)
Q Consensus 376 CIryGd~k~~~~DVkKaLe~Ai~~q~vvk~~lg 408 (524)
++-...+-+.+..|||||..||.++.+++..++
T Consensus 258 ~~N~~~~~~~d~~vR~Al~~aidr~~i~~~~~~ 290 (476)
T cd08512 258 ALNTKKAPFDNPKVRQAIAYAIDYDGIIDQVLK 290 (476)
T ss_pred EeeCCCCCCCCHHHHHHHHHhcCHHHHHHHHhc
Confidence 344455678899999999999999999998865
No 34
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=27.28 E-value=2.8e+02 Score=33.53 Aligned_cols=37 Identities=27% Similarity=0.465 Sum_probs=19.9
Q ss_pred HHHHhhhhcccccCCCccccch--hhcCCCCCCCchHHHHHHH
Q 009849 355 LLALNTLKIERVVPSEANITDC--IRYGEPKHRNTDVRKALNC 395 (524)
Q Consensus 355 L~aL~~LK~Eki~PtE~nI~DC--IryGd~k~~~~DVkKaLe~ 395 (524)
+.-+|-.| |.|++-. -+| ++.-+-|+.+-|.=--|+.
T Consensus 626 Mrr~nW~k---I~p~d~s-~~cFWvkv~Edk~en~dlfakL~~ 664 (1102)
T KOG1924|consen 626 MRRFNWSK---IVPRDLS-ENCFWVKVNEDKLENDDLFAKLAL 664 (1102)
T ss_pred cccCCccc---cCccccC-ccceeeecchhhccchHHHHHHHH
Confidence 33445544 6666521 245 4556777777776444443
No 35
>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=27.14 E-value=46 Score=34.40 Aligned_cols=31 Identities=26% Similarity=0.295 Sum_probs=25.9
Q ss_pred cCCCCCCCchHHHHHHHHHHHhHHHHHhcCC
Q 009849 379 YGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 409 (524)
Q Consensus 379 yGd~k~~~~DVkKaLe~Ai~~q~vvk~~lg~ 409 (524)
+..+.+.+..|||||-.||-.+.++++.+|.
T Consensus 249 ~~~~~~~d~~vR~Al~~aiDr~~i~~~~~~g 279 (488)
T cd08489 249 TASEPLSDLKVREAINYAIDKEAISKGILYG 279 (488)
T ss_pred CCCCccccHHHHHHHHHhcCHHHHHHHHhcC
Confidence 4455678899999999999999999987653
No 36
>PF03033 Glyco_transf_28: Glycosyltransferase family 28 N-terminal domain; InterPro: IPR004276 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 28 GT28 from CAZY comprises enzymes with a number of known activities; 1,2-diacylglycerol 3-beta-galactosyltransferase (2.4.1.46 from EC); 1,2-diacylglycerol 3-beta-glucosyltransferase (2.4.1.157 from EC); beta-N-acetylglucosamine transferase (2.4.1 from EC).; GO: 0016758 transferase activity, transferring hexosyl groups, 0005975 carbohydrate metabolic process, 0030259 lipid glycosylation; PDB: 2IYF_B 2YJN_A 2P6P_A 1PNV_A 3H4T_A 3H4I_A 1PN3_B 3IA7_B 1NLM_B 1F0K_B ....
Probab=27.00 E-value=79 Score=26.75 Aligned_cols=29 Identities=28% Similarity=0.291 Sum_probs=21.0
Q ss_pred hHHHHHHHhhcCceEEEEccCCCCHHHHh
Q 009849 23 FSNALHQLRMRRYNILLAQPHKASAPLVA 51 (524)
Q Consensus 23 FS~ALh~LRmR~YNILLA~P~~ASasL~s 51 (524)
|......|+.|||.|.+++++..-..+.+
T Consensus 15 ~lala~~L~~rGh~V~~~~~~~~~~~v~~ 43 (139)
T PF03033_consen 15 FLALARALRRRGHEVRLATPPDFRERVEA 43 (139)
T ss_dssp HHHHHHHHHHTT-EEEEEETGGGHHHHHH
T ss_pred HHHHHHHHhccCCeEEEeecccceecccc
Confidence 44555689999999999999886555533
No 37
>cd08492 PBP2_NikA_DppA_OppA_like_15 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=26.95 E-value=60 Score=33.38 Aligned_cols=28 Identities=25% Similarity=0.446 Sum_probs=24.3
Q ss_pred CCCCCCchHHHHHHHHHHHhHHHHHhcC
Q 009849 381 EPKHRNTDVRKALNCAIEQHMVIKRSLG 408 (524)
Q Consensus 381 d~k~~~~DVkKaLe~Ai~~q~vvk~~lg 408 (524)
.+-+.+.+|||||-.||-++.|++..++
T Consensus 261 ~~~~~d~~vR~Ai~~aidr~~i~~~~~~ 288 (484)
T cd08492 261 RPPFDDVRVRQALQLAIDREAIVETVFF 288 (484)
T ss_pred CCCCCCHHHHHHHHHhhhHHHHHHHHhc
Confidence 4557789999999999999999988754
No 38
>PRK14813 NADH dehydrogenase subunit B; Provisional
Probab=26.91 E-value=54 Score=32.47 Aligned_cols=28 Identities=18% Similarity=0.316 Sum_probs=22.9
Q ss_pred CCCCCCCccchhhHHHHHHHHHhhhhccccc
Q 009849 337 TQGRLTPSEYVQGLIGVILLALNTLKIERVV 367 (524)
Q Consensus 337 ~~g~p~ps~~~qglI~viL~aL~~LK~Eki~ 367 (524)
-||||| .++.+|+-||.+++.++.|++.
T Consensus 132 IPGCPP---~PeaIl~gl~~l~~~i~~~~~~ 159 (189)
T PRK14813 132 VPGCPP---RPEALIGGLMKVQELIRMEQIG 159 (189)
T ss_pred ccCCCC---CHHHHHHHHHHHHHHHHhcccc
Confidence 499999 4677888889999999987653
No 39
>PF03054 tRNA_Me_trans: tRNA methyl transferase; InterPro: IPR004506 tRNA-specific 2-thiouridylase catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34.; GO: 0016740 transferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 2DET_A 2DER_A 2DEU_A 2HMA_A.
Probab=26.86 E-value=60 Score=34.40 Aligned_cols=28 Identities=25% Similarity=0.329 Sum_probs=23.4
Q ss_pred EEEEeCCcchHHHHHHHhhcCceEEEEc
Q 009849 14 YLLISGDRDFSNALHQLRMRRYNILLAQ 41 (524)
Q Consensus 14 IvLISGDrDFS~ALh~LRmR~YNILLA~ 41 (524)
+|.+||-.|=|-|+..|+.+||+|+-++
T Consensus 4 ~vamSGGVDSsvaA~LLk~~G~~V~Gv~ 31 (356)
T PF03054_consen 4 LVAMSGGVDSSVAAALLKEQGYDVIGVT 31 (356)
T ss_dssp EEE--SSHHHHHHHHHHHHCT-EEEEEE
T ss_pred EEEccCCHHHHHHHHHHHhhcccceEEE
Confidence 5889999999999999999999998877
No 40
>TIGR00364 exsB protein. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown.
Probab=26.56 E-value=61 Score=30.27 Aligned_cols=28 Identities=18% Similarity=0.325 Sum_probs=24.4
Q ss_pred EEEEeCCcchHHHHHHHhhcCceEEEEc
Q 009849 14 YLLISGDRDFSNALHQLRMRRYNILLAQ 41 (524)
Q Consensus 14 IvLISGDrDFS~ALh~LRmR~YNILLA~ 41 (524)
+|++||..|=+.+++.|+.++++|..++
T Consensus 2 vv~lSGG~DSs~~~~~~~~~g~~v~~~~ 29 (201)
T TIGR00364 2 VVVLSGGQDSTTCLAIAKDEGYEVHAIT 29 (201)
T ss_pred EEEeccHHHHHHHHHHHHHcCCcEEEEE
Confidence 6899999998888999988899888766
No 41
>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=26.44 E-value=50 Score=33.78 Aligned_cols=29 Identities=21% Similarity=0.461 Sum_probs=25.1
Q ss_pred CCCCCCchHHHHHHHHHHHhHHHHHhcCC
Q 009849 381 EPKHRNTDVRKALNCAIEQHMVIKRSLGA 409 (524)
Q Consensus 381 d~k~~~~DVkKaLe~Ai~~q~vvk~~lg~ 409 (524)
.+-+.+.+|||||..||.++.+++..++.
T Consensus 257 ~~~~~d~~vR~Al~~aidr~~i~~~~~~g 285 (480)
T cd08517 257 NPPLKDVRVRQAIAHAIDRQFIVDTVFFG 285 (480)
T ss_pred CCccCCHHHHHHHHHhcCHHHHHHHHHcC
Confidence 45678899999999999999999988653
No 42
>TIGR01957 nuoB_fam NADH-quinone oxidoreductase, B subunit. This model describes the B chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. The quinone is plastoquinone in Synechocystis (where the chain is designated K) and in chloroplast, where NADH may be replaced by NADPH. In the methanogenic archaeal genus Methanosarcina, NADH is replaced by F420H2.
Probab=26.37 E-value=57 Score=30.82 Aligned_cols=25 Identities=20% Similarity=0.129 Sum_probs=18.3
Q ss_pred CCCCCCCccchhhHHHHHHHHHhhhhcc
Q 009849 337 TQGRLTPSEYVQGLIGVILLALNTLKIE 364 (524)
Q Consensus 337 ~~g~p~ps~~~qglI~viL~aL~~LK~E 364 (524)
-+|||+ .++-+++.|+..+..+|.|
T Consensus 121 IPGCPp---~Pe~i~~~l~~l~~~~~~~ 145 (145)
T TIGR01957 121 IPGCPP---RPEALIYGLIKLQKKIKRE 145 (145)
T ss_pred eCCCCC---CHHHHHHHHHHHHHHhhcC
Confidence 489998 4566777778777777754
No 43
>PF11553 DUF3231: Protein of unknown function (DUF3231); InterPro: IPR021617 This bacterial family of proteins has no known function. ; PDB: 2RBD_B.
Probab=26.37 E-value=80 Score=28.98 Aligned_cols=71 Identities=14% Similarity=0.207 Sum_probs=29.4
Q ss_pred cCCCCCCCchHH-HHHHHHHHhCCccc-hhhhccccHHHHHHHHHHhcccchhhhHHHHHHHHhhccccceeeCCC
Q 009849 426 LYGNPNQYPKEV-WDRIQKFLTSSSGR-SAIMASQCRYEAALILKNSCLPELALGEILKILNMVITPKKWIIHHQS 499 (524)
Q Consensus 426 ~~gnpk~fpK~~-WD~Iq~FisS~~G~-saI~~SqsRyeaA~~LKk~CLk~LalgDVLQILnmlIs~KKWi~~hpS 499 (524)
....|..|+..+ ..-|...+...-+. +....+-.|.+.....++...+.+.+.+ ++++++ -+|.|++..|.
T Consensus 87 ~~~~~~lfsD~~~l~~~~~~~~~~~~~~~~al~~s~R~Dl~~~f~~~~~~~~~~~~--~~~~l~-~~KGwl~~pP~ 159 (166)
T PF11553_consen 87 TDSAPPLFSDKFMLFYISFMSQAGITNYGRALSSSVRNDLRAFFMKFLMEALELYD--KIVKLM-KEKGWLERPPY 159 (166)
T ss_dssp -GGGS-G--HHHHHHHHHHHHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHH--HHHHHH-HHTT------B
T ss_pred CCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH--HHHHHH-HHCCCcCCCCC
Confidence 666888899983 33333332222221 2222333588876666665554444443 234444 47899998774
No 44
>TIGR00342 thiazole biosynthesis/tRNA modification protein ThiI. The protein product of the thiI gene is required for the synthesis of the thiazole moiety in thiamine biosynthesis. It also acts in the generation of 4-thiouridine in tRNA, and may occur in species (such as Mycoplasma genitalium) that lack de novo thiamine biosynthesis.
Probab=26.21 E-value=76 Score=33.18 Aligned_cols=29 Identities=21% Similarity=0.212 Sum_probs=26.4
Q ss_pred eEEEEeCCcchHHHHHHHhhcCceEEEEc
Q 009849 13 NYLLISGDRDFSNALHQLRMRRYNILLAQ 41 (524)
Q Consensus 13 nIvLISGDrDFS~ALh~LRmR~YNILLA~ 41 (524)
-++++||..|=+.|++.|..||++|+.++
T Consensus 175 vlvllSGGiDS~vaa~ll~krG~~V~av~ 203 (371)
T TIGR00342 175 VLALLSGGIDSPVAAFMMMKRGCRVVAVH 203 (371)
T ss_pred EEEEecCCchHHHHHHHHHHcCCeEEEEE
Confidence 57999999999999999999999998776
No 45
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=25.71 E-value=1.1e+02 Score=24.12 Aligned_cols=32 Identities=25% Similarity=0.274 Sum_probs=24.3
Q ss_pred CCCceEEEEeCCcchHH-----HHHHHhhcCceEEEE
Q 009849 9 PAPSNYLLISGDRDFSN-----ALHQLRMRRYNILLA 40 (524)
Q Consensus 9 PpPAnIvLISGDrDFS~-----ALh~LRmR~YNILLA 40 (524)
..++++|+|..+..+.. .|..+-.+|-.|+|+
T Consensus 33 ~~~~tll~i~~~~~~~~~~~~~~l~~~v~~G~~lvl~ 69 (70)
T PF14258_consen 33 ADDGTLLVIGPDLRLSEPEEAEALLEWVEAGNTLVLA 69 (70)
T ss_pred CCCCEEEEEeCCCCCCchHHHHHHHHHHHcCCEEEEe
Confidence 47899999999977653 555555699888886
No 46
>PF04009 DUF356: Protein of unknown function (DUF356); InterPro: IPR007154 Members of this family are around 120 amino acids in length and are found in some archaebacteria. The function of this family is unknown. However it contains a conserved motif IHPPAH that may be involved in its function.
Probab=25.29 E-value=69 Score=29.43 Aligned_cols=22 Identities=23% Similarity=0.501 Sum_probs=17.0
Q ss_pred CCCceEEEEeCCcc-hHHHHHHH
Q 009849 9 PAPSNYLLISGDRD-FSNALHQL 30 (524)
Q Consensus 9 PpPAnIvLISGDrD-FS~ALh~L 30 (524)
.||||||+||.+-| |...+..+
T Consensus 78 HPPAHIiVis~~~~~y~eL~~~~ 100 (107)
T PF04009_consen 78 HPPAHIIVISPRHDVYEELLEMF 100 (107)
T ss_pred CCCceEEEECCCchHHHHHHHHh
Confidence 68999999999987 66555443
No 47
>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=25.03 E-value=53 Score=33.91 Aligned_cols=29 Identities=21% Similarity=0.408 Sum_probs=24.8
Q ss_pred CCCCCCCchHHHHHHHHHHHhHHHHHhcC
Q 009849 380 GEPKHRNTDVRKALNCAIEQHMVIKRSLG 408 (524)
Q Consensus 380 Gd~k~~~~DVkKaLe~Ai~~q~vvk~~lg 408 (524)
..+-+.+.+|||||..||.++.+++..++
T Consensus 263 ~~~~~~d~~vR~Al~~aidr~~i~~~~~~ 291 (482)
T cd08493 263 QKPPFDDPKVRQAIAHAINKEAIVDAVYQ 291 (482)
T ss_pred CCCccCCHHHHHHHHHhcCHHHHHHHHhc
Confidence 34567789999999999999999998765
No 48
>cd05014 SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.
Probab=24.94 E-value=2.1e+02 Score=24.13 Aligned_cols=49 Identities=20% Similarity=0.177 Sum_probs=36.0
Q ss_pred CceEEEEeCCc---chHHHHHHHhhcCceEEEEccCCCCHHHHhhcceEEEcc
Q 009849 11 PSNYLLISGDR---DFSNALHQLRMRRYNILLAQPHKASAPLVAAAKSVWLWT 60 (524)
Q Consensus 11 PAnIvLISGDr---DFS~ALh~LRmR~YNILLA~P~~ASasL~sAAS~vWlW~ 60 (524)
-..+++||-.+ +...++..+|.+|-.|++++....+. |...|..+....
T Consensus 48 ~d~vi~iS~sG~t~~~~~~~~~a~~~g~~vi~iT~~~~s~-la~~ad~~l~~~ 99 (128)
T cd05014 48 GDVVIAISNSGETDELLNLLPHLKRRGAPIIAITGNPNST-LAKLSDVVLDLP 99 (128)
T ss_pred CCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEeCCCCCc-hhhhCCEEEECC
Confidence 35667777654 68889999999999999999766544 555566666554
No 49
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=24.37 E-value=1.8e+02 Score=32.92 Aligned_cols=59 Identities=14% Similarity=0.254 Sum_probs=36.7
Q ss_pred CCCCchHHHHHHHHHHhCCcc-chhhhccccHHHHHHHHHHhc----ccchhhhHHHHHHHHhh
Q 009849 430 PNQYPKEVWDRIQKFLTSSSG-RSAIMASQCRYEAALILKNSC----LPELALGEILKILNMVI 488 (524)
Q Consensus 430 pk~fpK~~WD~Iq~FisS~~G-~saI~~SqsRyeaA~~LKk~C----Lk~LalgDVLQILnmlI 488 (524)
+..++++.++.+.++|-.+.+ ...|..+..|...-..|++.| |+.+...|+.+.|.-+.
T Consensus 130 a~~Ls~~a~naLLK~LEepp~~tifIL~tt~~~kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia 193 (614)
T PRK14971 130 VHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVA 193 (614)
T ss_pred cccCCHHHHHHHHHHHhCCCCCeEEEEEeCCchhchHHHHhhhheeecCCCCHHHHHHHHHHHH
Confidence 455677889999999888644 445555555554444455555 56666666665554433
No 50
>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=23.95 E-value=60 Score=33.43 Aligned_cols=27 Identities=33% Similarity=0.545 Sum_probs=24.4
Q ss_pred CCCCCchHHHHHHHHHHHhHHHHHhcC
Q 009849 382 PKHRNTDVRKALNCAIEQHMVIKRSLG 408 (524)
Q Consensus 382 ~k~~~~DVkKaLe~Ai~~q~vvk~~lg 408 (524)
+-+.+..|||||..||-++.+++..++
T Consensus 255 ~~~~d~~vR~Al~~aiDr~~i~~~~~~ 281 (482)
T cd08513 255 PILADVRVRQALAYAIDRDAIVKTLYG 281 (482)
T ss_pred CccCCHHHHHHHHhhcCHHHHHHHHhc
Confidence 568899999999999999999998865
No 51
>PF10686 DUF2493: Protein of unknown function (DUF2493); InterPro: IPR019627 This entry is represented by Mycobacteriophage D29, Gp61. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family are mainly Proteobacteria. The function is not known.
Probab=23.90 E-value=1.1e+02 Score=25.32 Aligned_cols=31 Identities=29% Similarity=0.509 Sum_probs=23.2
Q ss_pred CceEEEEeCCcch------HHHHHHHhhcCceEEEEc
Q 009849 11 PSNYLLISGDRDF------SNALHQLRMRRYNILLAQ 41 (524)
Q Consensus 11 PAnIvLISGDrDF------S~ALh~LRmR~YNILLA~ 41 (524)
....|||+|.||| -.+|..++.+.=.++|++
T Consensus 2 ~g~rVli~GgR~~~D~~~i~~~Ld~~~~~~~~~~lvh 38 (71)
T PF10686_consen 2 EGMRVLITGGRDWTDHELIWAALDKVHARHPDMVLVH 38 (71)
T ss_pred CCCEEEEEECCccccHHHHHHHHHHHHHhCCCEEEEE
Confidence 4567999999986 346777777777777776
No 52
>TIGR03679 arCOG00187 arCOG00187 universal archaeal metal-binding-domain/4Fe-4S-binding-domain containing ABC transporter, ATP-binding protein. This model has the same scope as an archaeal COG (arCOG00187) and is found in all completely sequenced archaea and does not recognize any known non-archaeal genes.
Probab=23.45 E-value=69 Score=31.07 Aligned_cols=25 Identities=24% Similarity=0.165 Sum_probs=22.2
Q ss_pred EEEEeCCcchHHHHHHHhhcCceEE
Q 009849 14 YLLISGDRDFSNALHQLRMRRYNIL 38 (524)
Q Consensus 14 IvLISGDrDFS~ALh~LRmR~YNIL 38 (524)
++|.||-.|=+.+|+.++.+||.|+
T Consensus 1 ~vl~SGGkDS~~al~~a~~~G~~v~ 25 (218)
T TIGR03679 1 AALYSGGKDSNYALYKALEEGHEVR 25 (218)
T ss_pred CeeecCcHHHHHHHHHHHHcCCEEE
Confidence 4789999999999999999999985
No 53
>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=23.37 E-value=63 Score=33.51 Aligned_cols=31 Identities=19% Similarity=0.260 Sum_probs=26.0
Q ss_pred cCCCCCCCchHHHHHHHHHHHhHHHHHhcCC
Q 009849 379 YGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 409 (524)
Q Consensus 379 yGd~k~~~~DVkKaLe~Ai~~q~vvk~~lg~ 409 (524)
...+-+.+..|||||-.||.++.|++..++.
T Consensus 253 ~~~~~~~d~~vR~Al~~aidr~~i~~~~~~g 283 (470)
T cd08508 253 ITKPPLDDLKVRQAIAAAVNVDEVVEFVGAG 283 (470)
T ss_pred cCCCCcCCHHHHHHHHHhcCHHHHHHHHhCC
Confidence 4456778899999999999999999977653
No 54
>cd04182 GT_2_like_f GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families.
Probab=23.07 E-value=1.5e+02 Score=25.87 Aligned_cols=77 Identities=14% Similarity=0.282 Sum_probs=47.3
Q ss_pred hhhHHHHHHHHHhhhhcccccCCCccccchhhcCCC-CCCCchHHHHHHHHHHHhHHHHHhcCCcceeecCCCccceecc
Q 009849 347 VQGLIGVILLALNTLKIERVVPSEANITDCIRYGEP-KHRNTDVRKALNCAIEQHMVIKRSLGALPLYVPKNEKLWNCEN 425 (524)
Q Consensus 347 ~qglI~viL~aL~~LK~Eki~PtE~nI~DCIryGd~-k~~~~DVkKaLe~Ai~~q~vvk~~lg~m~lyv~kne~lWkCVn 425 (524)
.+|...-|..||..++. ..|. + .|..+|. -...-++++.++.+.+... .+.+. +.+
T Consensus 73 ~~G~~~~i~~al~~~~~----~~~~-v--lv~~~D~P~i~~~~i~~l~~~~~~~~~---------~~v~~-------~~~ 129 (186)
T cd04182 73 EEGMSSSLAAGLEALPA----DADA-V--LILLADQPLVTAETLRALIDAFREDGA---------GIVAP-------VYQ 129 (186)
T ss_pred hhCHHHHHHHHHHhccc----cCCE-E--EEEeCCCCCCCHHHHHHHHHHHHhCCC---------eEEEE-------ecC
Confidence 46888889999988762 1221 1 4667786 4555667777765432111 11111 112
Q ss_pred -cCCCCCCCchHHHHHHHHHHh
Q 009849 426 -LYGNPNQYPKEVWDRIQKFLT 446 (524)
Q Consensus 426 -~~gnpk~fpK~~WD~Iq~Fis 446 (524)
..+.|-.|+++.+..+++++.
T Consensus 130 g~~~~P~~~~~~~~~~l~~~~g 151 (186)
T cd04182 130 GRRGHPVLFPRSLFPELLALSG 151 (186)
T ss_pred CccCCCeeECHHHHHHHHccCC
Confidence 356788899999999998863
No 55
>PRK09755 putative ABC transporter periplasmic-binding protein; Provisional
Probab=22.57 E-value=69 Score=34.24 Aligned_cols=30 Identities=23% Similarity=0.576 Sum_probs=26.1
Q ss_pred cCCCCCCCchHHHHHHHHHHHhHHHHHhcC
Q 009849 379 YGEPKHRNTDVRKALNCAIEQHMVIKRSLG 408 (524)
Q Consensus 379 yGd~k~~~~DVkKaLe~Ai~~q~vvk~~lg 408 (524)
.-.+.+.+.+|||||-.||-++.|++..+|
T Consensus 298 ~~~~~~~d~~vRqAl~~AIDr~~i~~~~~g 327 (535)
T PRK09755 298 LEKPPFNDVRVRRALYLTVDRQLIAQKVLG 327 (535)
T ss_pred CCCCccCCHHHHHHHHHHhCHHHHHHHHhC
Confidence 345678899999999999999999998776
No 56
>KOG0258 consensus Alanine aminotransferase [Amino acid transport and metabolism]
Probab=22.28 E-value=1.8e+02 Score=32.43 Aligned_cols=70 Identities=29% Similarity=0.423 Sum_probs=57.1
Q ss_pred eecc--cCCCCCCCchHHHHHHHHHHhCCccch-hhhcccc----HHHHHHHHHHh----------cccchhhhHHHHHH
Q 009849 422 NCEN--LYGNPNQYPKEVWDRIQKFLTSSSGRS-AIMASQC----RYEAALILKNS----------CLPELALGEILKIL 484 (524)
Q Consensus 422 kCVn--~~gnpk~fpK~~WD~Iq~FisS~~G~s-aI~~Sqs----RyeaA~~LKk~----------CLk~LalgDVLQIL 484 (524)
-|++ +-..|+ ||.|.-++-+++|..-.|+. |-++||- |.+.|.-+++- ||-.=|-.-|..||
T Consensus 75 l~~~p~lLd~~~-fp~Dai~RA~~~L~~~gGs~GaYS~SqGv~~vR~~VA~~I~rRDG~p~~p~dI~LT~GAS~ai~~il 153 (475)
T KOG0258|consen 75 LCQYPELLDSPE-FPTDAIKRAKRILNDCGGSLGAYSDSQGVPGVRKHVAEFIERRDGIPADPEDIFLTTGASPAIRSIL 153 (475)
T ss_pred HhcChhhcCCCC-CCHHHHHHHHHHHHhcCCcccccccccCChhHHHHHHHHHHhccCCCCCHHHeeecCCCcHHHHHHH
Confidence 4777 556677 99999999999999999832 4555665 89999888875 68888888899999
Q ss_pred HHhhcccc
Q 009849 485 NMVITPKK 492 (524)
Q Consensus 485 nmlIs~KK 492 (524)
.|||..+|
T Consensus 154 ~l~~~~~~ 161 (475)
T KOG0258|consen 154 SLLIAGKK 161 (475)
T ss_pred HHHhcCCC
Confidence 99999865
No 57
>PRK13883 conjugal transfer protein TrbH; Provisional
Probab=22.18 E-value=1.1e+02 Score=29.21 Aligned_cols=33 Identities=27% Similarity=0.395 Sum_probs=24.5
Q ss_pred ceEEEEeCCc-chHHHHH-HHhhcCceEEEEccCC
Q 009849 12 SNYLLISGDR-DFSNALH-QLRMRRYNILLAQPHK 44 (524)
Q Consensus 12 AnIvLISGDr-DFS~ALh-~LRmR~YNILLA~P~~ 44 (524)
++|.|-.+.. .|..+|- .||.+||-|+=-.+..
T Consensus 53 Tt~~l~q~~~D~Fg~aL~~aLR~~GYaV~e~~~~~ 87 (151)
T PRK13883 53 TRFELQQPTPDAFGQALVKALRDKGYALLEYNPAG 87 (151)
T ss_pred eEEEEecCCCcHHHHHHHHHHHHcCeEEEecCCcc
Confidence 4455555555 4999876 8999999999877654
No 58
>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=21.97 E-value=71 Score=32.84 Aligned_cols=33 Identities=21% Similarity=0.388 Sum_probs=26.1
Q ss_pred hhhcCCCCCCCchHHHHHHHHHHHhHHHHHhcC
Q 009849 376 CIRYGEPKHRNTDVRKALNCAIEQHMVIKRSLG 408 (524)
Q Consensus 376 CIryGd~k~~~~DVkKaLe~Ai~~q~vvk~~lg 408 (524)
++..-.+-+.+.+|||||-.||..+.|++...|
T Consensus 239 ~~N~~~~~~~d~~vRkAl~~aidr~~i~~~~~~ 271 (466)
T cd08506 239 AINTNVPPFDDVKVRQAVAYAVDRAALVRAFGG 271 (466)
T ss_pred EecCCCCCCCCHHHHHHHHHhcCHHHHHHHhcC
Confidence 344445668889999999999999999985443
No 59
>PF09832 DUF2059: Uncharacterized protein conserved in bacteria (DUF2059); InterPro: IPR018637 This entry contains proteins that have no known function. ; PDB: 2X3O_B 3OAO_A.
Probab=21.82 E-value=51 Score=25.74 Aligned_cols=28 Identities=21% Similarity=0.387 Sum_probs=23.3
Q ss_pred CCCchHHHHHHHHHHhCCccchhhhccc
Q 009849 431 NQYPKEVWDRIQKFLTSSSGRSAIMASQ 458 (524)
Q Consensus 431 k~fpK~~WD~Iq~FisS~~G~saI~~Sq 458 (524)
+.|+.+..+.|-.|..||.|...+...-
T Consensus 15 ~~ft~~El~~i~~FY~Sp~Gqk~~~~~~ 42 (64)
T PF09832_consen 15 EHFTEEELDAILAFYESPLGQKIVAKEP 42 (64)
T ss_dssp HHS-HHHHHHHHHHHHSHHHHHHHHHHH
T ss_pred HHCCHHHHHHHHHHHCCHHhHHHHHHhH
Confidence 3589999999999999999999887654
No 60
>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=21.64 E-value=72 Score=32.47 Aligned_cols=28 Identities=18% Similarity=0.358 Sum_probs=24.0
Q ss_pred CCCCCCchHHHHHHHHHHHhHHHHHhcC
Q 009849 381 EPKHRNTDVRKALNCAIEQHMVIKRSLG 408 (524)
Q Consensus 381 d~k~~~~DVkKaLe~Ai~~q~vvk~~lg 408 (524)
.+-+.+.+|||||..||-.+.+++..++
T Consensus 245 ~~~~~d~~vR~Al~~aidr~~i~~~~~~ 272 (457)
T cd08516 245 REPFDDPKVRQAIAYAIDRDAIVDAAFF 272 (457)
T ss_pred CCCCCCHHHHHHHHHhcCHHHHHHHHhc
Confidence 4567789999999999999999988754
No 61
>PF12146 Hydrolase_4: Putative lysophospholipase; InterPro: IPR022742 This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins.
Probab=21.55 E-value=1.9e+02 Score=23.94 Aligned_cols=38 Identities=16% Similarity=0.401 Sum_probs=30.5
Q ss_pred eecccCCCCceEEEEeCCcc----hHHHHHHHhhcCceEEEE
Q 009849 3 FWAVDNPAPSNYLLISGDRD----FSNALHQLRMRRYNILLA 40 (524)
Q Consensus 3 ~WAlDNPpPAnIvLISGDrD----FS~ALh~LRmR~YNILLA 40 (524)
.|.-++++=++|+|+.|=.+ |......|..+||.|+..
T Consensus 8 ~w~p~~~~k~~v~i~HG~~eh~~ry~~~a~~L~~~G~~V~~~ 49 (79)
T PF12146_consen 8 RWKPENPPKAVVVIVHGFGEHSGRYAHLAEFLAEQGYAVFAY 49 (79)
T ss_pred EecCCCCCCEEEEEeCCcHHHHHHHHHHHHHHHhCCCEEEEE
Confidence 46777776688888888865 777888899999999864
No 62
>CHL00023 ndhK NADH dehydrogenase subunit K
Probab=21.49 E-value=91 Score=31.78 Aligned_cols=45 Identities=13% Similarity=0.019 Sum_probs=33.7
Q ss_pred CCCCCCCccchhhHHHHHHHHHhhhhcccccCCCccccchhhcCCCCCC
Q 009849 337 TQGRLTPSEYVQGLIGVILLALNTLKIERVVPSEANITDCIRYGEPKHR 385 (524)
Q Consensus 337 ~~g~p~ps~~~qglI~viL~aL~~LK~Eki~PtE~nI~DCIryGd~k~~ 385 (524)
-+|||+ .++.+|..|+..+..++.|.+... .++..-=||=..+|+
T Consensus 136 IPGCPP---~PeaIi~~l~~L~~ki~~~~~~~~-~~~~~~~r~~~~~h~ 180 (225)
T CHL00023 136 LPGCPP---KPEAVIDAITKLRKKISREIYEDR-IRSQQENRCFTTNHK 180 (225)
T ss_pred ecCCCC---CHHHHHHHHHHHHHHHhcccccch-hcccccceeeccccc
Confidence 489999 566788889999999999987643 556666666666664
No 63
>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=21.47 E-value=71 Score=32.64 Aligned_cols=29 Identities=24% Similarity=0.292 Sum_probs=24.8
Q ss_pred CCCCCCCchHHHHHHHHHHHhHHHHHhcC
Q 009849 380 GEPKHRNTDVRKALNCAIEQHMVIKRSLG 408 (524)
Q Consensus 380 Gd~k~~~~DVkKaLe~Ai~~q~vvk~~lg 408 (524)
..+-+.+..|||||..||-.+.+++..++
T Consensus 239 ~~~~~~d~~vR~Ai~~aidr~~i~~~~~~ 267 (470)
T cd08490 239 EKGPLADVRVRQALSLAIDREGIADSVLE 267 (470)
T ss_pred CCCccCCHHHHHHHHhhcCHHHHHHHHhc
Confidence 34567788999999999999999998764
No 64
>PRK08384 thiamine biosynthesis protein ThiI; Provisional
Probab=21.29 E-value=1.1e+02 Score=32.85 Aligned_cols=31 Identities=19% Similarity=0.128 Sum_probs=27.4
Q ss_pred eEEEEeCCcchHHHHHHHhhcCceEEEEccC
Q 009849 13 NYLLISGDRDFSNALHQLRMRRYNILLAQPH 43 (524)
Q Consensus 13 nIvLISGDrDFS~ALh~LRmR~YNILLA~P~ 43 (524)
-++|+||..|=.-|+..|..|||.|..++-.
T Consensus 183 vlvllSGGiDSpVAa~ll~krG~~V~~v~f~ 213 (381)
T PRK08384 183 VVALLSGGIDSPVAAFLMMKRGVEVIPVHIY 213 (381)
T ss_pred EEEEEeCChHHHHHHHHHHHcCCeEEEEEEE
Confidence 4799999999999999999999999987743
No 65
>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=21.10 E-value=69 Score=33.06 Aligned_cols=27 Identities=30% Similarity=0.509 Sum_probs=23.8
Q ss_pred CCCCchHHHHHHHHHHHhHHHHHhcCC
Q 009849 383 KHRNTDVRKALNCAIEQHMVIKRSLGA 409 (524)
Q Consensus 383 k~~~~DVkKaLe~Ai~~q~vvk~~lg~ 409 (524)
-+.+..|||||-.||-++.+++..++.
T Consensus 247 ~~~d~~vR~Ai~~aiDr~~i~~~~~~g 273 (464)
T cd08518 247 VTSDPAIRKALNYAIDRQAIVDGVLNG 273 (464)
T ss_pred cccCHHHHHHHHhhcCHHHHHHHHhcC
Confidence 578889999999999999999987553
No 66
>PRK14665 mnmA tRNA-specific 2-thiouridylase MnmA; Provisional
Probab=20.94 E-value=1e+02 Score=32.59 Aligned_cols=29 Identities=28% Similarity=0.154 Sum_probs=26.6
Q ss_pred eEEEEeCCcchHHHHHHHhhcCceEEEEc
Q 009849 13 NYLLISGDRDFSNALHQLRMRRYNILLAQ 41 (524)
Q Consensus 13 nIvLISGDrDFS~ALh~LRmR~YNILLA~ 41 (524)
-+|++||..|=+-+++.|+.+||+|+.++
T Consensus 8 VlValSGGVDSsvaa~LL~~~G~~V~~v~ 36 (360)
T PRK14665 8 VLLGMSGGTDSSVAAMLLLEAGYEVTGVT 36 (360)
T ss_pred EEEEEcCCHHHHHHHHHHHHcCCeEEEEE
Confidence 57999999999999999999999998876
No 67
>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=20.91 E-value=79 Score=32.57 Aligned_cols=30 Identities=30% Similarity=0.461 Sum_probs=25.6
Q ss_pred CCCCCCCchHHHHHHHHHHHhHHHHHhcCC
Q 009849 380 GEPKHRNTDVRKALNCAIEQHMVIKRSLGA 409 (524)
Q Consensus 380 Gd~k~~~~DVkKaLe~Ai~~q~vvk~~lg~ 409 (524)
..+-+.+.+|||||..||..+.+++..++.
T Consensus 247 ~~~~~~d~~vR~Ai~~aidr~~i~~~~~~g 276 (474)
T cd08499 247 QKEPFDDVRVRQAINYAIDKEAIIKGILNG 276 (474)
T ss_pred CCCCCCCHHHHHHHHHhcCHHHHHHHHhcC
Confidence 356688999999999999999999987653
No 68
>KOG2805 consensus tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=20.89 E-value=1e+02 Score=33.41 Aligned_cols=31 Identities=29% Similarity=0.225 Sum_probs=27.4
Q ss_pred CceEEEEeCCcchHHHHHHHhhcCceEEEEc
Q 009849 11 PSNYLLISGDRDFSNALHQLRMRRYNILLAQ 41 (524)
Q Consensus 11 PAnIvLISGDrDFS~ALh~LRmR~YNILLA~ 41 (524)
+--+|..||..|-|-|++.|+.|||||.-+.
T Consensus 6 ~~VvvamSgGVDSsVaa~Ll~~~g~~v~gv~ 36 (377)
T KOG2805|consen 6 DRVVVAMSGGVDSSVAARLLAARGYNVTGVF 36 (377)
T ss_pred ceEEEEecCCchHHHHHHHHHhcCCCeeEEe
Confidence 3456899999999999999999999998776
No 69
>KOG1610 consensus Corticosteroid 11-beta-dehydrogenase and related short chain-type dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism; General function prediction only]
Probab=20.85 E-value=1.5e+02 Score=31.78 Aligned_cols=45 Identities=18% Similarity=0.353 Sum_probs=33.6
Q ss_pred CCCceEEEEeC-CcchHHHHH-HHhhcCceEEEEccCC-CCHHHHhhc
Q 009849 9 PAPSNYLLISG-DRDFSNALH-QLRMRRYNILLAQPHK-ASAPLVAAA 53 (524)
Q Consensus 9 PpPAnIvLISG-DrDFS~ALh-~LRmR~YNILLA~P~~-ASasL~sAA 53 (524)
+-+...|||+| |..|...|+ +|-.+||.|+-+|... ..+.|...+
T Consensus 26 ~~~~k~VlITGCDSGfG~~LA~~L~~~Gf~V~Agcl~~~gae~L~~~~ 73 (322)
T KOG1610|consen 26 SLSDKAVLITGCDSGFGRLLAKKLDKKGFRVFAGCLTEEGAESLRGET 73 (322)
T ss_pred ccCCcEEEEecCCcHHHHHHHHHHHhcCCEEEEEeecCchHHHHhhhh
Confidence 45677788887 567999888 7888999999999554 335565443
No 70
>TIGR00420 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase. tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (trmU, asuE, or mnmA) is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine (mnm5s2U34) present in the wobble position of some tRNAs. This enzyme appears not to occur in the Archaea.
Probab=20.77 E-value=1.1e+02 Score=32.15 Aligned_cols=29 Identities=21% Similarity=0.175 Sum_probs=26.2
Q ss_pred eEEEEeCCcchHHHHHHHhhcCceEEEEc
Q 009849 13 NYLLISGDRDFSNALHQLRMRRYNILLAQ 41 (524)
Q Consensus 13 nIvLISGDrDFS~ALh~LRmR~YNILLA~ 41 (524)
-+|++||..|=+.+++.|+.+||+|+.++
T Consensus 3 VlValSGGvDSsv~a~lL~~~G~~V~~v~ 31 (352)
T TIGR00420 3 VIVGLSGGVDSSVSAYLLKQQGYEVVGVF 31 (352)
T ss_pred EEEEEeCCHHHHHHHHHHHHcCCeEEEEE
Confidence 36899999999999999999999998876
No 71
>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=20.47 E-value=80 Score=32.50 Aligned_cols=31 Identities=32% Similarity=0.537 Sum_probs=25.9
Q ss_pred cCCCCCCCchHHHHHHHHHHHhHHHHHhcCC
Q 009849 379 YGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 409 (524)
Q Consensus 379 yGd~k~~~~DVkKaLe~Ai~~q~vvk~~lg~ 409 (524)
...+.+.+.+|||||..||..+.+++..++.
T Consensus 250 ~~~~~~~d~~vR~Al~~aidr~~i~~~~~~g 280 (460)
T cd08515 250 AAGPPLKDVRVRQALNHAIDRQAIVKALWGG 280 (460)
T ss_pred CCCCCccCHHHHHHHHhhcCHHHHHHHHhcC
Confidence 3456678999999999999999999887653
No 72
>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=20.43 E-value=73 Score=32.95 Aligned_cols=31 Identities=26% Similarity=0.398 Sum_probs=26.4
Q ss_pred cCCCCCCCchHHHHHHHHHHHhHHHHHhcCC
Q 009849 379 YGEPKHRNTDVRKALNCAIEQHMVIKRSLGA 409 (524)
Q Consensus 379 yGd~k~~~~DVkKaLe~Ai~~q~vvk~~lg~ 409 (524)
...+-+.+.+|||||..||-++.+++..++.
T Consensus 258 ~~~~~~~d~~vR~Ai~~aiDr~~i~~~~~~g 288 (486)
T cd08501 258 TKSPALADVAVRKAFLKAIDRDTIARIAFGG 288 (486)
T ss_pred CCCcccCCHHHHHHHHHhCCHHHHHHHHhcC
Confidence 3456688999999999999999999887654
No 73
>cd01986 Alpha_ANH_like Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases and ATP sulphurylases. The domain forms a apha/beta/apha fold which binds to Adenosine group..
Probab=20.32 E-value=1.2e+02 Score=25.30 Aligned_cols=28 Identities=25% Similarity=0.350 Sum_probs=23.9
Q ss_pred EEEEeCCcchHHHHHHHhhcCceEEEEc
Q 009849 14 YLLISGDRDFSNALHQLRMRRYNILLAQ 41 (524)
Q Consensus 14 IvLISGDrDFS~ALh~LRmR~YNILLA~ 41 (524)
+|.+||..|=+..++.|+..+++|+.++
T Consensus 2 ~v~~SGG~DS~~ll~~l~~~~~~~~~~~ 29 (103)
T cd01986 2 LVAFSGGKDSSVAAALLKKLGYQVIAVT 29 (103)
T ss_pred EEEEeCcHHHHHHHHHHHHhCCCEEEEE
Confidence 6889999999999999998887777665
No 74
>PRK15104 oligopeptide ABC transporter substrate-binding protein OppA; Provisional
Probab=20.23 E-value=85 Score=33.57 Aligned_cols=29 Identities=17% Similarity=0.477 Sum_probs=24.6
Q ss_pred CCCCCCchHHHHHHHHHHHhHHHHHhcCC
Q 009849 381 EPKHRNTDVRKALNCAIEQHMVIKRSLGA 409 (524)
Q Consensus 381 d~k~~~~DVkKaLe~Ai~~q~vvk~~lg~ 409 (524)
.+-+.+..|||||..||-++.+|++.++.
T Consensus 307 ~~~~~d~~vRqAi~~AiDr~~iv~~~~~g 335 (543)
T PRK15104 307 KPPFNDVRVRTALKLGLDRDIIVNKVKNQ 335 (543)
T ss_pred CCCCCCHHHHHHHHHhhCHHHHHHHHHcC
Confidence 45577889999999999999999987653
No 75
>cd08511 PBP2_NikA_DppA_OppA_like_5 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family 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 mos
Probab=20.11 E-value=85 Score=32.20 Aligned_cols=30 Identities=23% Similarity=0.376 Sum_probs=25.2
Q ss_pred CCCCCCCchHHHHHHHHHHHhHHHHHhcCC
Q 009849 380 GEPKHRNTDVRKALNCAIEQHMVIKRSLGA 409 (524)
Q Consensus 380 Gd~k~~~~DVkKaLe~Ai~~q~vvk~~lg~ 409 (524)
..+-+.+..|||||..||.++++++..++.
T Consensus 248 ~~~~~~d~~vRkAi~~aidr~~i~~~~~~g 277 (467)
T cd08511 248 GNGPFNDPRVRQALALAIDREAINQVVFNG 277 (467)
T ss_pred CCCCCCCHHHHHHHHhhcCHHHHHHHHhcC
Confidence 345678899999999999999999877554
No 76
>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=20.11 E-value=79 Score=32.73 Aligned_cols=29 Identities=34% Similarity=0.453 Sum_probs=24.4
Q ss_pred CCCCCCCchHHHHHHHHHHHhHHHHHhcC
Q 009849 380 GEPKHRNTDVRKALNCAIEQHMVIKRSLG 408 (524)
Q Consensus 380 Gd~k~~~~DVkKaLe~Ai~~q~vvk~~lg 408 (524)
..+-+.+..|||||..||.++.|++..++
T Consensus 259 ~~~~~~d~~vRkAi~~aidr~~i~~~~~~ 287 (482)
T cd08495 259 AEGPLSDPRVRQALNLAIDREGLVDLLLG 287 (482)
T ss_pred CCCcccCHHHHHHHHHhcCHHHHHHHHhc
Confidence 34556788999999999999999998763
No 77
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=20.09 E-value=1.3e+02 Score=23.29 Aligned_cols=41 Identities=20% Similarity=0.129 Sum_probs=27.4
Q ss_pred hhhccccHHHHHHHHHHh--cccchhhhHHHHHHHHhhccccce
Q 009849 453 AIMASQCRYEAALILKNS--CLPELALGEILKILNMVITPKKWI 494 (524)
Q Consensus 453 aI~~SqsRyeaA~~LKk~--CLk~LalgDVLQILnmlIs~KKWi 494 (524)
++...++.+|++..|.+. +=++-+..||.++|+.|.. ++||
T Consensus 25 ~~~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~-~glI 67 (68)
T PF05402_consen 25 LLDGPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLRE-KGLI 67 (68)
T ss_dssp H--SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHH-TT--
T ss_pred HccCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH-CcCc
Confidence 344567889999999888 5566679999999999875 4444
Done!