Query psy654
Match_columns 224
No_of_seqs 158 out of 380
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 20:37:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy654.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/654hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2680|consensus 100.0 1.2E-61 2.7E-66 446.4 8.4 173 2-207 117-292 (454)
2 PF06068 TIP49: TIP49 C-termin 100.0 3.3E-58 7.2E-63 428.2 10.9 171 1-207 100-282 (398)
3 COG1224 TIP49 DNA helicase TIP 100.0 3.2E-55 6.9E-60 408.4 11.1 172 1-207 115-295 (450)
4 KOG1942|consensus 100.0 1E-55 2.2E-60 406.8 1.3 172 1-207 114-300 (456)
5 KOG1942|consensus 97.9 3.2E-06 7E-11 79.8 1.7 43 161-203 188-230 (456)
6 PF06068 TIP49: TIP49 C-termin 97.8 7E-06 1.5E-10 78.2 1.3 43 161-203 173-215 (398)
7 KOG2680|consensus 97.6 2.7E-05 5.8E-10 73.8 1.6 46 159-204 183-230 (454)
8 COG1224 TIP49 DNA helicase TIP 97.1 0.00024 5.1E-09 68.3 2.0 44 161-204 189-233 (450)
9 COG0090 RplB Ribosomal protein 81.6 2.4 5.2E-05 39.4 4.6 54 11-77 66-119 (275)
10 TIGR03595 Obg_CgtA_exten Obg f 71.4 3.9 8.5E-05 30.1 2.5 19 59-77 45-63 (69)
11 PF00181 Ribosomal_L2: Ribosom 69.4 12 0.00025 27.9 4.8 47 16-75 30-76 (77)
12 PF09269 DUF1967: Domain of un 68.3 4.2 9.2E-05 29.8 2.1 18 59-76 45-62 (69)
13 PF04014 Antitoxin-MazE: Antid 66.3 9.6 0.00021 25.5 3.4 33 48-83 4-37 (47)
14 PF01336 tRNA_anti-codon: OB-f 59.1 54 0.0012 22.2 6.5 58 19-86 3-60 (75)
15 PF10015 DUF2258: Uncharacteri 52.3 11 0.00024 29.0 2.0 23 54-76 39-62 (75)
16 COG3212 Predicted membrane pro 52.2 33 0.00072 28.8 5.0 44 20-87 97-141 (144)
17 PF03459 TOBE: TOBE domain; I 49.0 82 0.0018 21.4 8.1 57 17-83 5-62 (64)
18 cd04489 ExoVII_LU_OBF ExoVII_L 48.2 83 0.0018 22.0 5.9 52 18-76 3-54 (78)
19 PF04565 RNA_pol_Rpb2_3: RNA p 47.4 12 0.00027 27.3 1.6 21 107-140 31-53 (68)
20 PTZ00180 60S ribosomal protein 45.8 38 0.00083 31.3 4.8 52 15-77 37-91 (260)
21 PRK11347 antitoxin ChpS; Provi 44.2 54 0.0012 25.1 4.7 41 42-85 3-43 (83)
22 KOG1728|consensus 44.0 36 0.00079 29.3 4.1 70 5-76 35-126 (156)
23 PRK09612 rpl2p 50S ribosomal p 43.8 63 0.0014 29.5 5.8 49 15-76 35-83 (238)
24 PF00924 MS_channel: Mechanose 43.2 11 0.00023 31.2 0.8 32 66-97 59-90 (206)
25 PF03120 DNA_ligase_OB: NAD-de 43.2 1.5E+02 0.0033 22.8 7.1 74 22-95 4-77 (82)
26 PTZ00031 ribosomal protein L2; 42.1 49 0.0011 31.5 5.0 53 12-77 98-150 (317)
27 PF03413 PepSY: Peptidase prop 40.5 23 0.0005 23.6 2.0 12 74-85 51-62 (64)
28 TIGR02609 doc_partner putative 39.7 57 0.0012 24.0 4.1 36 47-85 6-41 (74)
29 PRK14812 hypothetical protein; 39.3 40 0.00087 27.7 3.5 34 53-88 42-75 (119)
30 CHL00052 rpl2 ribosomal protei 39.2 63 0.0014 30.0 5.2 53 12-77 65-117 (273)
31 PRK10929 putative mechanosensi 38.7 20 0.00044 39.0 2.2 36 63-98 931-966 (1109)
32 PRK11281 hypothetical protein; 36.5 20 0.00043 39.0 1.7 35 64-98 935-969 (1113)
33 PF13128 DUF3954: Protein of u 35.4 74 0.0016 22.8 3.9 30 8-39 5-34 (50)
34 TIGR03106 trio_M42_hydro hydro 34.5 34 0.00074 32.0 2.7 32 49-80 138-169 (343)
35 TIGR01171 rplB_bact ribosomal 33.7 93 0.002 28.9 5.4 48 17-77 70-117 (273)
36 PF01967 MoaC: MoaC family; I 33.5 32 0.00068 29.0 2.1 35 42-76 9-43 (136)
37 PF02237 BPL_C: Biotin protein 33.4 1.2E+02 0.0027 20.3 4.7 32 10-51 6-37 (48)
38 PF09285 Elong-fact-P_C: Elong 33.0 31 0.00067 24.9 1.7 16 67-82 37-52 (56)
39 PRK14699 replication factor A; 32.1 1E+02 0.0022 30.7 5.6 58 18-76 71-132 (484)
40 PRK09374 rplB 50S ribosomal pr 30.7 86 0.0019 29.2 4.6 48 17-77 72-119 (276)
41 PF06434 Aconitase_2_N: Aconit 30.6 42 0.00092 30.2 2.5 20 66-85 122-141 (204)
42 COG3264 Small-conductance mech 30.4 31 0.00067 36.7 1.8 43 63-109 656-698 (835)
43 cd04484 polC_OBF polC_OBF: A s 29.6 2.3E+02 0.0051 20.9 6.4 54 18-76 3-59 (82)
44 PHA02600 FII major tail tube p 29.5 3.5E+02 0.0075 22.9 8.6 70 7-77 7-84 (169)
45 PRK10334 mechanosensitive chan 29.1 38 0.00082 30.9 2.0 34 64-97 126-159 (286)
46 PF03829 PTSIIA_gutA: PTS syst 27.9 30 0.00064 28.1 1.0 26 64-89 48-73 (117)
47 PRK03955 hypothetical protein; 27.2 56 0.0012 27.2 2.5 23 65-87 108-130 (131)
48 PF01568 Molydop_binding: Moly 26.8 64 0.0014 23.9 2.6 31 52-85 31-61 (110)
49 PF14578 GTP_EFTU_D4: Elongati 26.6 1.3E+02 0.0028 23.2 4.2 27 43-76 55-81 (81)
50 PRK09606 DNA-directed RNA poly 26.6 33 0.00071 33.6 1.2 20 108-140 436-457 (494)
51 TIGR00581 moaC molybdenum cofa 26.4 47 0.001 28.4 2.0 35 42-76 20-54 (147)
52 cd05794 S1_EF-P_repeat_2 S1_EF 26.0 52 0.0011 23.8 1.9 16 67-82 37-52 (56)
53 PRK09364 moaC molybdenum cofac 25.7 43 0.00093 28.9 1.6 35 42-76 23-57 (159)
54 PRK06033 hypothetical protein; 25.2 71 0.0015 24.3 2.6 14 67-80 27-40 (83)
55 PRK15491 replication factor A; 25.0 1.6E+02 0.0035 28.1 5.5 61 17-78 70-134 (374)
56 cd01420 MoaC_PE MoaC family, p 24.0 56 0.0012 27.7 2.0 35 42-76 9-43 (140)
57 PF11776 DUF3315: Domain of un 23.8 83 0.0018 22.0 2.5 16 71-86 37-52 (52)
58 PF13670 PepSY_2: Peptidase pr 23.5 55 0.0012 24.0 1.7 12 74-85 70-81 (83)
59 cd00528 MoaC MoaC family. Memb 23.4 60 0.0013 27.4 2.1 35 42-76 9-43 (136)
60 PRK10377 PTS system glucitol/s 23.4 44 0.00095 27.3 1.2 24 66-89 50-73 (120)
61 cd03524 RPA2_OBF_family RPA2_O 23.1 2.1E+02 0.0046 18.2 7.2 57 20-84 3-60 (75)
62 PF07883 Cupin_2: Cupin domain 22.9 98 0.0021 20.8 2.7 14 67-80 40-53 (71)
63 PRK12343 putative molybdenum c 22.3 64 0.0014 27.7 2.0 35 42-76 17-51 (151)
64 smart00841 Elong-fact-P_C Elon 22.3 67 0.0015 23.2 1.9 16 67-82 37-52 (56)
65 cd02790 MopB_CT_Formate-Dh_H F 22.2 1E+02 0.0022 23.0 3.0 32 50-84 34-65 (116)
66 COG1363 FrvX Cellulase M and r 22.0 62 0.0014 31.0 2.1 36 49-84 135-170 (355)
67 cd02786 MopB_CT_3 The MopB_CT_ 21.9 1.1E+02 0.0024 23.0 3.1 32 50-84 30-61 (116)
68 PF05343 Peptidase_M42: M42 gl 21.7 64 0.0014 29.5 2.1 42 49-90 89-133 (292)
69 PRK11465 putative mechanosensi 21.4 64 0.0014 33.9 2.2 35 64-98 570-604 (741)
70 TIGR00849 gutA PTS system, glu 21.4 51 0.0011 27.0 1.2 23 67-89 51-73 (121)
71 TIGR02084 leud 3-isopropylmala 20.9 1.4E+02 0.0031 25.3 3.9 27 55-86 100-126 (156)
72 COG3848 Phosphohistidine swive 20.8 80 0.0017 26.0 2.2 19 66-84 86-104 (111)
73 PF11495 Regulator_TrmB: Archa 20.5 2.5E+02 0.0055 24.3 5.5 36 15-57 181-216 (233)
74 cd00508 MopB_CT_Fdh-Nap-like T 20.5 1.2E+02 0.0025 22.7 3.0 32 50-84 34-65 (120)
75 cd02785 MopB_CT_4 The MopB_CT_ 20.5 1.2E+02 0.0026 23.3 3.2 31 51-84 32-62 (124)
76 PF00501 AMP-binding: AMP-bind 20.2 2E+02 0.0043 25.5 4.8 52 39-91 359-412 (417)
77 PRK14736 atpC F0F1 ATP synthas 20.2 4.7E+02 0.01 21.4 6.7 73 14-102 11-95 (133)
No 1
>KOG2680|consensus
Probab=100.00 E-value=1.2e-61 Score=446.42 Aligned_cols=173 Identities=55% Similarity=0.756 Sum_probs=171.7
Q ss_pred cccceeeceeEEEeeeEEEEEEEEEEEccCCCCCCCeEEEEEEEecCceeeeeccHHHHHHHHHccccccceEEEEcCCC
Q psy654 2 SQMSTHSDTNHIEETEMIEGEVVEIQIERPATGLGSKVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITIDKATG 81 (224)
Q Consensus 2 ~~~r~sigvrikE~~ev~EGeVvei~i~~~~~~~~~~v~~itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~Id~~tG 81 (224)
||||||||+|||||+||+|||||+|+|+||++|.|+++|||||||+|||+.|+||.||+++|.||||++||||+||+++|
T Consensus 117 QAfRksiGvrIKEetevIEGEVVeiqidRp~tg~g~k~GKlt~kTtdMEt~ydlG~Kmi~~l~KeKV~aGDVI~idka~G 196 (454)
T KOG2680|consen 117 QAFRKSIGVRIKEETEVIEGEVVEIQIDRPATGMGSKVGKLTLKTTDMETIYDLGMKMIESLTKEKVQAGDVITIDKASG 196 (454)
T ss_pred HHHHHhhceEeeheeeeecceEEEEEeeccccCcCcccceeEEeecchhhHHHHHHHHHHHhhHhhccCCceEEEEcccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEEeeccccccccccccccccccccCCCcccccccccccccccccccCccCCCCCCCCceeeeeeeeccccceeeeee-
Q psy654 82 KITRLGRSFTRARDYDATGAQTRNTLPSRSRHVSSWGVQKDVVQSISNNIICPVVPRPESSRSEDSGSTVTLHEIVDVQ- 160 (224)
Q Consensus 82 ~v~rlGRs~~~a~~yD~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~P~Gev~k~ke~v~~vTLHdlD~VN- 160 (224)
+|+|+||||++++|||++|++|+|| | || +||++|+||++|+|||||||++|
T Consensus 197 kitKlGrSf~rsrdyDamG~~tkfV------------------q-------CP---eGElqkrkevvhtvsLHeIDViNS 248 (454)
T KOG2680|consen 197 KITKLGRSFTRSRDYDAMGSQTKFV------------------Q-------CP---EGELQKRKEVVHTVSLHEIDVINS 248 (454)
T ss_pred eeehhhccccccccCCccCCcccee------------------c-------CC---chhhhheeeeeEeeeecccccccc
Confidence 9999999999999999999999999 9 99 99999999999999999999999
Q ss_pred --cCceEEecCCCCccccchhcccccchhhhhccccccccCeeEecccc
Q psy654 161 --AGDVITIDKATGKITRLGRSFTRARDYDATGAQTRQCNLNEIVPTTH 207 (224)
Q Consensus 161 --qGDVIlId~~tGEITkegRses~a~dIDk~VnK~V~eGKAEivpgvl 207 (224)
||++++|..++|||+.+.|.+ +|..|.+|.++||||||||||
T Consensus 249 rtqG~lALFsGdTGEIr~EvRdq-----in~KV~eWreEGKAeivpGVL 292 (454)
T KOG2680|consen 249 RTQGFLALFSGDTGEIRSEVRDQ-----INTKVAEWREEGKAEIVPGVL 292 (454)
T ss_pred cccceEEEEeCCcccccHHHHHH-----HHHHHHHHHhcCCeeeccceE
Confidence 899999999999999999999 999999999999999999997
No 2
>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.
Probab=100.00 E-value=3.3e-58 Score=428.24 Aligned_cols=171 Identities=37% Similarity=0.517 Sum_probs=138.1
Q ss_pred CcccceeeceeEEEeeeEEEEEEEEEEE---ccCCCCCCC--eEEEEEEEecCceeeeeccHHHHHHHHHccccccceEE
Q psy654 1 MSQMSTHSDTNHIEETEMIEGEVVEIQI---ERPATGLGS--KVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVIT 75 (224)
Q Consensus 1 m~~~r~sigvrikE~~ev~EGeVvei~i---~~~~~~~~~--~v~~itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~ 75 (224)
|||||||||+||+|+++||||||+||++ ++|.+ |++ ..++|+|||+||+++|+||++|++||+||||++|||||
T Consensus 100 ~qa~RraIGvrIkE~~eV~EGeVvei~~~~~~~~~~-~~~~~~~~~i~LkT~~~~~~l~l~~~i~~~l~kekV~~GDVI~ 178 (398)
T PF06068_consen 100 TQAFRRAIGVRIKEEKEVYEGEVVEIKIEEAENPLN-YGKTIKHGKITLKTTDMEKTLKLGPKIYEQLQKEKVRVGDVIY 178 (398)
T ss_dssp HHHHHCSEEEEEEEEECEEEEEEEEEEE---E-TTS--SSSS-EEEEEEEETTCEEEEEE-CHHHHHHHHTT--TTCEEE
T ss_pred HHHHHHhheEEEEEEEEEEEEEEEEEEEeeccCccc-cCCcceEEEEEEEEcCCceEecCCHHHHHHHHHhCCccCcEEE
Confidence 7999999999999999999999999999 66666 444 56899999999999999999999999999999999999
Q ss_pred EEcCCCcEEEeeccccccccccccccccccccCCCcccccccccccccccccccCccCCCCCCCCceeeeeeeeccccce
Q psy654 76 IDKATGKITRLGRSFTRARDYDATGAQTRNTLPSRSRHVSSWGVQKDVVQSISNNIICPVVPRPESSRSEDSGSTVTLHE 155 (224)
Q Consensus 76 Id~~tG~v~rlGRs~~~a~~yD~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~P~Gev~k~ke~v~~vTLHd 155 (224)
||++||+|+|+|||++++++||++. ++|| | || +|+++|+||++|+|||||
T Consensus 179 Id~~tG~V~k~Grs~~~~~~~D~~~--~~~V------------------~-------~P---~Gev~K~KEiv~~vTLHD 228 (398)
T PF06068_consen 179 IDKNTGRVKKVGRSDSYAKDYDLEA--TKFV------------------P-------CP---KGEVHKRKEIVQTVTLHD 228 (398)
T ss_dssp EETTTTEEEEEEEECCCS-TTSECC--TTEE-------------------------------SS-SEEEEEEEEEEEHHH
T ss_pred EECCCCeEEEEecccchhhcccccc--ceEe------------------e-------CC---CCcceEEEEEEEEEeHHH
Confidence 9999999999999999999999966 4699 8 88 999999999999999999
Q ss_pred eeeee---cCceEEe----cCCCCccccchhcccccchhhhhccccccccCeeEecccc
Q psy654 156 IVDVQ---AGDVITI----DKATGKITRLGRSFTRARDYDATGAQTRQCNLNEIVPTTH 207 (224)
Q Consensus 156 lD~VN---qGDVIlI----d~~tGEITkegRses~a~dIDk~VnK~V~eGKAEivpgvl 207 (224)
||++| +|.+.+| .++++||++++|.+ +|+.|++|+++|+||||||||
T Consensus 229 lD~~Nsr~q~~lslf~~~~~~~~~EI~~elR~e-----Ink~V~~wieegkAelvpGVL 282 (398)
T PF06068_consen 229 LDVANSRPQDFLSLFGQLFKGDTGEITDELREE-----INKKVNKWIEEGKAELVPGVL 282 (398)
T ss_dssp HHHHCC---------------------HHHHHH-----HHHHHHHHHHCTSEEEEE-EE
T ss_pred hhhhhhccccHHHHHHhhcCCCcccchHHHHHH-----HhHHHHHHHhcCceEEecceE
Confidence 99999 4445555 88999999999999 999999999999999999996
No 3
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=100.00 E-value=3.2e-55 Score=408.42 Aligned_cols=172 Identities=33% Similarity=0.421 Sum_probs=161.8
Q ss_pred CcccceeeceeEEEeeeEEEEEEEEEEEccCCCCCCCeE-----EEEEEEecCceeeeeccHHHHHHHHHccccccceEE
Q psy654 1 MSQMSTHSDTNHIEETEMIEGEVVEIQIERPATGLGSKV-----GKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVIT 75 (224)
Q Consensus 1 m~~~r~sigvrikE~~ev~EGeVvei~i~~~~~~~~~~v-----~~itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~ 75 (224)
|||||||||+||+|+++||||||+++++++..+||+||. +.|+|||+||+++|+||++|++||.++||.+||||+
T Consensus 115 ~qa~RraIGvrikE~reV~EGeV~~l~i~~~~~p~~~y~~~~~~~~i~LkT~d~~k~~~lg~~i~~ql~~~~V~~GDVI~ 194 (450)
T COG1224 115 TQALRRAIGVRIKETREVYEGEVVELEIRRARNPLNPYGKVPSGAIITLKTKDEEKTLRLGPEIAEQLVKEGVEEGDVIY 194 (450)
T ss_pred HHHHHHhhceEeeeeeEEEEEEEEEEEEeeccCCCCCccccccceEEEEEecccceEeecCHHHHHHHHHhCcccCCEEE
Confidence 699999999999999999999999999988777777763 579999999999999999999999999999999999
Q ss_pred EEcCCCcEEEeeccccccc-cccccccccccccCCCcccccccccccccccccccCccCCCCCCCCceeeeeeeeccccc
Q psy654 76 IDKATGKITRLGRSFTRAR-DYDATGAQTRNTLPSRSRHVSSWGVQKDVVQSISNNIICPVVPRPESSRSEDSGSTVTLH 154 (224)
Q Consensus 76 Id~~tG~v~rlGRs~~~a~-~yD~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~P~Gev~k~ke~v~~vTLH 154 (224)
||++||+|+++|||+.+++ +||++. ++|| | || +|||+|+||++|+||||
T Consensus 195 Id~etG~V~klGrs~~~~~~~~dl~~--~~~V------------------~-------~P---~Gev~K~KEi~~~vTLH 244 (450)
T COG1224 195 IDAETGRVKKLGRSKARAREDFDLED--TRFV------------------P-------LP---EGEVQKRKEIVQTVTLH 244 (450)
T ss_pred EEccccEEEEeecccccccccccccc--eEEE------------------E-------CC---CCceeeeEEEEEEEEeh
Confidence 9999999999999999996 777766 5699 8 88 99999999999999999
Q ss_pred eeeeee---cCceEEecCCCCccccchhcccccchhhhhccccccccCeeEecccc
Q psy654 155 EIVDVQ---AGDVITIDKATGKITRLGRSFTRARDYDATGAQTRQCNLNEIVPTTH 207 (224)
Q Consensus 155 dlD~VN---qGDVIlId~~tGEITkegRses~a~dIDk~VnK~V~eGKAEivpgvl 207 (224)
|||++| +|.+.+|...+++|++++|.+ +|..|++|+++|+||||||||
T Consensus 245 DlDv~nar~~G~~sl~~~~~~eI~~evR~~-----vn~~V~~~ieeGkAElVpGVL 295 (450)
T COG1224 245 DLDVANARAQGILSLFSGGTGEITDEVREE-----VNEKVKKWIEEGKAELVPGVL 295 (450)
T ss_pred hhhhhhccccchHhhhcCCcccCCHHHHHH-----HHHHHHHHHhcCcEEeecceE
Confidence 999999 667788888999999999999 999999999999999999997
No 4
>KOG1942|consensus
Probab=100.00 E-value=1e-55 Score=406.79 Aligned_cols=172 Identities=27% Similarity=0.400 Sum_probs=164.6
Q ss_pred CcccceeeceeEEEeeeEEEEEEEEEEE---ccCCCCCCCeEEE--EEEEecCceeeeeccHHHHHHHHHccccccceEE
Q psy654 1 MSQMSTHSDTNHIEETEMIEGEVVEIQI---ERPATGLGSKVGK--LTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVIT 75 (224)
Q Consensus 1 m~~~r~sigvrikE~~ev~EGeVvei~i---~~~~~~~~~~v~~--itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~ 75 (224)
|++||||||+||||.+|||||||+|+.+ ++|.+|||+++++ |+|||.+++++|+|+|++||+|+||+|.+|||||
T Consensus 114 menfRRaIglRikEtKeVYEGEVtEl~p~e~enp~ggygKtIshv~i~LKtaKgtKqLkLdPsiyesi~kerv~~GDViY 193 (456)
T KOG1942|consen 114 MENFRRAIGLRIKETKEVYEGEVTELTPVEAENPLGGYGKTISHVVIGLKTAKGTKQLKLDPSIYESIQKERVEVGDVIY 193 (456)
T ss_pred HHHHHHHhhhhhhhhhhhhcceeeEeccccccCCCCccCceeeeeEEEEeecCCcceeccChHHHHHHHHhhhccCcEEE
Confidence 7899999999999999999999999975 8999999999998 6999999999999999999999999999999999
Q ss_pred EEcCCCcEEEeeccccccccccccccccccccCCCcccccccccccccccccccCccCCCCCCCCceeeeeeeeccccce
Q psy654 76 IDKATGKITRLGRSFTRARDYDATGAQTRNTLPSRSRHVSSWGVQKDVVQSISNNIICPVVPRPESSRSEDSGSTVTLHE 155 (224)
Q Consensus 76 Id~~tG~v~rlGRs~~~a~~yD~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~P~Gev~k~ke~v~~vTLHd 155 (224)
|++|||.|+|+|||+++|.+||+++++ || | +| +|+|+|+||++|+|||||
T Consensus 194 IEaNsGavKrvGRsda~ateFDLEaee--yV------------------P-------lP---KGeVhKkKeivQdVtLhD 243 (456)
T KOG1942|consen 194 IEANSGAVKRVGRSDAYATEFDLEAEE--YV------------------P-------LP---KGEVHKKKEIVQDVTLHD 243 (456)
T ss_pred EEeccchhhcccccccchhhcccccce--ee------------------c-------CC---ccchhhhHHHhhhcchhh
Confidence 999999999999999999999999976 99 8 55 999999999999999999
Q ss_pred eeeee---cC--ce-----EEecCCCCccccchhcccccchhhhhccccccccCeeEecccc
Q psy654 156 IVDVQ---AG--DV-----ITIDKATGKITRLGRSFTRARDYDATGAQTRQCNLNEIVPTTH 207 (224)
Q Consensus 156 lD~VN---qG--DV-----IlId~~tGEITkegRses~a~dIDk~VnK~V~eGKAEivpgvl 207 (224)
||++| || |+ +++.++++|||+++|.+ +|++||+|+++|.|||+||||
T Consensus 244 LD~ANARPqGgqdvlsmmgqlmkPkKTEITdkLR~e-----iNkvVn~Yid~GvAElvPGVL 300 (456)
T KOG1942|consen 244 LDVANARPQGGQDVLSMMGQLMKPKKTEITDKLRGE-----INKVVNKYIDQGVAELVPGVL 300 (456)
T ss_pred cccccCCCCccchHHHHHHHhcCCccchhHHHHHHH-----HHHHHHHHHhcchhhhcCcce
Confidence 99999 55 43 68999999999999999 999999999999999999997
No 5
>KOG1942|consensus
Probab=97.95 E-value=3.2e-06 Score=79.78 Aligned_cols=43 Identities=30% Similarity=0.468 Sum_probs=41.3
Q ss_pred cCceEEecCCCCccccchhcccccchhhhhccccccccCeeEe
Q psy654 161 AGDVITIDKATGKITRLGRSFTRARDYDATGAQTRQCNLNEIV 203 (224)
Q Consensus 161 qGDVIlId~~tGEITkegRses~a~dIDk~VnK~V~eGKAEiv 203 (224)
.||++||+.++|.|++.|||++||+|||++..+|++.||||+.
T Consensus 188 ~GDViYIEaNsGavKrvGRsda~ateFDLEaeeyVPlPKGeVh 230 (456)
T KOG1942|consen 188 VGDVIYIEANSGAVKRVGRSDAYATEFDLEAEEYVPLPKGEVH 230 (456)
T ss_pred cCcEEEEEeccchhhcccccccchhhcccccceeecCCccchh
Confidence 6999999999999999999999999999999999999999864
No 6
>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.
Probab=97.80 E-value=7e-06 Score=78.25 Aligned_cols=43 Identities=42% Similarity=0.694 Sum_probs=36.3
Q ss_pred cCceEEecCCCCccccchhcccccchhhhhccccccccCeeEe
Q psy654 161 AGDVITIDKATGKITRLGRSFTRARDYDATGAQTRQCNLNEIV 203 (224)
Q Consensus 161 qGDVIlId~~tGEITkegRses~a~dIDk~VnK~V~eGKAEiv 203 (224)
.||+++|++++|.|++.||++++++|||+...+|+++|+||+.
T Consensus 173 ~GDVI~Id~~tG~V~k~Grs~~~~~~~D~~~~~~V~~P~Gev~ 215 (398)
T PF06068_consen 173 VGDVIYIDKNTGRVKKVGRSDSYAKDYDLEATKFVPCPKGEVH 215 (398)
T ss_dssp TTCEEEEETTTTEEEEEEEECCCS-TTSECCTTEE---SS-SE
T ss_pred cCcEEEEECCCCeEEEEecccchhhccccccceEeeCCCCcce
Confidence 6899999999999999999999999999999999999999764
No 7
>KOG2680|consensus
Probab=97.58 E-value=2.7e-05 Score=73.82 Aligned_cols=46 Identities=70% Similarity=1.022 Sum_probs=41.5
Q ss_pred eecCceEEecCCCCccccchhcccccchhhhhcc--ccccccCeeEec
Q psy654 159 VQAGDVITIDKATGKITRLGRSFTRARDYDATGA--QTRQCNLNEIVP 204 (224)
Q Consensus 159 VNqGDVIlId~~tGEITkegRses~a~dIDk~Vn--K~V~eGKAEivp 204 (224)
+.+||+|.+++++|.|++.|||+++++|||++.. +|++||.|||..
T Consensus 183 V~aGDVI~idka~GkitKlGrSf~rsrdyDamG~~tkfVqCPeGElqk 230 (454)
T KOG2680|consen 183 VQAGDVITIDKASGKITKLGRSFTRSRDYDAMGSQTKFVQCPEGELQK 230 (454)
T ss_pred ccCCceEEEEcccceeehhhccccccccCCccCCccceecCCchhhhh
Confidence 4469999999999999999999999999999865 589999999864
No 8
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=97.10 E-value=0.00024 Score=68.34 Aligned_cols=44 Identities=41% Similarity=0.608 Sum_probs=41.3
Q ss_pred cCceEEecCCCCccccchhcccccc-hhhhhccccccccCeeEec
Q psy654 161 AGDVITIDKATGKITRLGRSFTRAR-DYDATGAQTRQCNLNEIVP 204 (224)
Q Consensus 161 qGDVIlId~~tGEITkegRses~a~-dIDk~VnK~V~eGKAEivp 204 (224)
.||+|+|+.++|.|++.||++++++ |+|....+|+++|+||+..
T Consensus 189 ~GDVI~Id~etG~V~klGrs~~~~~~~~dl~~~~~V~~P~Gev~K 233 (450)
T COG1224 189 EGDVIYIDAETGRVKKLGRSKARAREDFDLEDTRFVPLPEGEVQK 233 (450)
T ss_pred cCCEEEEEccccEEEEeecccccccccccccceEEEECCCCceee
Confidence 5899999999999999999999996 9999999999999998753
No 9
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=81.62 E-value=2.4 Score=39.41 Aligned_cols=54 Identities=20% Similarity=0.361 Sum_probs=41.9
Q ss_pred eEEEeeeEEEEEEEEEEEccCCCCCCCeEEEEEEEecCceeeeeccHHHHHHHHHccccccceEEEE
Q psy654 11 NHIEETEMIEGEVVEIQIERPATGLGSKVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITID 77 (224)
Q Consensus 11 rikE~~ev~EGeVvei~i~~~~~~~~~~v~~itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~Id 77 (224)
.++..+..++|+|++|+.|...+ ..|+.|.. .|+|+.|-|.++ ++.+||+|++=
T Consensus 66 dfkr~k~~i~g~V~~IeyDP~Rs---A~IAlv~y--~dGek~yilAp~--------Gl~vGd~I~sG 119 (275)
T COG0090 66 DFKRNKDGIPGKVEDIEYDPNRS---APIALVVY--EDGEKRYILAPE--------GLKVGDVIESG 119 (275)
T ss_pred ccccccCCccEEEEEEEECCCCC---cceEEEEe--cCCCEEEEEccC--------ccccCCEEEeC
Confidence 45566778999999999876553 34565544 599999999886 99999999874
No 10
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=71.36 E-value=3.9 Score=30.06 Aligned_cols=19 Identities=26% Similarity=0.483 Sum_probs=17.4
Q ss_pred HHHHHHHccccccceEEEE
Q psy654 59 MIEAIGKEKVQAGDVITID 77 (224)
Q Consensus 59 m~e~l~kekV~~GDVI~Id 77 (224)
+.++|.+.|++.||.|.|-
T Consensus 45 v~~~L~~~G~~~GD~V~Ig 63 (69)
T TIGR03595 45 VEDALRKAGAKDGDTVRIG 63 (69)
T ss_pred HHHHHHHcCCCCCCEEEEc
Confidence 6889999999999999983
No 11
>PF00181 Ribosomal_L2: Ribosomal Proteins L2, RNA binding domain; InterPro: IPR022666 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YIT_A 1Q7Y_C 1YJN_A 3CPW_A 3I56_A 1VQ9_A 1M1K_C 3CC7_A 1YIJ_A 1K9M_C ....
Probab=69.42 E-value=12 Score=27.94 Aligned_cols=47 Identities=19% Similarity=0.410 Sum_probs=35.0
Q ss_pred eeEEEEEEEEEEEccCCCCCCCeEEEEEEEecCceeeeeccHHHHHHHHHccccccceEE
Q psy654 16 TEMIEGEVVEIQIERPATGLGSKVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVIT 75 (224)
Q Consensus 16 ~ev~EGeVvei~i~~~~~~~~~~v~~itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~ 75 (224)
..-++|.|++|+.+...+ ..++.+-. .+++..|=|.++ ++.+||+|.
T Consensus 30 ~~~~~g~V~~i~~DP~Rs---a~iAlV~~--~~g~~~yiiA~e--------g~~vGd~I~ 76 (77)
T PF00181_consen 30 KGNIKGIVIDIEYDPNRS---APIALVKY--EDGEKRYIIAPE--------GMKVGDIIE 76 (77)
T ss_dssp TTSEEEEEEEEEEETTTS---SEEEEEEE--TTSEEEEEEEBT--------TEBTTEEEE
T ss_pred CCCCcEEEEEEEecCCcC---ccEEEEEe--cCCcEEEEEeEC--------CCcCCCEEE
Confidence 345899999998876543 35666544 558888888875 999999985
No 12
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=68.25 E-value=4.2 Score=29.83 Aligned_cols=18 Identities=28% Similarity=0.486 Sum_probs=13.7
Q ss_pred HHHHHHHccccccceEEE
Q psy654 59 MIEAIGKEKVQAGDVITI 76 (224)
Q Consensus 59 m~e~l~kekV~~GDVI~I 76 (224)
+.++|.+.|++.||.|.|
T Consensus 45 v~~~L~~~G~~~GD~V~I 62 (69)
T PF09269_consen 45 VEKALRKAGAKEGDTVRI 62 (69)
T ss_dssp HHHHHHTTT--TT-EEEE
T ss_pred HHHHHHHcCCCCCCEEEE
Confidence 578999999999999998
No 13
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=66.32 E-value=9.6 Score=25.47 Aligned_cols=33 Identities=18% Similarity=0.299 Sum_probs=25.7
Q ss_pred CceeeeeccHHHHHHHHHccccccceEEEEcCCC-cE
Q psy654 48 EMETSYDLGAKMIEAIGKEKVQAGDVITIDKATG-KI 83 (224)
Q Consensus 48 ~~e~~~~lg~~m~e~l~kekV~~GDVI~Id~~tG-~v 83 (224)
.......|+..+.+++ ++++||.|.|....+ ++
T Consensus 4 g~s~~v~iPk~~~~~l---~l~~Gd~v~i~~~~~g~i 37 (47)
T PF04014_consen 4 GNSGQVTIPKEIREKL---GLKPGDEVEIEVEGDGKI 37 (47)
T ss_dssp TTCSEEEE-HHHHHHT---TSSTTTEEEEEEETTSEE
T ss_pred CCCceEECCHHHHHHc---CCCCCCEEEEEEeCCCEE
Confidence 3455678899998887 899999999988877 44
No 14
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=59.05 E-value=54 Score=22.23 Aligned_cols=58 Identities=28% Similarity=0.447 Sum_probs=39.5
Q ss_pred EEEEEEEEEEccCCCCCCCeEEEEEEEecCceeeeeccHHHHHHHHHccccccceEEEEcCCCcEEEe
Q psy654 19 IEGEVVEIQIERPATGLGSKVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITIDKATGKITRL 86 (224)
Q Consensus 19 ~EGeVvei~i~~~~~~~~~~v~~itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~Id~~tG~v~rl 86 (224)
++|.|..++ + -+++...++|.-..+.-...+-...+.++. +.++.||.+.+- |++++-
T Consensus 3 v~G~V~~~~--~----~~~~~~~~~l~D~tg~i~~~~~~~~~~~~~-~~l~~g~~v~v~---G~v~~~ 60 (75)
T PF01336_consen 3 VEGRVTSIR--R----SGGKIVFFTLEDGTGSIQVVFFNEEYERFR-EKLKEGDIVRVR---GKVKRY 60 (75)
T ss_dssp EEEEEEEEE--E----EETTEEEEEEEETTEEEEEEEETHHHHHHH-HTS-TTSEEEEE---EEEEEE
T ss_pred EEEEEEEEE--c----CCCCEEEEEEEECCccEEEEEccHHhhHHh-hcCCCCeEEEEE---EEEEEE
Confidence 689999887 1 134466788876667777777774444444 468899999995 777654
No 15
>PF10015 DUF2258: Uncharacterized protein conserved in archaea (DUF2258); InterPro: IPR017140 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=52.31 E-value=11 Score=28.99 Aligned_cols=23 Identities=35% Similarity=0.484 Sum_probs=20.9
Q ss_pred eccHHHHHHHH-HccccccceEEE
Q psy654 54 DLGAKMIEAIG-KEKVQAGDVITI 76 (224)
Q Consensus 54 ~lg~~m~e~l~-kekV~~GDVI~I 76 (224)
+|...+|+-|+ +.||..||||.|
T Consensus 39 eLNk~ly~~lv~~~~i~K~DVVRI 62 (75)
T PF10015_consen 39 ELNKKLYEKLVNKMKIDKLDVVRI 62 (75)
T ss_pred HHHHHHHHHHHHHhCCCcccEEEE
Confidence 46778999999 999999999999
No 16
>COG3212 Predicted membrane protein [Function unknown]
Probab=52.22 E-value=33 Score=28.75 Aligned_cols=44 Identities=30% Similarity=0.457 Sum_probs=32.0
Q ss_pred EEEEEEEEEccCCCCCCCeEEEEEEEec-CceeeeeccHHHHHHHHHccccccceEEEEcCCCcEEEee
Q psy654 20 EGEVVEIQIERPATGLGSKVGKLTMKTT-EMETSYDLGAKMIEAIGKEKVQAGDVITIDKATGKITRLG 87 (224)
Q Consensus 20 EGeVvei~i~~~~~~~~~~v~~itLkT~-~~e~~~~lg~~m~e~l~kekV~~GDVI~Id~~tG~v~rlG 87 (224)
.|.|.++++++.. |..+=.+.++.. .++.. +.||++||+|-+.+
T Consensus 97 ~G~v~dieLe~~~---g~~vYevei~~~d~~e~e---------------------v~iDA~TG~Il~~~ 141 (144)
T COG3212 97 PGKVDDIELEEDN---GRLVYEVEIVKDDGQEYE---------------------VEIDAKTGKILKIE 141 (144)
T ss_pred CCceeEEEEeccC---CEEEEEEEEEeCCCcEEE---------------------EEEecCCCCccccc
Confidence 4677888877654 556667788886 66665 77899999987654
No 17
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=49.00 E-value=82 Score=21.37 Aligned_cols=57 Identities=14% Similarity=0.153 Sum_probs=39.1
Q ss_pred eEEEEEEEEEEEccCCCCCCCeEEEEEEEecCce-eeeeccHHHHHHHHHccccccceEEEEcCCCcE
Q psy654 17 EMIEGEVVEIQIERPATGLGSKVGKLTMKTTEME-TSYDLGAKMIEAIGKEKVQAGDVITIDKATGKI 83 (224)
Q Consensus 17 ev~EGeVvei~i~~~~~~~~~~v~~itLkT~~~e-~~~~lg~~m~e~l~kekV~~GDVI~Id~~tG~v 83 (224)
-.++|+|..++-.. ....+++...+++ -+-.+.+ +++.+.+++.||-+|+--...+|
T Consensus 5 N~l~g~V~~ie~~g-------~~~~v~~~~~~~~~l~a~it~---~~~~~L~L~~G~~V~~~ik~~~v 62 (64)
T PF03459_consen 5 NQLPGTVESIENLG-------SEVEVTLDLGGGETLTARITP---ESAEELGLKPGDEVYASIKASSV 62 (64)
T ss_dssp EEEEEEEEEEEESS-------SEEEEEEEETTSEEEEEEEEH---HHHHHCT-STT-EEEEEE-GGG-
T ss_pred cEEEEEEEEEEECC-------CeEEEEEEECCCCEEEEEEcH---HHHHHcCCCCCCEEEEEEehhhe
Confidence 46889999988422 2467888888888 6667766 67778899999999875444333
No 18
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=48.24 E-value=83 Score=21.97 Aligned_cols=52 Identities=15% Similarity=0.257 Sum_probs=40.1
Q ss_pred EEEEEEEEEEEccCCCCCCCeEEEEEEEecCceeeeeccHHHHHHHHHccccccceEEE
Q psy654 18 MIEGEVVEIQIERPATGLGSKVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITI 76 (224)
Q Consensus 18 v~EGeVvei~i~~~~~~~~~~v~~itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~I 76 (224)
.+.|+|.+++. ... | .+-++|.-..++-..-+-++.++++ +..++.|+.|.|
T Consensus 3 ~v~g~v~~i~~--tk~--g--~~~~~L~D~~~~i~~~~f~~~~~~~-~~~l~~g~~v~v 54 (78)
T cd04489 3 WVEGEISNLKR--PSS--G--HLYFTLKDEDASIRCVMWRSNARRL-GFPLEEGMEVLV 54 (78)
T ss_pred EEEEEEecCEE--CCC--c--EEEEEEEeCCeEEEEEEEcchhhhC-CCCCCCCCEEEE
Confidence 46899999987 222 3 6778898887777778888888774 478999999888
No 19
>PF04565 RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; InterPro: IPR007645 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 3, is also known as the fork domain and is proximal to catalytic site [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_B 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C 3AOH_H 1IW7_M 2O5J_C 2CW0_M ....
Probab=47.38 E-value=12 Score=27.27 Aligned_cols=21 Identities=48% Similarity=0.898 Sum_probs=14.6
Q ss_pred cCCCcccccccccccccccccccCccCCCC--CCCC
Q psy654 107 LPSRSRHVSSWGVQKDVVQSISNNIICPVV--PRPE 140 (224)
Q Consensus 107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~--P~Ge 140 (224)
...|.-|.|+|| - ||| + |+|+
T Consensus 31 ~~~R~lh~s~~G------~------iCP-veTPEG~ 53 (68)
T PF04565_consen 31 TEPRQLHPSQYG------R------ICP-VETPEGE 53 (68)
T ss_dssp STTTSTTGGGTT------T------BSS-SSS-SST
T ss_pred ccccccccccee------E------Eee-cccCCCc
Confidence 345777999999 3 599 4 7775
No 20
>PTZ00180 60S ribosomal protein L8; Provisional
Probab=45.75 E-value=38 Score=31.32 Aligned_cols=52 Identities=10% Similarity=0.175 Sum_probs=37.0
Q ss_pred eeeEEEEEEEEEEEccCCCCCCCeEEEEEEEecC---ceeeeeccHHHHHHHHHccccccceEEEE
Q psy654 15 ETEMIEGEVVEIQIERPATGLGSKVGKLTMKTTE---METSYDLGAKMIEAIGKEKVQAGDVITID 77 (224)
Q Consensus 15 ~~ev~EGeVvei~i~~~~~~~~~~v~~itLkT~~---~e~~~~lg~~m~e~l~kekV~~GDVI~Id 77 (224)
...-++|.|++|+.|...+ ..++.|...... .++.|-|.++ ++++||.|+.-
T Consensus 37 ~~~~~~g~V~~IeyDPnRs---A~IAlv~~~d~~~~~g~~~YIlAp~--------gl~vGd~I~~g 91 (260)
T PTZ00180 37 RHGYIRGVVKDIEHDPGRG---APLARVEFRDPYKYKRVKELMVAPE--------GMYTGQYVYCG 91 (260)
T ss_pred ccCCcCEEEEEEEECCCCC---ceEEEEEecCCccccCceEEEEeeC--------CCCCCCEEEeC
Confidence 3344689999999876554 357766655443 3567887775 99999999973
No 21
>PRK11347 antitoxin ChpS; Provisional
Probab=44.16 E-value=54 Score=25.05 Aligned_cols=41 Identities=10% Similarity=0.216 Sum_probs=33.1
Q ss_pred EEEEecCceeeeeccHHHHHHHHHccccccceEEEEcCCCcEEE
Q psy654 42 LTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITIDKATGKITR 85 (224)
Q Consensus 42 itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~Id~~tG~v~r 85 (224)
.+++.--.+.-++|++.+.++| +++.||.+.|...-|.+.-
T Consensus 3 ~~v~kwGNS~~vriPk~il~~l---~l~~G~~v~i~v~~~~iii 43 (83)
T PRK11347 3 ITIKRWGNSAGMVIPNIVMKEL---NLQPGQSVEAQVSNNQLIL 43 (83)
T ss_pred EEEEEEcCceeEEeCHHHHHHc---CCCCCCEEEEEEECCEEEE
Confidence 3566666777889999998776 7999999999998887654
No 22
>KOG1728|consensus
Probab=44.05 E-value=36 Score=29.31 Aligned_cols=70 Identities=24% Similarity=0.358 Sum_probs=48.4
Q ss_pred ceeeceeEEEeeeEEEEEEEEEEEccCCCCCCCeEEEE---EEEecCceeeeeccHHHHHHHHH----------------
Q psy654 5 STHSDTNHIEETEMIEGEVVEIQIERPATGLGSKVGKL---TMKTTEMETSYDLGAKMIEAIGK---------------- 65 (224)
Q Consensus 5 r~sigvrikE~~ev~EGeVvei~i~~~~~~~~~~v~~i---tLkT~~~e~~~~lg~~m~e~l~k---------------- 65 (224)
-+.+|+-+|--+|-|||.=.+= .-|-+|.-+.=|+| +....+|+.+.=+-.....-+-|
T Consensus 35 ~~~iglGFKtP~eAiegtYIDK--KCPftG~vsIRGril~G~V~k~Km~rTIvvrrdYlHy~~KY~ryekrHkN~svh~S 112 (156)
T KOG1728|consen 35 YKNIGLGFKTPREAIEGTYIDK--KCPFTGNVSIRGRILTGTVVKMKMQRTIVVRRDYLHYIKKYNRYEKRHKNMSVHVS 112 (156)
T ss_pred hhhcCcccCChHHhhcceeecc--cCCcccceeEeeEEEeeEEeeeceeEEEEEEhhhhhHhHHhhHHHHhccCCccccc
Confidence 3568888888899999976653 45666654444665 77788999987766444333222
Q ss_pred ---ccccccceEEE
Q psy654 66 ---EKVQAGDVITI 76 (224)
Q Consensus 66 ---ekV~~GDVI~I 76 (224)
.-|+.||+++|
T Consensus 113 PcFrdi~~gDiVtv 126 (156)
T KOG1728|consen 113 PCFRDIQEGDIVTV 126 (156)
T ss_pred hhhhccccCCEEEE
Confidence 14999999998
No 23
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated
Probab=43.79 E-value=63 Score=29.48 Aligned_cols=49 Identities=22% Similarity=0.300 Sum_probs=36.6
Q ss_pred eeeEEEEEEEEEEEccCCCCCCCeEEEEEEEecCceeeeeccHHHHHHHHHccccccceEEE
Q psy654 15 ETEMIEGEVVEIQIERPATGLGSKVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITI 76 (224)
Q Consensus 15 ~~ev~EGeVvei~i~~~~~~~~~~v~~itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~I 76 (224)
..+.++|.|++|+.|...+. .++.|.. .+.++.|-|.++ +..+||+|+.
T Consensus 35 ~~~~~~g~V~~IeyDPnRsa---~IAlv~~--~~g~~~YIiAp~--------gl~~Gd~I~s 83 (238)
T PRK09612 35 KDGTLRGKVVDILHDPGRNA---PVAKVKF--ENGEEFLILAPE--------GLYVGQEIEI 83 (238)
T ss_pred cCCceeEEEEEEEECCCCCC---eEEEEEe--CCCCEEEEEccC--------CCCCCCEEEe
Confidence 33567899999998765543 4665554 566778888775 9999999996
No 24
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=43.22 E-value=11 Score=31.18 Aligned_cols=32 Identities=31% Similarity=0.564 Sum_probs=23.2
Q ss_pred ccccccceEEEEcCCCcEEEeecccccccccc
Q psy654 66 EKVQAGDVITIDKATGKITRLGRSFTRARDYD 97 (224)
Q Consensus 66 ekV~~GDVI~Id~~tG~v~rlGRs~~~a~~yD 97 (224)
.-.++||.|.|+...|+|..+|=-.+.-+++|
T Consensus 59 ~pf~vGD~I~i~~~~G~V~~I~l~~t~l~~~~ 90 (206)
T PF00924_consen 59 RPFKVGDRIEIGGVEGRVEEIGLRSTRLRTWD 90 (206)
T ss_dssp -SS-TT-EEESSS-EEEEEEE-SSEEEEEETT
T ss_pred CCccCCCEEEEEEeehHHHhcCcceeeeecCC
Confidence 36789999999999999999997777777655
No 25
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=43.15 E-value=1.5e+02 Score=22.80 Aligned_cols=74 Identities=18% Similarity=0.170 Sum_probs=39.4
Q ss_pred EEEEEEEccCCCCCCCeEEEEEEEecCceeeeeccHHHHHHHHHccccccceEEEEcCCCcEEEeecccccccc
Q psy654 22 EVVEIQIERPATGLGSKVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITIDKATGKITRLGRSFTRARD 95 (224)
Q Consensus 22 eVvei~i~~~~~~~~~~v~~itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~Id~~tG~v~rlGRs~~~a~~ 95 (224)
+|.+|+..-..+|.=..++.+.=-.-++.+.=+..--=++.+.+.++..||.|.|-++-.-|=++=+.-...++
T Consensus 4 ~v~~I~~~vGRtG~itPva~lePV~l~G~~VsratLhN~~~i~~~~i~~Gd~V~V~raGdVIP~I~~vv~~~r~ 77 (82)
T PF03120_consen 4 KVRDIEWQVGRTGKITPVAVLEPVELDGTTVSRATLHNYDYIKELDIRIGDTVLVTRAGDVIPKIVGVVKEKRT 77 (82)
T ss_dssp EEEEEEEEE-TTSBEEEEEEEEEEECTTCEEEEEE--SHHHHHHTT-BBT-EEEEEEETTTEEEEEEE-GGG--
T ss_pred EEEEEEEecCCCeEEEEEEEEEEEEECCeEEEEEEecCHHHHHHcCCCCCCEEEEEECCCccceEeEeehhcCC
Confidence 34555554444443222344333333444333333334667888999999999999998888777665544443
No 26
>PTZ00031 ribosomal protein L2; Provisional
Probab=42.05 E-value=49 Score=31.51 Aligned_cols=53 Identities=19% Similarity=0.235 Sum_probs=38.1
Q ss_pred EEEeeeEEEEEEEEEEEccCCCCCCCeEEEEEEEecCceeeeeccHHHHHHHHHccccccceEEEE
Q psy654 12 HIEETEMIEGEVVEIQIERPATGLGSKVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITID 77 (224)
Q Consensus 12 ikE~~ev~EGeVvei~i~~~~~~~~~~v~~itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~Id 77 (224)
+++...-++|.|++|+.|...+. .++.+.. .+++..|-|.++ ++.+||+|+.-
T Consensus 98 fkr~~~~i~g~V~~IeyDPnRsA---~IALV~~--~dg~~~YIlApe--------Gl~vGd~I~sg 150 (317)
T PTZ00031 98 FKRSRKDIYSTVLRIEYDPSRSA---HIALLQY--EDGVLSYILAPL--------LLRPGDKIIAS 150 (317)
T ss_pred cccccCCcCEEEEEEEeCCCCCC---cEEEEEe--cCCcEEEEEccC--------CCCCCCEEEeC
Confidence 34444456899999998765543 4666554 566777887775 99999999863
No 27
>PF03413 PepSY: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification. ; InterPro: IPR005075 This signature, PepSY, is found in the propeptide of members of the MEROPS peptidase family M4 (clan MA(E)), which contains the thermostable thermolysins (3.4.24.27 from EC), and related thermolabile neutral proteases (bacillolysins) (3.4.24.28 from EC) from various species of Bacillus. It is also in many non-peptidase proteins, including Bacillus subtilis YpeB protein - a regulator of SleB spore cortex lytic enzyme - and a large number of eubacterial and archaeal cell wall-associated and secreted proteins which are mostly annotated as 'hypothetical protein'. Many extracellular bacterial proteases are produced as proenzymes. The propeptides usually have a dual function, i.e. they function as an intramolecular chaperone required for the folding of the polypeptide and as an inhibitor preventing premature activation of the enzyme. Analysis of the propeptide region of the M4 family of peptidases reveals two regions of conservation, the PepSY domain and a second domain, proximate to the N terminus, the FTP domain (IPR011096 from INTERPRO), which is also found in isolation in the propeptide of eukaryotic peptidases belong to MEROPS peptidase family M36. Propeptide domain swapping experiments, for example swapping the propeptide domain of PA protease with that of vibrolysin, both propeptides contain the FTP and PepSY domains, allows the PA protease domain to fold correctly and inhibits the C-terminal autoprocessing activity. However, swapping the propeptide of PA protease for the thermolysin propeptide, does not facilitate the correct folding nor the processing of the chimaeric protein into an active peptidase []. Mutational analysis of the Pseudomonas aeruginosa elastase gene revealed two mutations in the propeptide which resulted in the loss of inhibitory activity but not chaperone activity: A-15V and T-153I (where +1 is defined as the first residue of the mature peptidase). Both mutations resulted in peptidase activity, the T-153V mutation being much less effective than the A-15I mutation [] in activating peptidase activity. The T-153V mutation lies N-terminal to the FTP domain while the A-15I mutation is C-terminal to the PepSY domain. Given the diverse range of other proteins, both domains occur in in isolation, the exact function of each is still unclear; though it has been proposed that the PepSY domain primarily has inhibitory activity and in conjunction with the FTP domain in chaperone activity. ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0005576 extracellular region; PDB: 2GU3_A 3NQZ_A 3NQY_A 2KGY_A.
Probab=40.52 E-value=23 Score=23.58 Aligned_cols=12 Identities=33% Similarity=0.534 Sum_probs=7.9
Q ss_pred EEEEcCCCcEEE
Q psy654 74 ITIDKATGKITR 85 (224)
Q Consensus 74 I~Id~~tG~v~r 85 (224)
++||+.||+|.+
T Consensus 51 v~VDa~tG~Il~ 62 (64)
T PF03413_consen 51 VYVDAYTGEILS 62 (64)
T ss_dssp EEEETTT--EEE
T ss_pred EEEECCCCeEEE
Confidence 349999999964
No 28
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=39.70 E-value=57 Score=24.01 Aligned_cols=36 Identities=17% Similarity=0.357 Sum_probs=28.4
Q ss_pred cCceeeeeccHHHHHHHHHccccccceEEEEcCCCcEEE
Q psy654 47 TEMETSYDLGAKMIEAIGKEKVQAGDVITIDKATGKITR 85 (224)
Q Consensus 47 ~~~e~~~~lg~~m~e~l~kekV~~GDVI~Id~~tG~v~r 85 (224)
...+....|+..+.++| ++..||-|.++...|.+.-
T Consensus 6 ~GNS~~vtIPk~i~~~l---gl~~Gd~v~v~~~~~~iii 41 (74)
T TIGR02609 6 VGNSLVVTLPKEVLESL---GLKEGDTLYVDEEEGGLKL 41 (74)
T ss_pred ECCeeEEEECHHHHHHc---CcCCCCEEEEEEECCEEEE
Confidence 34556778999988776 7999999999988886543
No 29
>PRK14812 hypothetical protein; Provisional
Probab=39.26 E-value=40 Score=27.65 Aligned_cols=34 Identities=18% Similarity=0.180 Sum_probs=28.3
Q ss_pred eeccHHHHHHHHHccccccceEEEEcCCCcEEEeec
Q psy654 53 YDLGAKMIEAIGKEKVQAGDVITIDKATGKITRLGR 88 (224)
Q Consensus 53 ~~lg~~m~e~l~kekV~~GDVI~Id~~tG~v~rlGR 88 (224)
+.+.+..++.|.+ ++.||.|+||-+++.|+--|.
T Consensus 42 i~~~~~~~~~l~~--~~~g~~i~vDL~~~~v~~~~~ 75 (119)
T PRK14812 42 IVQPREVREKLAQ--LKPTDQVTVDLEQQKIISPVE 75 (119)
T ss_pred ccCCHHHHHHHhc--cCCCCEEEEEcCCCEEEcCCe
Confidence 4577888888885 499999999999999987663
No 30
>CHL00052 rpl2 ribosomal protein L2
Probab=39.22 E-value=63 Score=30.03 Aligned_cols=53 Identities=19% Similarity=0.279 Sum_probs=38.4
Q ss_pred EEEeeeEEEEEEEEEEEccCCCCCCCeEEEEEEEecCceeeeeccHHHHHHHHHccccccceEEEE
Q psy654 12 HIEETEMIEGEVVEIQIERPATGLGSKVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITID 77 (224)
Q Consensus 12 ikE~~ev~EGeVvei~i~~~~~~~~~~v~~itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~Id 77 (224)
+++...-++|.|++|+.+...+ ..++.+.. .+++..|-|.++ ++++||+|+.-
T Consensus 65 f~r~~~~i~~~V~~IeyDP~Rs---a~IAlv~~--~~g~~~YIlAp~--------gl~~Gd~I~~g 117 (273)
T CHL00052 65 FRRNKKDIYGRIVTIEYDPNRN---AYICLIHY--GDGEKRYILHPR--------GLKIGDTIVSG 117 (273)
T ss_pred cccccCCCcEEEEEEEECCCCC---ccEEEEEe--CCCcEEEEEccC--------CCCCCCEEEeC
Confidence 3444445789999999876543 45676544 566888888775 99999999973
No 31
>PRK10929 putative mechanosensitive channel protein; Provisional
Probab=38.68 E-value=20 Score=39.00 Aligned_cols=36 Identities=28% Similarity=0.513 Sum_probs=30.9
Q ss_pred HHHccccccceEEEEcCCCcEEEeeccccccccccc
Q psy654 63 IGKEKVQAGDVITIDKATGKITRLGRSFTRARDYDA 98 (224)
Q Consensus 63 l~kekV~~GDVI~Id~~tG~v~rlGRs~~~a~~yD~ 98 (224)
+...-+++||.|.|+-.+|.|.++|=-.++-+++|-
T Consensus 931 L~erPfrVGD~I~I~~~~GtV~~I~lRsT~Irt~Dg 966 (1109)
T PRK10929 931 LFEKPIRIGDTVTIRDLTGSVTKINTRATTISDWDR 966 (1109)
T ss_pred HHhCCCCCCCEEEECCEEEEEEEEeeeEEEEEeCCC
Confidence 345678999999999999999999977788888873
No 32
>PRK11281 hypothetical protein; Provisional
Probab=36.47 E-value=20 Score=39.01 Aligned_cols=35 Identities=26% Similarity=0.442 Sum_probs=30.3
Q ss_pred HHccccccceEEEEcCCCcEEEeeccccccccccc
Q psy654 64 GKEKVQAGDVITIDKATGKITRLGRSFTRARDYDA 98 (224)
Q Consensus 64 ~kekV~~GDVI~Id~~tG~v~rlGRs~~~a~~yD~ 98 (224)
...-+++||.|.|+..+|.|.++|=-.++-+++|-
T Consensus 935 ~eRPfrIGD~I~I~~~~G~V~~I~lRsT~Irt~D~ 969 (1113)
T PRK11281 935 FERPVRIGDTVTIGTFSGTVSKIRIRATTITDFDR 969 (1113)
T ss_pred HcCCcCCCCEEEECCEEEEEEEEEeEEEEEEcCCC
Confidence 34568999999999999999999977788888873
No 33
>PF13128 DUF3954: Protein of unknown function (DUF3954)
Probab=35.44 E-value=74 Score=22.80 Aligned_cols=30 Identities=33% Similarity=0.459 Sum_probs=19.7
Q ss_pred eceeEEEeeeEEEEEEEEEEEccCCCCCCCeE
Q psy654 8 SDTNHIEETEMIEGEVVEIQIERPATGLGSKV 39 (224)
Q Consensus 8 igvrikE~~ev~EGeVvei~i~~~~~~~~~~v 39 (224)
|++..--.--|-.|+|..+ +-|.+|||..+
T Consensus 5 Id~~~ngiYiV~~G~v~~i--~pP~sGfGeq~ 34 (50)
T PF13128_consen 5 IDVKENGIYIVKDGEVTFI--EPPESGFGEQV 34 (50)
T ss_pred eeccCCeEEEEECCeEEEc--CCCCCCcceEE
Confidence 3333333334568998876 68899999865
No 34
>TIGR03106 trio_M42_hydro hydrolase, peptidase M42 family. This model describes a subfamily of MEROPS peptidase family M42, a glutamyl aminopeptidase family that also includes the cellulase CelM from Clostridium thermocellum and deblocking aminopeptidases that can remove acylated amino acids. Members of this family occur in a three gene cassette with an amidotransferase (TIGR03104)in the asparagine synthase (glutamine-hydrolyzing) family, and a probable acetyltransferase (TIGR03103) in the GNAT family.
Probab=34.48 E-value=34 Score=31.97 Aligned_cols=32 Identities=19% Similarity=0.284 Sum_probs=28.0
Q ss_pred ceeeeeccHHHHHHHHHccccccceEEEEcCC
Q psy654 49 METSYDLGAKMIEAIGKEKVQAGDVITIDKAT 80 (224)
Q Consensus 49 ~e~~~~lg~~m~e~l~kekV~~GDVI~Id~~t 80 (224)
|+--+|+|.+=.|...+.||++||.+++|...
T Consensus 138 ~~l~iDiG~~s~ee~~~lGV~~Gd~v~~~~~~ 169 (343)
T TIGR03106 138 VEVRVDARASCRADLVRLGISVGDFVAFDPQP 169 (343)
T ss_pred cEEEEECCcCCHHHHHHcCCCCCCEEEECCcc
Confidence 46777899988899999999999999999865
No 35
>TIGR01171 rplB_bact ribosomal protein L2, bacterial/organellar. This model distinguishes bacterial and organellar ribosomal protein L2 from its counterparts in the archaea nad in the eukaryotic cytosol. Plant mitochondrial examples tend to have long, variable inserts.
Probab=33.68 E-value=93 Score=28.91 Aligned_cols=48 Identities=21% Similarity=0.371 Sum_probs=36.0
Q ss_pred eEEEEEEEEEEEccCCCCCCCeEEEEEEEecCceeeeeccHHHHHHHHHccccccceEEEE
Q psy654 17 EMIEGEVVEIQIERPATGLGSKVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITID 77 (224)
Q Consensus 17 ev~EGeVvei~i~~~~~~~~~~v~~itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~Id 77 (224)
.-++|.|++|+.+...+ ..++.+.. .+++..|-|.++ ++.+||.|+.-
T Consensus 70 ~~i~g~V~~IeyDP~Rs---a~IAlv~~--~~g~~~YIlap~--------gl~~Gd~I~~g 117 (273)
T TIGR01171 70 DGIPAKVAAIEYDPNRS---ARIALLHY--ADGEKRYILAPK--------GLKVGDTVISG 117 (273)
T ss_pred CCCcEEEEEEEeCCCCC---cCEEEEEe--cCCcEEEEEccC--------CCCCCCEEEEC
Confidence 34579999998876554 35676644 567788888875 99999999974
No 36
>PF01967 MoaC: MoaC family; InterPro: IPR002820 The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cis-dithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism [, ]. In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which converts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner []. MoCF is the active co-factor in eukaryotic and some prokaryotic molybdo-enzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdo-enzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF []. Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 (Q39054 from SWISSPROT) of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) []. This entry contains the molybdenum cofactor biosynthesis protein MoaC.; GO: 0006777 Mo-molybdopterin cofactor biosynthetic process; PDB: 2EKN_B 1EKS_A 1EKR_A 3JQM_D 2IIH_A 3JQJ_I 2IDE_K 3JQK_A 2OHD_B 2EEY_A.
Probab=33.45 E-value=32 Score=28.96 Aligned_cols=35 Identities=29% Similarity=0.420 Sum_probs=29.5
Q ss_pred EEEEecCceeeeeccHHHHHHHHHccccccceEEE
Q psy654 42 LTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITI 76 (224)
Q Consensus 42 itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~I 76 (224)
.|.+|.--+-...|++..++.|....+..|||+.+
T Consensus 9 ~t~R~A~A~g~i~l~~~~~~~i~~~~~~KGdvl~v 43 (136)
T PF01967_consen 9 VTYRTAIASGRIRLSPETIELIRDGEVPKGDVLAV 43 (136)
T ss_dssp -EEEEEEEEEEEEE-HHHHHHHHTTSSTTC-HHHH
T ss_pred CeeEEEEEEEEEEECHHHHHHHHhCCCCCCCHHHh
Confidence 67888888999999999999999999999999865
No 37
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=33.42 E-value=1.2e+02 Score=20.29 Aligned_cols=32 Identities=22% Similarity=0.178 Sum_probs=24.5
Q ss_pred eeEEEeeeEEEEEEEEEEEccCCCCCCCeEEEEEEEecCcee
Q psy654 10 TNHIEETEMIEGEVVEIQIERPATGLGSKVGKLTMKTTEMET 51 (224)
Q Consensus 10 vrikE~~ev~EGeVvei~i~~~~~~~~~~v~~itLkT~~~e~ 51 (224)
|++....+.++|.+..|. . -|.|.++|.+++.
T Consensus 6 V~v~~~~~~~~G~~~gId--~--------~G~L~v~~~~g~~ 37 (48)
T PF02237_consen 6 VRVETGDGEIEGIAEGID--D--------DGALLVRTEDGSI 37 (48)
T ss_dssp EEEEETSCEEEEEEEEEE--T--------TSEEEEEETTEEE
T ss_pred EEEEECCeEEEEEEEEEC--C--------CCEEEEEECCCCE
Confidence 566777888999999886 1 2579999999843
No 38
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=33.03 E-value=31 Score=24.92 Aligned_cols=16 Identities=31% Similarity=0.609 Sum_probs=11.5
Q ss_pred cccccceEEEEcCCCc
Q psy654 67 KVQAGDVITIDKATGK 82 (224)
Q Consensus 67 kV~~GDVI~Id~~tG~ 82 (224)
=|+.||.|.||-.+|.
T Consensus 37 FI~~Gd~I~VdT~~g~ 52 (56)
T PF09285_consen 37 FIEEGDKIKVDTRDGS 52 (56)
T ss_dssp T--TT-EEEEETTTTE
T ss_pred eecCCCEEEEECCCCe
Confidence 3688999999999985
No 39
>PRK14699 replication factor A; Provisional
Probab=32.14 E-value=1e+02 Score=30.65 Aligned_cols=58 Identities=24% Similarity=0.324 Sum_probs=43.0
Q ss_pred EEEEEEEEEE----EccCCCCCCCeEEEEEEEecCceeeeeccHHHHHHHHHccccccceEEE
Q psy654 18 MIEGEVVEIQ----IERPATGLGSKVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITI 76 (224)
Q Consensus 18 v~EGeVvei~----i~~~~~~~~~~v~~itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~I 76 (224)
-++|.|..+. +++.. |--.+++.++|.=.-+...|.|=..+++.+...++++||+|.|
T Consensus 71 ~i~~rVl~i~~~r~f~r~d-G~~g~v~~~~iaDeTG~ir~tlW~~~a~~~~~g~l~~GDvv~I 132 (484)
T PRK14699 71 NFIARVVSVFDTKEFTRND-GTIGRVGNLIVGDETGKIKLTLWDNMADLIKAGKIKAGQTLQI 132 (484)
T ss_pred EEEEEEEEecCceEEecCC-CCceEEEEEEEecCCCeEEEEEecCccchhhhcCCCCCCEEEE
Confidence 5789999884 23322 2223567778887777888888888877777668999999999
No 40
>PRK09374 rplB 50S ribosomal protein L2; Validated
Probab=30.68 E-value=86 Score=29.22 Aligned_cols=48 Identities=21% Similarity=0.364 Sum_probs=35.8
Q ss_pred eEEEEEEEEEEEccCCCCCCCeEEEEEEEecCceeeeeccHHHHHHHHHccccccceEEEE
Q psy654 17 EMIEGEVVEIQIERPATGLGSKVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITID 77 (224)
Q Consensus 17 ev~EGeVvei~i~~~~~~~~~~v~~itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~Id 77 (224)
.-+.|.|++|+.|...+ ..++.+.. .+++..|-|.++ ++++||+|+.-
T Consensus 72 ~~i~~~V~~IeyDP~Rs---a~IAlv~~--~~g~~~YIlAp~--------gl~~Gd~I~~g 119 (276)
T PRK09374 72 DGIPAKVERIEYDPNRS---ARIALLHY--ADGEKRYILAPK--------GLKVGDTVVSG 119 (276)
T ss_pred CCCCEEEEEEEeCCCCC---cCEEEEEe--cCCCEEEEEecC--------CCCCCCEEEeC
Confidence 33579999999876554 35776655 467788888875 99999999973
No 41
>PF06434 Aconitase_2_N: Aconitate hydratase 2 N-terminus; InterPro: IPR015929 Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [, ]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) []. Below is a description of some of the multi-functional activities associated with different aconitases. Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway []. The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA. Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [, ]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated []. IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis []. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system. Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [, ]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress. This entry represents the N-terminal region of bacterial aconitase B (AcnB), which consists of both a HEAT-like domain and a 'swivel' domain. HEAT-like domains are usually implicated in protein-protein interactions, while the 'swivel' domain is usually a mobile unit in proteins that carry it. In AcnB, this N-terminal region was shown to be sufficient for dimerisation and for AcnB binding to mRNA. An iron-mediated dimerisation mechanism may be responsible for switching AcnB between its catalytic and regulatory roles, as dimerisation requires iron while mRNA binding is inhibited by iron. More information about these proteins can be found at Protein of the Month: Aconitase [].; GO: 0003994 aconitate hydratase activity, 0006099 tricarboxylic acid cycle; PDB: 1L5J_B.
Probab=30.59 E-value=42 Score=30.18 Aligned_cols=20 Identities=45% Similarity=0.625 Sum_probs=15.7
Q ss_pred ccccccceEEEEcCCCcEEE
Q psy654 66 EKVQAGDVITIDKATGKITR 85 (224)
Q Consensus 66 ekV~~GDVI~Id~~tG~v~r 85 (224)
.++.-||||.|++..|+|.+
T Consensus 122 ~~l~~Gdvi~I~p~~gki~~ 141 (204)
T PF06434_consen 122 SSLNTGDVITIYPYEGKIYK 141 (204)
T ss_dssp TT--TT-EEEEETTTTEEEE
T ss_pred cccCCCcEEEEecCCcEEEC
Confidence 47788999999999999998
No 42
>COG3264 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=30.36 E-value=31 Score=36.71 Aligned_cols=43 Identities=23% Similarity=0.471 Sum_probs=33.7
Q ss_pred HHHccccccceEEEEcCCCcEEEeeccccccccccccccccccccCC
Q psy654 63 IGKEKVQAGDVITIDKATGKITRLGRSFTRARDYDATGAQTRNTLPS 109 (224)
Q Consensus 63 l~kekV~~GDVI~Id~~tG~v~rlGRs~~~a~~yD~~~~~~~~v~~~ 109 (224)
|.+..|++||.|+|---+|-|+|+.=-.+.-++||= .+.++|.
T Consensus 656 L~ErpvkvGD~It~g~~~G~V~~I~vRAT~I~~fd~----~~vIVPN 698 (835)
T COG3264 656 LFERPVKVGDTVTIGTVSGTVRKISVRATTIRTFDR----KEVIVPN 698 (835)
T ss_pred heecCcccCCEEEECCceEEEEEEEeeEEEEEeCCC----CeEEecc
Confidence 445689999999999999999999966677777773 2255564
No 43
>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=29.64 E-value=2.3e+02 Score=20.93 Aligned_cols=54 Identities=24% Similarity=0.413 Sum_probs=28.0
Q ss_pred EEEEEEEEEEEccCCCCCCCeEEEEEEE--ecCceeeeeccHHHHHHHHHcccc-ccceEEE
Q psy654 18 MIEGEVVEIQIERPATGLGSKVGKLTMK--TTEMETSYDLGAKMIEAIGKEKVQ-AGDVITI 76 (224)
Q Consensus 18 v~EGeVvei~i~~~~~~~~~~v~~itLk--T~~~e~~~~lg~~m~e~l~kekV~-~GDVI~I 76 (224)
+++|+|-.++...-.+ |+.+-.+.|- |.-..-..-+. +-.+.+ +.++ .||.|.+
T Consensus 3 ~i~G~Vf~~e~re~k~--g~~i~~~~itD~t~Si~~K~F~~-~~~~~~--~~ik~~G~~v~v 59 (82)
T cd04484 3 VVEGEVFDLEIRELKS--GRKILTFKVTDYTSSITVKKFLR-KDEKDK--EELKSKGDWVRV 59 (82)
T ss_pred EEEEEEEEEEEEEecC--CCEEEEEEEEcCCCCEEEEEecc-CChhHH--hhcccCCCEEEE
Confidence 6899999988754444 3444333331 22111111121 223333 4678 8998876
No 44
>PHA02600 FII major tail tube protein; Provisional
Probab=29.55 E-value=3.5e+02 Score=22.85 Aligned_cols=70 Identities=17% Similarity=0.300 Sum_probs=45.0
Q ss_pred eeceeEEEeeeEEEEEEEEEEEcc---CC---CCCCCeEEEE--EEEecCceeeeeccHHHHHHHHHccccccceEEEE
Q psy654 7 HSDTNHIEETEMIEGEVVEIQIER---PA---TGLGSKVGKL--TMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITID 77 (224)
Q Consensus 7 sigvrikE~~ev~EGeVvei~i~~---~~---~~~~~~v~~i--tLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~Id 77 (224)
-...++...-.=|=|++.|++... .. .| |--.|.+ .+--.+++.++++..-..+-|..-++..||-..+.
T Consensus 7 l~~~n~f~dG~~~~G~~~evtlP~l~~kte~~rg-gGm~g~i~~~~G~e~le~~f~~~g~~~~~l~~~g~~~~~~~~l~ 84 (169)
T PHA02600 7 LKNFNVFNDGASYQGVVEEVTLPKLTRKLEAYRG-GGMNGPVKVDMGLEDLELEWTVGGFEVELLKQYGAVSVDGVPLR 84 (169)
T ss_pred eeeEEEEECCeeeEEEEeeccCCcccceeeeeEc-CCceeEEEccCCccceEEEEEEcCccHHHHHHhcCCCCCeEEEE
Confidence 344556666667889999986522 11 11 1112333 33345588888888888888888898888887773
No 45
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=29.15 E-value=38 Score=30.94 Aligned_cols=34 Identities=18% Similarity=0.205 Sum_probs=29.0
Q ss_pred HHccccccceEEEEcCCCcEEEeecccccccccc
Q psy654 64 GKEKVQAGDVITIDKATGKITRLGRSFTRARDYD 97 (224)
Q Consensus 64 ~kekV~~GDVI~Id~~tG~v~rlGRs~~~a~~yD 97 (224)
...-.++||.|.++-.+|.|..+|=-.++-+.+|
T Consensus 126 ~~rpf~vGD~I~i~~~~G~V~~I~~r~T~i~t~d 159 (286)
T PRK10334 126 MFRPFRAGEYVDLGGVAGTVLSVQIFSTTMRTAD 159 (286)
T ss_pred hcCCCCCCCEEEECCEEEEEEEEEeEEEEEEcCC
Confidence 3456899999999999999999997777777766
No 46
>PF03829 PTSIIA_gutA: PTS system glucitol/sorbitol-specific IIA component; InterPro: IPR004716 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. The Man family is unique in several respects among PTS permease families: It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria. The system in Escherichia coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 2F9H_A.
Probab=27.89 E-value=30 Score=28.13 Aligned_cols=26 Identities=27% Similarity=0.371 Sum_probs=17.6
Q ss_pred HHccccccceEEEEcCCCcEEEeecc
Q psy654 64 GKEKVQAGDVITIDKATGKITRLGRS 89 (224)
Q Consensus 64 ~kekV~~GDVI~Id~~tG~v~rlGRs 89 (224)
.++-+++||++.||-..=.|+.+|-.
T Consensus 48 ~~~~i~~Gd~l~i~~~~y~ItaVG~~ 73 (117)
T PF03829_consen 48 LKGDIKPGDTLIIGGQEYTITAVGSV 73 (117)
T ss_dssp GG----TT-EEEETTEEEEEEEE-TT
T ss_pred ccCCcCCCCEEEECCeEEEEEEEhHH
Confidence 45679999999999999999999943
No 47
>PRK03955 hypothetical protein; Reviewed
Probab=27.18 E-value=56 Score=27.20 Aligned_cols=23 Identities=26% Similarity=0.502 Sum_probs=19.8
Q ss_pred HccccccceEEEEcCCCcEEEee
Q psy654 65 KEKVQAGDVITIDKATGKITRLG 87 (224)
Q Consensus 65 kekV~~GDVI~Id~~tG~v~rlG 87 (224)
-+.++-||.|.+|..+|.|..+.
T Consensus 108 ~~~l~~G~~V~Vdg~~G~V~i~~ 130 (131)
T PRK03955 108 ISKLKDGDRVVVDGDEGEVEILE 130 (131)
T ss_pred ceecCCCCEEEEeCCCCEEEEcc
Confidence 45789999999999999998764
No 48
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=26.82 E-value=64 Score=23.92 Aligned_cols=31 Identities=13% Similarity=0.291 Sum_probs=22.1
Q ss_pred eeeccHHHHHHHHHccccccceEEEEcCCCcEEE
Q psy654 52 SYDLGAKMIEAIGKEKVQAGDVITIDKATGKITR 85 (224)
Q Consensus 52 ~~~lg~~m~e~l~kekV~~GDVI~Id~~tG~v~r 85 (224)
.+.+.|+-+ .+.+++.||.|.|....|++.-
T Consensus 31 ~v~inp~dA---~~~Gi~~Gd~V~v~s~~G~v~~ 61 (110)
T PF01568_consen 31 FVEINPEDA---AKLGIKDGDWVRVSSPRGSVEV 61 (110)
T ss_dssp EEEEEHHHH---HHCT--TTCEEEEEETTEEEEE
T ss_pred EEEEcHHHH---HHhcCcCCCEEEEEeccceEee
Confidence 456666654 4568999999999999997763
No 49
>PF14578 GTP_EFTU_D4: Elongation factor Tu domain 4; PDB: 1G7R_A 1G7S_A 1G7T_A 1XE1_A.
Probab=26.64 E-value=1.3e+02 Score=23.21 Aligned_cols=27 Identities=11% Similarity=0.302 Sum_probs=15.0
Q ss_pred EEEecCceeeeeccHHHHHHHHHccccccceEEE
Q psy654 43 TMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITI 76 (224)
Q Consensus 43 tLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~I 76 (224)
.....-++-.+.+...+ .+..||++|+
T Consensus 55 ~~A~~G~eVai~Ieg~~-------~i~eGDiLyV 81 (81)
T PF14578_consen 55 DEAKKGDEVAISIEGPT-------QIKEGDILYV 81 (81)
T ss_dssp SEEETT-EEEEEEET---------TB-TT-EEEE
T ss_pred cccCCCCEEEEEEeCCc-------cCCCCCEEeC
Confidence 34455666666666655 8888999885
No 50
>PRK09606 DNA-directed RNA polymerase subunit B''; Validated
Probab=26.58 E-value=33 Score=33.57 Aligned_cols=20 Identities=40% Similarity=0.996 Sum_probs=15.3
Q ss_pred CCCcccccccccccccccccccCccCCCC--CCCC
Q psy654 108 PSRSRHVSSWGVQKDVVQSISNNIICPVV--PRPE 140 (224)
Q Consensus 108 ~~~~~~~~~~~~~~~~~~~~~~~~~~P~~--P~Ge 140 (224)
--|.-|.|+|| - ||| + |+|+
T Consensus 436 ~vR~lhps~~G------~------iCP-veTPEG~ 457 (494)
T PRK09606 436 EARDLHPTQWG------R------ICP-SETPEGP 457 (494)
T ss_pred cccccCcccce------e------ccc-CcCCCCC
Confidence 45777999999 3 599 5 7775
No 51
>TIGR00581 moaC molybdenum cofactor biosynthesis protein MoaC. MoaC catalyzes an early step in molybdenum cofactor biosynthesis in E. coli. The Arabidopsis homolog Cnx3 complements MoaC deficiency in E. coli (MUID:95197640). Eukarotic members of this family branch within the bacterial branch, with the archaeal members as an apparent outgroup. This protein is absent in a number of the pathogens with smaller genomes, including Mycoplasmas, Chlamydias, and spirochetes, but is found in most other complete genomes to date. The homolog form Synechocystis sp. is fused to a MobA-homologous region and is an outlier to all other bacterial forms by both neighbor-joining and UPGMA analyses. Members of this family are well-conserved. The seed for this model excludes both archaeal sequences and the most divergent bacterial sequences, but still finds all candidate MoaC sequences easily between trusted and noise cutoffs. We suggest that sequences branching outside the set that contains all seed members
Probab=26.43 E-value=47 Score=28.38 Aligned_cols=35 Identities=20% Similarity=0.328 Sum_probs=31.9
Q ss_pred EEEEecCceeeeeccHHHHHHHHHccccccceEEE
Q psy654 42 LTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITI 76 (224)
Q Consensus 42 itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~I 76 (224)
.|.+|.--+-...|+++.+++|....+..|||+..
T Consensus 20 ~t~R~A~A~g~I~l~~~~~~~i~~~~~~KGdvl~~ 54 (147)
T TIGR00581 20 ETVREARASGFVRMKPETVKMISEGRVPKGDVIAT 54 (147)
T ss_pred CceeEEEEEEEEEECHHHHHHHHhCCCCCccHHHH
Confidence 57888888899999999999999999999999865
No 52
>cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=25.97 E-value=52 Score=23.76 Aligned_cols=16 Identities=31% Similarity=0.638 Sum_probs=13.9
Q ss_pred cccccceEEEEcCCCc
Q psy654 67 KVQAGDVITIDKATGK 82 (224)
Q Consensus 67 kV~~GDVI~Id~~tG~ 82 (224)
=|+.||.|-||-.+|.
T Consensus 37 FI~~Gd~I~V~T~~g~ 52 (56)
T cd05794 37 FIKEGEKIKVDTRTGE 52 (56)
T ss_pred eecCCCEEEEECCCCc
Confidence 3688999999999986
No 53
>PRK09364 moaC molybdenum cofactor biosynthesis protein MoaC; Provisional
Probab=25.74 E-value=43 Score=28.94 Aligned_cols=35 Identities=23% Similarity=0.335 Sum_probs=32.0
Q ss_pred EEEEecCceeeeeccHHHHHHHHHccccccceEEE
Q psy654 42 LTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITI 76 (224)
Q Consensus 42 itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~I 76 (224)
.|.+|.--+-...|+++.+++|....+..|||+..
T Consensus 23 ~t~R~A~A~g~I~l~~e~~~~i~~~~~~KGdvl~~ 57 (159)
T PRK09364 23 ETVRTAVAEGSVRMSPETLALIRDGTAKKGDVLAT 57 (159)
T ss_pred CcccEEEEEEEEEECHHHHHHHHhCCCCCccHHHH
Confidence 57888888899999999999999999999999865
No 54
>PRK06033 hypothetical protein; Validated
Probab=25.18 E-value=71 Score=24.31 Aligned_cols=14 Identities=29% Similarity=0.574 Sum_probs=11.9
Q ss_pred cccccceEEEEcCC
Q psy654 67 KVQAGDVITIDKAT 80 (224)
Q Consensus 67 kV~~GDVI~Id~~t 80 (224)
+.++||||.+|+..
T Consensus 27 ~L~~GDVI~L~~~~ 40 (83)
T PRK06033 27 RMGRGAVIPLDATE 40 (83)
T ss_pred CCCCCCEEEeCCCC
Confidence 77899999999854
No 55
>PRK15491 replication factor A; Provisional
Probab=25.00 E-value=1.6e+02 Score=28.08 Aligned_cols=61 Identities=18% Similarity=0.274 Sum_probs=43.2
Q ss_pred eEEEEEEEEEEE----ccCCCCCCCeEEEEEEEecCceeeeeccHHHHHHHHHccccccceEEEEc
Q psy654 17 EMIEGEVVEIQI----ERPATGLGSKVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITIDK 78 (224)
Q Consensus 17 ev~EGeVvei~i----~~~~~~~~~~v~~itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~Id~ 78 (224)
--+.|.|+++.- .|.. |--.+++.+.|--.-++-.+.|=...++.+....+++|||++|..
T Consensus 70 v~i~arVl~~~~~R~f~r~d-Gs~g~v~~~~v~DeTG~ir~tlW~~~a~~~~~~~le~G~v~~I~~ 134 (374)
T PRK15491 70 VNFTAKVVSIFEPKEFNRND-GTTGRVGNIIVADETGSIRLTLWDDLADLIKTGDIEVGKSLNISG 134 (374)
T ss_pred eEEEEEEeeccCCeeeecCC-CCceEEEEEEEEcCCCeEEEEEECchhhhhccCCcCCCCEEEEee
Confidence 356788887732 2211 112357777888777788888888888887767899999999964
No 56
>cd01420 MoaC_PE MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis.
Probab=24.03 E-value=56 Score=27.69 Aligned_cols=35 Identities=20% Similarity=0.401 Sum_probs=30.5
Q ss_pred EEEEecCceeeeeccHHHHHHHHHccccccceEEE
Q psy654 42 LTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITI 76 (224)
Q Consensus 42 itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~I 76 (224)
.|.++.--+-...|+++.+++|....+..|||+..
T Consensus 9 ~t~R~A~A~g~i~l~~~~~~~i~~~~~~KGdvl~v 43 (140)
T cd01420 9 VTERTAVAEGRVRMSPETLDLITEGQLPKGDVLAV 43 (140)
T ss_pred CceeEEEEEEEEEECHHHHHHHHhCCCCCccHHHH
Confidence 46677777788899999999999999999999865
No 57
>PF11776 DUF3315: Domain of unknown function (DUF3315); InterPro: IPR024572 This is a bacterial family of uncharacterised proteins, which include YohN from Escherichia coli K12.; PDB: 2L1S_A.
Probab=23.76 E-value=83 Score=22.00 Aligned_cols=16 Identities=38% Similarity=0.590 Sum_probs=13.3
Q ss_pred cceEEEEcCCCcEEEe
Q psy654 71 GDVITIDKATGKITRL 86 (224)
Q Consensus 71 GDVI~Id~~tG~v~rl 86 (224)
||.+-|+.+||.|..+
T Consensus 37 ~dyvLv~~~tG~I~~V 52 (52)
T PF11776_consen 37 GDYVLVAIATGIIASV 52 (52)
T ss_dssp SEEEEEETTT-BEEEE
T ss_pred CeEEEEEcCCCeEEeC
Confidence 8999999999999764
No 58
>PF13670 PepSY_2: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification.
Probab=23.51 E-value=55 Score=23.98 Aligned_cols=12 Identities=33% Similarity=0.747 Sum_probs=10.9
Q ss_pred EEEEcCCCcEEE
Q psy654 74 ITIDKATGKITR 85 (224)
Q Consensus 74 I~Id~~tG~v~r 85 (224)
|++|+.||+|.+
T Consensus 70 v~vD~~tG~V~~ 81 (83)
T PF13670_consen 70 VYVDPATGEVVK 81 (83)
T ss_pred EEEcCCCCeEee
Confidence 799999999976
No 59
>cd00528 MoaC MoaC family. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis.
Probab=23.44 E-value=60 Score=27.38 Aligned_cols=35 Identities=23% Similarity=0.414 Sum_probs=30.7
Q ss_pred EEEEecCceeeeeccHHHHHHHHHccccccceEEE
Q psy654 42 LTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITI 76 (224)
Q Consensus 42 itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~I 76 (224)
.|.++.--+-...+.++.+++|....+..|||+..
T Consensus 9 ~t~R~A~A~g~i~l~~~~~~~i~~~~~~KGdvl~~ 43 (136)
T cd00528 9 VTERTAVAEGRVRLSPETLDLIREGQLPKGDVLAV 43 (136)
T ss_pred CceeEEEEEEEEEECHHHHHHHHhCCCCCccHHHH
Confidence 46677777888899999999999999999999865
No 60
>PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional
Probab=23.37 E-value=44 Score=27.33 Aligned_cols=24 Identities=17% Similarity=0.232 Sum_probs=21.3
Q ss_pred ccccccceEEEEcCCCcEEEeecc
Q psy654 66 EKVQAGDVITIDKATGKITRLGRS 89 (224)
Q Consensus 66 ekV~~GDVI~Id~~tG~v~rlGRs 89 (224)
..+++||.+.||..+=.|+.+|..
T Consensus 50 ~~i~~Gd~l~i~~~~Y~ItaVG~~ 73 (120)
T PRK10377 50 GALQPGLQFELGQHRYPVTAVGSV 73 (120)
T ss_pred CccCCCCEEEECCEEEEEEEEhHH
Confidence 458999999999999999999943
No 61
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=23.15 E-value=2.1e+02 Score=18.24 Aligned_cols=57 Identities=25% Similarity=0.324 Sum_probs=37.7
Q ss_pred EEEEEEEEEccCCCCCCCeEEEEEEEecC-ceeeeeccHHHHHHHHHccccccceEEEEcCCCcEE
Q psy654 20 EGEVVEIQIERPATGLGSKVGKLTMKTTE-METSYDLGAKMIEAIGKEKVQAGDVITIDKATGKIT 84 (224)
Q Consensus 20 EGeVvei~i~~~~~~~~~~v~~itLkT~~-~e~~~~lg~~m~e~l~kekV~~GDVI~Id~~tG~v~ 84 (224)
.|.|+++.-... |.....++|.-.. +.-...+-+..++.+ ...++.|+++.|. |++.
T Consensus 3 ~g~v~~~~~~~~----~~~~~~~~l~D~~~~~i~~~~~~~~~~~~-~~~~~~g~~v~v~---g~v~ 60 (75)
T cd03524 3 VGIVVAVEEIRT----EGKVLIFTLTDGTGGTIRVTLFGELAEEL-ENLLKEGQVVYIK---GKVK 60 (75)
T ss_pred EEEEEeeccccc----CCeEEEEEEEcCCCCEEEEEEEchHHHHH-HhhccCCCEEEEE---EEEE
Confidence 577777754332 4456777776544 556666667766654 4568999999995 6664
No 62
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=22.90 E-value=98 Score=20.75 Aligned_cols=14 Identities=29% Similarity=0.513 Sum_probs=11.9
Q ss_pred cccccceEEEEcCC
Q psy654 67 KVQAGDVITIDKAT 80 (224)
Q Consensus 67 kV~~GDVI~Id~~t 80 (224)
.+++||.++|.+.+
T Consensus 40 ~l~~Gd~~~i~~~~ 53 (71)
T PF07883_consen 40 ELKPGDAIYIPPGV 53 (71)
T ss_dssp EEETTEEEEEETTS
T ss_pred EccCCEEEEECCCC
Confidence 66889999999874
No 63
>PRK12343 putative molybdenum cofactor biosynthesis protein MoaC; Reviewed
Probab=22.31 E-value=64 Score=27.74 Aligned_cols=35 Identities=26% Similarity=0.349 Sum_probs=32.2
Q ss_pred EEEEecCceeeeeccHHHHHHHHHccccccceEEE
Q psy654 42 LTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITI 76 (224)
Q Consensus 42 itLkT~~~e~~~~lg~~m~e~l~kekV~~GDVI~I 76 (224)
.|.+|.--+-...+.+..+++|.+..+..|||+..
T Consensus 17 ~t~R~A~A~g~i~~~~~~~~~i~~~~~~KGdvl~~ 51 (151)
T PRK12343 17 DVLRIAVAEGFIKLKPETIEAIREGEVEKGNVLAT 51 (151)
T ss_pred CceEEEEEEEEEEECHHHHHHHHhCCCCCccHHHH
Confidence 68888888999999999999999999999999865
No 64
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970.
Probab=22.31 E-value=67 Score=23.19 Aligned_cols=16 Identities=38% Similarity=0.663 Sum_probs=13.8
Q ss_pred cccccceEEEEcCCCc
Q psy654 67 KVQAGDVITIDKATGK 82 (224)
Q Consensus 67 kV~~GDVI~Id~~tG~ 82 (224)
=|+.||.|-||-.+|.
T Consensus 37 FI~~Gd~I~V~T~~g~ 52 (56)
T smart00841 37 FINEGDKIKVDTRTGE 52 (56)
T ss_pred cccCCCEEEEECCCCc
Confidence 3688999999999885
No 65
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=22.18 E-value=1e+02 Score=22.97 Aligned_cols=32 Identities=9% Similarity=0.308 Sum_probs=25.2
Q ss_pred eeeeeccHHHHHHHHHccccccceEEEEcCCCcEE
Q psy654 50 ETSYDLGAKMIEAIGKEKVQAGDVITIDKATGKIT 84 (224)
Q Consensus 50 e~~~~lg~~m~e~l~kekV~~GDVI~Id~~tG~v~ 84 (224)
+-.+.+.++-+ .+.+|+.||.|.|.-..|+++
T Consensus 34 ~~~v~in~~dA---~~lgi~~Gd~V~v~~~~G~~~ 65 (116)
T cd02790 34 EEYVEINPEDA---KRLGIEDGEKVRVSSRRGSVE 65 (116)
T ss_pred CcEEEECHHHH---HHcCCCCCCEEEEEcCCEEEE
Confidence 44567777655 456899999999999999875
No 66
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=21.98 E-value=62 Score=30.99 Aligned_cols=36 Identities=22% Similarity=0.310 Sum_probs=30.2
Q ss_pred ceeeeeccHHHHHHHHHccccccceEEEEcCCCcEE
Q psy654 49 METSYDLGAKMIEAIGKEKVQAGDVITIDKATGKIT 84 (224)
Q Consensus 49 ~e~~~~lg~~m~e~l~kekV~~GDVI~Id~~tG~v~ 84 (224)
++--+|+|.+=-|.-.+.||++||.|.+|..+-...
T Consensus 135 ~el~iDiga~skeea~~lGI~vGd~v~~~~~~~~l~ 170 (355)
T COG1363 135 DELFIDIGASSKEEAEELGIRVGDFVVFDPRFRELA 170 (355)
T ss_pred hhEEEECCcCCHHHHHhcCCCCCCEEEEcCceEEec
Confidence 556689999999999999999999999998764443
No 67
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=21.87 E-value=1.1e+02 Score=23.00 Aligned_cols=32 Identities=19% Similarity=0.318 Sum_probs=25.7
Q ss_pred eeeeeccHHHHHHHHHccccccceEEEEcCCCcEE
Q psy654 50 ETSYDLGAKMIEAIGKEKVQAGDVITIDKATGKIT 84 (224)
Q Consensus 50 e~~~~lg~~m~e~l~kekV~~GDVI~Id~~tG~v~ 84 (224)
+-...+.|+-+++ .+|+.||.|.|....|+++
T Consensus 30 ~~~v~i~p~dA~~---lgi~~Gd~V~v~s~~G~~~ 61 (116)
T cd02786 30 EPTLLIHPADAAA---RGIADGDLVVVFNDRGSVT 61 (116)
T ss_pred CCEEEECHHHHHH---cCCCCCCEEEEEcCCeEEE
Confidence 3456778877655 5899999999999999886
No 68
>PF05343 Peptidase_M42: M42 glutamyl aminopeptidase; InterPro: IPR008007 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M42 (glutamyl aminopeptidase family, clan MH). For members of this family and family M28 the predicted metal ligands occur in the same order in the sequence: H, D, E, D/E, H; and the active site residues occur in the motifs HXD and EE. ; PDB: 2WYR_C 2CF4_A 1VHO_A 3ISX_A 3KL9_G 1YLO_F 3CPX_C 1VHE_A 2GRE_F 1XFO_A ....
Probab=21.66 E-value=64 Score=29.49 Aligned_cols=42 Identities=21% Similarity=0.364 Sum_probs=27.6
Q ss_pred ceeeeeccHHHHHHHHHccccccceEEEEcCCCcE---EEeeccc
Q psy654 49 METSYDLGAKMIEAIGKEKVQAGDVITIDKATGKI---TRLGRSF 90 (224)
Q Consensus 49 ~e~~~~lg~~m~e~l~kekV~~GDVI~Id~~tG~v---~rlGRs~ 90 (224)
++--+|+|.+=.|+..+.||++||.+..|...-.. .-.||+.
T Consensus 89 ~~l~iDiGa~s~ee~~~~GV~iGd~v~~~~~~~~~~~~~i~gkal 133 (292)
T PF05343_consen 89 DDLFIDIGASSKEEVEELGVRIGDPVVFDPPFRELGNGRIVGKAL 133 (292)
T ss_dssp GGEEEECSGSSHHHHHHTTS-TT-EEEES---EEETTTEEEETTH
T ss_pred ceEEEEeccCCHHHHHhCCCCCCCEEeecCCeEEeCCCEEEEEeC
Confidence 34468999988888999999999999999865332 1455553
No 69
>PRK11465 putative mechanosensitive channel protein; Provisional
Probab=21.37 E-value=64 Score=33.88 Aligned_cols=35 Identities=23% Similarity=0.352 Sum_probs=30.3
Q ss_pred HHccccccceEEEEcCCCcEEEeeccccccccccc
Q psy654 64 GKEKVQAGDVITIDKATGKITRLGRSFTRARDYDA 98 (224)
Q Consensus 64 ~kekV~~GDVI~Id~~tG~v~rlGRs~~~a~~yD~ 98 (224)
...-.++||.|.++..+|.|.++|=-.++-+++|-
T Consensus 570 ~e~pf~vGD~I~v~g~~GtVe~I~lRsT~iRt~dg 604 (741)
T PRK11465 570 FENGMNTGDLVTIGPLTGTVERMSIRSVGVRQDTG 604 (741)
T ss_pred HcCCcCCCCEEEECCeEEEEEEEeeeEEEEEcCCC
Confidence 44567899999999999999999977788888873
No 70
>TIGR00849 gutA PTS system, glucitol/sorbitol-specific IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria.The system in E.Coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component.
Probab=21.35 E-value=51 Score=27.03 Aligned_cols=23 Identities=22% Similarity=0.368 Sum_probs=20.9
Q ss_pred cccccceEEEEcCCCcEEEeecc
Q psy654 67 KVQAGDVITIDKATGKITRLGRS 89 (224)
Q Consensus 67 kV~~GDVI~Id~~tG~v~rlGRs 89 (224)
.+++||.+.||..+=.|+.+|..
T Consensus 51 ~i~~Gd~l~i~~~~Y~ItaVG~~ 73 (121)
T TIGR00849 51 TLKPGQVFMIGGIAYPVTAVGDV 73 (121)
T ss_pred CcCCCCEEEECCEEEEEEEEhHH
Confidence 58999999999999999999953
No 71
>TIGR02084 leud 3-isopropylmalate dehydratase, small subunit. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain. The members of the seed for this model are those sequences which are gene clustered with other genes involved in leucine biosynthesis and include some archaea.
Probab=20.85 E-value=1.4e+02 Score=25.31 Aligned_cols=27 Identities=26% Similarity=0.503 Sum_probs=21.6
Q ss_pred ccHHHHHHHHHccccccceEEEEcCCCcEEEe
Q psy654 55 LGAKMIEAIGKEKVQAGDVITIDKATGKITRL 86 (224)
Q Consensus 55 lg~~m~e~l~kekV~~GDVI~Id~~tG~v~rl 86 (224)
+.+..++.| +.||.|.||-++|.|+..
T Consensus 100 ~~~~~~~~l-----~~gd~i~idl~~~~v~~~ 126 (156)
T TIGR02084 100 ESEEAVDEI-----EEGDEVEVDLEKGIIKNL 126 (156)
T ss_pred cCHHHHHHh-----CCCCEEEEECCCCEEEEe
Confidence 456666654 699999999999999766
No 72
>COG3848 Phosphohistidine swiveling domain [Signal transduction mechanisms]
Probab=20.77 E-value=80 Score=26.04 Aligned_cols=19 Identities=21% Similarity=0.562 Sum_probs=17.0
Q ss_pred ccccccceEEEEcCCCcEE
Q psy654 66 EKVQAGDVITIDKATGKIT 84 (224)
Q Consensus 66 ekV~~GDVI~Id~~tG~v~ 84 (224)
..|+.|+.|++|.+.|.|.
T Consensus 86 ~~i~dG~~vTvD~~rG~VY 104 (111)
T COG3848 86 QLIRDGAIVTVDAQRGVVY 104 (111)
T ss_pred hhccCCCEEEEecccceEE
Confidence 3678999999999999985
No 73
>PF11495 Regulator_TrmB: Archaeal transcriptional regulator TrmB; InterPro: IPR021586 TrmB is an alpha-glucoside sensing transcriptional regulator. The protein is the transcriptional repressor for gene cluster encoding trehalose/maltose ABC transporter in T.litoralis and P.furiosus []. TrmB has lost its DNA binding domain but retained its sugar recognition site. A nonreducing glucosyl residue is shared by all substrates bound to TrmB which suggests that its a common recognition motif []. ; PDB: 3QPH_A 2F5T_X.
Probab=20.55 E-value=2.5e+02 Score=24.27 Aligned_cols=36 Identities=25% Similarity=0.412 Sum_probs=24.8
Q ss_pred eeeEEEEEEEEEEEccCCCCCCCeEEEEEEEecCceeeeeccH
Q psy654 15 ETEMIEGEVVEIQIERPATGLGSKVGKLTMKTTEMETSYDLGA 57 (224)
Q Consensus 15 ~~ev~EGeVvei~i~~~~~~~~~~v~~itLkT~~~e~~~~lg~ 57 (224)
+...++|+|+++..+.. +-++.++++|.++ +|.+|-
T Consensus 181 ~~~~i~G~v~~~~~~~~-----~~~~~~~vet~~g--~~~VGG 216 (233)
T PF11495_consen 181 EPVTITGRVVDVRFNSF-----PGVASFTVETDDG--EVTVGG 216 (233)
T ss_dssp -EEEEEEEEEEEEEETT-----TTEEEEEEEETTE--EEEEE-
T ss_pred CceEEEEEEEEEEeccC-----CceeEEEEEeCCc--eEEecC
Confidence 34567999999875442 2367899999887 666664
No 74
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=20.53 E-value=1.2e+02 Score=22.67 Aligned_cols=32 Identities=13% Similarity=0.354 Sum_probs=25.3
Q ss_pred eeeeeccHHHHHHHHHccccccceEEEEcCCCcEE
Q psy654 50 ETSYDLGAKMIEAIGKEKVQAGDVITIDKATGKIT 84 (224)
Q Consensus 50 e~~~~lg~~m~e~l~kekV~~GDVI~Id~~tG~v~ 84 (224)
+-.+.+.|+-+ .+.+++.||.|.|.-..|+++
T Consensus 34 ~~~v~inp~dA---~~lgi~~Gd~V~v~~~~G~~~ 65 (120)
T cd00508 34 EPFVEIHPEDA---ARLGIKDGDLVRVSSRRGSVV 65 (120)
T ss_pred CCEEEECHHHH---HHcCCCCCCEEEEEeCCEEEE
Confidence 34567777654 456899999999999999876
No 75
>cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=20.51 E-value=1.2e+02 Score=23.31 Aligned_cols=31 Identities=13% Similarity=0.294 Sum_probs=25.4
Q ss_pred eeeeccHHHHHHHHHccccccceEEEEcCCCcEE
Q psy654 51 TSYDLGAKMIEAIGKEKVQAGDVITIDKATGKIT 84 (224)
Q Consensus 51 ~~~~lg~~m~e~l~kekV~~GDVI~Id~~tG~v~ 84 (224)
-...+.|+.+++ .+|+.||.|.|....|+|+
T Consensus 32 ~~v~i~p~dA~~---~gi~~Gd~V~v~s~~G~i~ 62 (124)
T cd02785 32 PRVKINPIDAAA---RGIAHGDLVEVYNDRGSVV 62 (124)
T ss_pred CeEEECHHHHHH---cCCCCCCEEEEEeCCCEEE
Confidence 356777877655 5899999999999999886
No 76
>PF00501 AMP-binding: AMP-binding enzyme; InterPro: IPR000873 A number of prokaryotic and eukaryotic enzymes, which appear to act via an ATP-dependent covalent binding of AMP to their substrate, share a region of sequence similarity [, , ]. This region is a Ser/Thr/Gly-rich domain that is further characterised by a conserved Pro-Lys-Gly triplet. The family of enzymes includes luciferase, long chain fatty acid Co-A ligase, acetyl-CoA synthetase and various other closely-related synthetases.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2V7B_A 2Y4O_B 2VSQ_A 3L8C_B 1RY2_A 3KXW_A 3LNV_A 3ETC_B 3A9U_A 3A9V_A ....
Probab=20.19 E-value=2e+02 Score=25.46 Aligned_cols=52 Identities=21% Similarity=0.311 Sum_probs=37.4
Q ss_pred EEEEEEEecCceeeeeccHHHHH-HHHH-ccccccceEEEEcCCCcEEEeecccc
Q psy654 39 VGKLTMKTTEMETSYDLGAKMIE-AIGK-EKVQAGDVITIDKATGKITRLGRSFT 91 (224)
Q Consensus 39 v~~itLkT~~~e~~~~lg~~m~e-~l~k-ekV~~GDVI~Id~~tG~v~rlGRs~~ 91 (224)
.|.|-++..-....|-=.++..+ ++.. .=..-||+.++|+. |.+.-+||++.
T Consensus 359 ~Gei~i~~~~~~~gy~~~~~~~~~~~~~~~~~~TGD~g~~d~~-G~~~~~GR~~~ 412 (417)
T PF00501_consen 359 PGEIVIRGPNVFSGYYNDPELTAEAFIDDGWYRTGDLGRLDED-GYLYILGRSDD 412 (417)
T ss_dssp EEEEEEESTTSBSEETTBHHHHHHHEETTSEEEEEEEEEEETT-SEEEEEEEGSC
T ss_pred cccccccCCccceeeeccccccccccccccceecceEEEECCC-CeEEEEEeeCC
Confidence 48888887665555544444443 3432 25899999999977 99999999873
No 77
>PRK14736 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=20.17 E-value=4.7e+02 Score=21.39 Aligned_cols=73 Identities=16% Similarity=0.208 Sum_probs=47.7
Q ss_pred EeeeEEEEEEEEEEEccCCCCCC------CeE-----EEEEEEecCcee-eeeccHHHHHHHHHccccccceEEEEcCCC
Q psy654 14 EETEMIEGEVVEIQIERPATGLG------SKV-----GKLTMKTTEMET-SYDLGAKMIEAIGKEKVQAGDVITIDKATG 81 (224)
Q Consensus 14 E~~ev~EGeVvei~i~~~~~~~~------~~v-----~~itLkT~~~e~-~~~lg~~m~e~l~kekV~~GDVI~Id~~tG 81 (224)
=++.+|+|+|..+.+.-..+.+| |.+ |.+++++.+++. .|- -.|=++.++++
T Consensus 11 P~~~~~~~~v~~V~vp~~~G~~gILp~H~P~it~L~~G~l~i~~~~~~~~~~~--------------v~gGf~eV~~n-- 74 (133)
T PRK14736 11 PERTLYSGEVEAVQLPGSEGEMTVLPGHAPVLTTLKVGVITVTETTGNGKRIY--------------VRGGFAEIGPT-- 74 (133)
T ss_pred CCccEEeeeeEEEEEecCccCeeEcCCChhhEeEecceEEEEEECCCcEEEEE--------------EeceEEEEECC--
Confidence 46688999999998866555443 222 667777655443 332 23667888777
Q ss_pred cEEEeeccccccccccccccc
Q psy654 82 KITRLGRSFTRARDYDATGAQ 102 (224)
Q Consensus 82 ~v~rlGRs~~~a~~yD~~~~~ 102 (224)
+|+-+--....+.+.|....+
T Consensus 75 ~v~Ila~~ae~~eeID~~~a~ 95 (133)
T PRK14736 75 SVTVLAERAAPVEELTPEMID 95 (133)
T ss_pred EEEEEeeeeEEhhhCCHHHHH
Confidence 677777656677777765443
Done!