Query 025704
Match_columns 249
No_of_seqs 56 out of 58
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 08:38:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025704.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025704hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12827 Peroxin-22: Peroxisom 94.7 0.0053 1.1E-07 50.7 -1.2 46 179-224 68-117 (117)
2 COG4502 5'(3')-deoxyribonucleo 84.4 3.4 7.5E-05 36.5 6.4 76 126-213 65-142 (180)
3 cd08556 GDPD Glycerophosphodie 81.9 2.7 5.8E-05 34.0 4.6 64 132-204 49-116 (189)
4 cd08562 GDPD_EcUgpQ_like Glyce 77.6 3.8 8.3E-05 34.8 4.4 63 136-204 90-157 (229)
5 cd08582 GDPD_like_2 Glyceropho 69.9 8 0.00017 33.4 4.6 62 135-202 89-154 (233)
6 PF06941 NT5C: 5' nucleotidase 69.6 8.3 0.00018 32.4 4.5 89 126-225 70-163 (191)
7 COG0144 Sun tRNA and rRNA cyto 63.4 7.9 0.00017 36.7 3.5 96 109-207 239-344 (355)
8 PF01644 Chitin_synth_1: Chiti 60.6 20 0.00044 31.4 5.3 29 176-204 105-143 (163)
9 cd08563 GDPD_TtGDE_like Glycer 55.4 20 0.00043 30.9 4.3 58 140-204 96-158 (230)
10 cd08579 GDPD_memb_like Glycero 54.4 24 0.00052 30.2 4.7 60 138-204 88-152 (220)
11 cd08567 GDPD_SpGDE_like Glycer 53.6 19 0.00042 31.2 4.0 66 131-204 109-188 (263)
12 PF04246 RseC_MucC: Positive r 52.2 14 0.00031 29.9 2.8 28 13-40 97-124 (135)
13 TIGR03510 XapX XapX domain. Th 51.2 18 0.0004 26.1 2.9 23 17-39 4-26 (49)
14 TIGR03778 VPDSG_CTERM VPDSG-CT 50.7 20 0.00043 23.1 2.6 21 12-32 2-22 (26)
15 cd08601 GDPD_SaGlpQ_like Glyce 48.3 38 0.00082 29.7 5.0 44 158-202 127-170 (256)
16 cd01028 TOPRIM_TopoIA TOPRIM_T 47.8 1.2E+02 0.0025 24.8 7.5 95 89-186 7-129 (142)
17 cd08564 GDPD_GsGDE_like Glycer 47.8 41 0.00089 29.9 5.2 49 146-201 120-171 (265)
18 cd08573 GDPD_GDE1 Glycerophosp 46.4 37 0.0008 30.4 4.7 63 136-204 92-156 (258)
19 TIGR02250 FCP1_euk FCP1-like p 44.3 1.4E+02 0.0031 25.1 7.7 55 126-187 55-110 (156)
20 PF13419 HAD_2: Haloacid dehal 44.1 1.3E+02 0.0028 23.1 6.9 58 125-191 73-131 (176)
21 PF01751 Toprim: Toprim domain 41.0 1.2E+02 0.0027 22.9 6.3 76 90-167 7-82 (100)
22 PF01102 Glycophorin_A: Glycop 40.9 24 0.00053 29.5 2.5 19 17-35 71-89 (122)
23 PRK07066 3-hydroxybutyryl-CoA 40.3 95 0.0021 29.4 6.7 73 140-220 79-174 (321)
24 TIGR03190 benz_CoA_bzdN benzoy 38.9 9 0.0002 36.4 -0.3 70 136-208 276-353 (377)
25 PF01171 ATP_bind_3: PP-loop f 38.8 68 0.0015 26.8 4.9 67 130-205 80-148 (182)
26 cd08561 GDPD_cytoplasmic_ScUgp 38.6 93 0.002 27.2 5.9 57 146-209 106-164 (249)
27 cd01427 HAD_like Haloacid deha 35.0 1.2E+02 0.0027 21.8 5.3 60 108-171 3-63 (139)
28 PF10389 CoatB: Bacteriophage 34.8 29 0.00063 24.9 1.8 11 27-37 35-45 (46)
29 PRK11009 aphA acid phosphatase 34.7 2.4E+02 0.0053 25.5 8.1 110 90-205 48-191 (237)
30 cd08568 GDPD_TmGDE_like Glycer 34.6 71 0.0015 27.6 4.5 52 146-204 92-143 (226)
31 cd08565 GDPD_pAtGDE_like Glyce 33.8 78 0.0017 27.9 4.7 60 135-202 84-150 (235)
32 COG4317 Uncharacterized protei 33.4 47 0.001 26.9 2.9 20 19-38 8-27 (93)
33 PF03672 UPF0154: Uncharacteri 31.6 55 0.0012 24.9 2.9 19 17-35 9-27 (64)
34 PRK06129 3-hydroxyacyl-CoA deh 30.5 1.6E+02 0.0035 26.8 6.3 88 140-235 78-192 (308)
35 PF12732 YtxH: YtxH-like prote 29.7 38 0.00082 25.0 1.8 14 17-30 7-20 (74)
36 cd04885 ACT_ThrD-I Tandem C-te 29.6 89 0.0019 22.2 3.6 30 142-171 35-64 (68)
37 TIGR02245 HAD_IIID1 HAD-superf 29.2 4E+02 0.0088 23.6 8.4 76 103-186 20-95 (195)
38 PF13844 Glyco_transf_41: Glyc 28.3 1.3E+02 0.0028 30.3 5.7 99 126-232 293-399 (468)
39 cd03362 TOPRIM_TopoIA_TopoIII 28.3 3.1E+02 0.0067 22.6 7.2 79 107-187 42-139 (151)
40 cd08566 GDPD_AtGDE_like Glycer 27.5 1.2E+02 0.0027 26.7 4.9 48 147-202 101-148 (240)
41 PF05729 NACHT: NACHT domain 27.0 1.1E+02 0.0024 23.5 4.1 44 177-220 118-165 (166)
42 TIGR03593 yidC_nterm membrane 26.7 1.3E+02 0.0029 28.0 5.2 19 22-40 9-27 (366)
43 cd04906 ACT_ThrD-I_1 First of 26.6 1E+02 0.0023 23.0 3.7 29 143-171 38-67 (85)
44 cd08559 GDPD_periplasmic_GlpQ_ 26.2 1.3E+02 0.0028 27.5 4.9 53 146-202 128-188 (296)
45 PRK09260 3-hydroxybutyryl-CoA 25.8 1.5E+02 0.0034 26.5 5.3 43 139-188 76-118 (288)
46 PF00891 Methyltransf_2: O-met 25.7 49 0.0011 28.6 2.0 27 141-168 156-182 (241)
47 cd08570 GDPD_YPL206cp_fungi Gl 25.3 1.4E+02 0.003 26.0 4.7 65 135-202 85-156 (234)
48 cd03363 TOPRIM_TopoIA_TopoI TO 25.1 3.7E+02 0.0081 21.7 7.4 93 89-186 7-110 (123)
49 PF06295 DUF1043: Protein of u 25.0 65 0.0014 26.5 2.5 16 20-35 3-18 (128)
50 PF06295 DUF1043: Protein of u 24.1 49 0.0011 27.3 1.7 21 17-37 4-24 (128)
51 COG4218 MtrF Tetrahydromethano 22.9 71 0.0015 25.0 2.2 18 17-34 48-65 (73)
52 TIGR00550 nadA quinolinate syn 22.9 49 0.0011 31.4 1.6 94 132-225 4-111 (310)
53 COG0241 HisB Histidinol phosph 22.9 2.1E+02 0.0045 25.4 5.4 84 106-197 7-105 (181)
54 cd06660 Aldo_ket_red Aldo-keto 22.7 1.6E+02 0.0034 25.7 4.6 86 90-178 58-148 (285)
55 PF09527 ATPase_gene1: Putativ 22.6 96 0.0021 21.6 2.7 19 17-35 37-55 (55)
56 COG4980 GvpP Gas vesicle prote 22.5 57 0.0012 27.3 1.8 14 17-30 13-26 (115)
57 PRK08942 D,D-heptose 1,7-bisph 22.2 2.6E+02 0.0057 23.0 5.7 72 106-186 5-92 (181)
58 TIGR01261 hisB_Nterm histidino 22.1 2.9E+02 0.0063 23.1 6.0 69 111-185 8-91 (161)
59 PF08370 PDR_assoc: Plant PDR 22.1 1.2E+02 0.0026 22.9 3.3 26 15-40 31-60 (65)
60 KOG0121 Nuclear cap-binding pr 22.0 1.1E+02 0.0025 26.8 3.5 55 130-185 22-78 (153)
61 PF13940 Ldr_toxin: Toxin Ldr, 22.0 49 0.0011 22.6 1.0 26 5-32 6-31 (35)
62 PF14155 DUF4307: Domain of un 21.7 87 0.0019 25.3 2.6 27 11-37 3-29 (112)
63 PRK06049 rpl30p 50S ribosomal 21.4 1.7E+02 0.0036 25.4 4.5 67 147-218 2-70 (154)
64 PF12263 DUF3611: Protein of u 20.7 1.1E+02 0.0025 27.1 3.4 21 16-36 62-82 (183)
65 PRK01294 lipase chaperone; Pro 20.4 5.7E+02 0.012 24.6 8.1 21 79-99 89-110 (336)
66 PRK11677 hypothetical protein; 20.3 56 0.0012 27.8 1.3 19 18-36 5-23 (134)
67 cd01657 Ribosomal_L7_archeal_e 20.1 1.6E+02 0.0035 25.4 4.0 66 147-217 1-68 (159)
No 1
>PF12827 Peroxin-22: Peroxisomal biogenesis protein family; InterPro: IPR024359 Peroxin-22 is an integral peroxisomal membrane protein. The N terminus of peroxin-22 is located in the matrix, while the C terminus is located in the cytosol. Peroxin-22 interacts with the ubiquitin-conjugating enzyme Pex4p, anchoring it at the peroxisomal membrane. Both proteins may act at the same step in peroxisome biogenesis [].; PDB: 2Y9O_B 2Y9M_B 2Y9P_B.
Probab=94.74 E-value=0.0053 Score=50.69 Aligned_cols=46 Identities=30% Similarity=0.494 Sum_probs=33.2
Q ss_pred cceEEeeccccCcchheeecccceeecCCHH----HHHHHHhhccceeee
Q 025704 179 KDKVLFCSTEIGRTSFVRQLEPDWHIDTNPE----IVSQLARFIKYQLHI 224 (249)
Q Consensus 179 rhKVLFCST~~Gr~sfVRQLeP~lHIDtd~~----vv~~L~rfVp~lv~I 224 (249)
.|||+-|+|.+|+-|-+|||.|+.-+=...+ +=..|.||+.+++.|
T Consensus 68 ~~KiI~Cdt~~G~~~~vK~Lk~d~llv~~ddl~~~ip~Di~rfv~~Ii~i 117 (117)
T PF12827_consen 68 NYKIIKCDTMQGYWSCVKHLKPDQLLVCSDDLGISIPEDINRFVKNIINI 117 (117)
T ss_dssp GGGEEEESSHHHHHHHHHHH--SEEEE-GGGT-SSS-GGGGGT-SEEEE-
T ss_pred ceeEEEecchhhHHHHHHhcCCCceEEehhhccccCHHHHHHHHHhhccC
Confidence 6999999999999999999999988742211 334699999998765
No 2
>COG4502 5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism]
Probab=84.41 E-value=3.4 Score=36.54 Aligned_cols=76 Identities=24% Similarity=0.393 Sum_probs=57.7
Q ss_pred ccceeehhHHHHHHHHhhcCceEEEEEeeC--hhhHHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeeccccee
Q 025704 126 KQVTVKSSVLEALLEITKFCDLYLMERVLD--NESEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDWH 203 (249)
Q Consensus 126 ~~a~v~esa~e~LleLak~~DvYLm~~V~d--D~eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~lH 203 (249)
-+..++|-+-+++-||++.+|||+.+.-.| +.=|++--.++|.. .-|...+++|| |+-.+| +.++-
T Consensus 65 RnL~V~p~aq~v~keLt~~y~vYivtaamdhp~s~~dK~eWl~E~F-----PFi~~qn~vfC----gnKniv---kaDil 132 (180)
T COG4502 65 RNLGVQPFAQTVLKELTSIYNVYIVTAAMDHPKSCEDKGEWLKEKF-----PFISYQNIVFC----GNKNIV---KADIL 132 (180)
T ss_pred hhcCccccHHHHHHHHHhhheEEEEEeccCCchhHHHHHHHHHHHC-----CCCChhhEEEe----cCCCeE---EeeEE
Confidence 367889999999999999999999876633 44456677777774 36677999999 444444 57899
Q ss_pred ecCCHHHHHH
Q 025704 204 IDTNPEIVSQ 213 (249)
Q Consensus 204 IDtd~~vv~~ 213 (249)
||.++-.++-
T Consensus 133 IDDnp~nLE~ 142 (180)
T COG4502 133 IDDNPLNLEN 142 (180)
T ss_pred ecCCchhhhh
Confidence 9999865443
No 3
>cd08556 GDPD Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins. The typical glycerophosphodiester phosphodiesterase domain (GDPD) consists of a TIM barrel and a small insertion domain named the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. This family corresponds to both typical GDPD domain and GDPD-like domain which lacks the GDPD-I region. Members in this family mainly consist of a large family of prokaryotic and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), and a number of uncharacterized homologs. Sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria are also included in this family. GDPD plays an essential role in glycerol metabolism and catalyzes the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcoho
Probab=81.85 E-value=2.7 Score=34.02 Aligned_cols=64 Identities=22% Similarity=0.267 Sum_probs=46.1
Q ss_pred hhHHHHHHHHhhcCceEEEEEeeChh----hHHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccceee
Q 025704 132 SSVLEALLEITKFCDLYLMERVLDNE----SEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDWHI 204 (249)
Q Consensus 132 esa~e~LleLak~~DvYLm~~V~dD~----eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~lHI 204 (249)
+.--|+| ++.+. +++++.-++++. -.+.+++++++.| ..++|+|||........+|++.|.+.+
T Consensus 49 ~tL~e~l-~~~~~-~~~i~leiK~~~~~~~~~~~l~~~i~~~~-------~~~~v~i~s~~~~~l~~~~~~~p~~~~ 116 (189)
T cd08556 49 PTLEEVL-ELVKG-GVGLNIELKEPTRYPGLEAKVAELLREYG-------LEERVVVSSFDHEALRALKELDPEVPT 116 (189)
T ss_pred CCHHHHH-Hhccc-CcEEEEEECCCCCchhHHHHHHHHHHHcC-------CcCCEEEEeCCHHHHHHHHHhCCCCcE
Confidence 3334444 33333 899999999973 5678999999865 237999999887777777777776654
No 4
>cd08562 GDPD_EcUgpQ_like Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46), UgpQ, and similar proteins. GP-GDE plays an essential role in the metabolic pathway of E. coli. It catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols, which are major sources of carbon and phosphate. E. coli possesses two major G3P uptake systems: Glp and Ugp, which contain genes coding for two distinct GP-GDEs. UgpQ gene from the E. coli ugp operon codes for a cytosolic phosphodiesterase GlpQ, which is the prototype of this family. Various glycerophosphodiesters, such as glycerophosphocholine (GPC), glycerophosphoethanolanmine (GPE), glycerophosphoglycerol (GPG)
Probab=77.60 E-value=3.8 Score=34.82 Aligned_cols=63 Identities=19% Similarity=0.207 Sum_probs=47.1
Q ss_pred HHHHHHhhcCceEEEEEeeChhh-----HHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccceee
Q 025704 136 EALLEITKFCDLYLMERVLDNES-----EKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDWHI 204 (249)
Q Consensus 136 e~LleLak~~DvYLm~~V~dD~e-----E~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~lHI 204 (249)
+-++++.+..+++++.-++++.+ ++.+..++++.|.. .+||+|||-...-...+|++.|.+-+
T Consensus 90 ~evl~~~~~~~~~l~iEiK~~~~~~~~~~~~v~~~l~~~~~~------~~~v~~~Sf~~~~l~~~~~~~p~~~~ 157 (229)
T cd08562 90 ADVLELARELGLGLNLEIKPDPGDEALTARVVAAALRELWPH------ASKLLLSSFSLEALRAARRAAPELPL 157 (229)
T ss_pred HHHHHHHHhcCCEEEEEECCCCCccHHHHHHHHHHHHHhcCC------cCCEEEECCCHHHHHHHHHhCCCCcE
Confidence 33445666667888888887653 35688888886543 48999999998888999999987654
No 5
>cd08582 GDPD_like_2 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterase and similar proteins. They show high sequence similarity to Escherichia coli glycerophosphodiester phosphodiesterase, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=69.87 E-value=8 Score=33.38 Aligned_cols=62 Identities=26% Similarity=0.366 Sum_probs=44.8
Q ss_pred HHHHHHHhhcCceEEEEEeeCh----hhHHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccce
Q 025704 135 LEALLEITKFCDLYLMERVLDN----ESEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDW 202 (249)
Q Consensus 135 ~e~LleLak~~DvYLm~~V~dD----~eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~l 202 (249)
++-++++.+..++.|+.-++++ .-.+.+.++++++| ...+||+|+|-..-....+|++.|.+
T Consensus 89 L~evl~~~~~~~~~l~ieiK~~~~~~~~~~~~~~~~~~~~------~~~~~v~~~Sf~~~~l~~~~~~~p~~ 154 (233)
T cd08582 89 LEEYLAIVPKYGKKLFIEIKHPRRGPEAEEELLKLLKESG------LLPEQIVIISFDAEALKRVRELAPTL 154 (233)
T ss_pred HHHHHHHHHhcCceEEEEeCCCccCccHHHHHHHHHHHcC------CCCCCEEEEecCHHHHHHHHHHCCCC
Confidence 3334455555689999999963 33467888888864 34589999998887888888888873
No 6
>PF06941 NT5C: 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); InterPro: IPR010708 This family consists of several 5' nucleotidase, deoxy (Pyrimidine), and cytosolic type C (NT5C) proteins. 5'(3')-deoxyribonucleotidase is a ubiquitous enzyme in mammalian cells whose physiological function is not known [].; GO: 0016791 phosphatase activity; PDB: 1Z4M_A 1Q92_A 1Q91_A 1Z4J_A 1Z4I_A 1Z4Q_A 1Z4K_A 2JAW_A 1MH9_A 1Z4L_A ....
Probab=69.59 E-value=8.3 Score=32.45 Aligned_cols=89 Identities=19% Similarity=0.196 Sum_probs=52.9
Q ss_pred ccceeehhHHHHHHHHhhcC-ceEEEEEeeCh-h--hHHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccc
Q 025704 126 KQVTVKSSVLEALLEITKFC-DLYLMERVLDN-E--SEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPD 201 (249)
Q Consensus 126 ~~a~v~esa~e~LleLak~~-DvYLm~~V~dD-~--eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~ 201 (249)
.+....+.|.|+|.+|.+.. .++.|+.-..+ . .++.-.+-|++. |. ++..+++.||.. | + .+..+
T Consensus 70 ~~l~p~~gA~e~l~~L~~~g~~~~~Itar~~~~~~~~~~~k~~Wl~~h--f~--~i~~~~~~~~~~---K-~---~v~~D 138 (191)
T PF06941_consen 70 SNLPPIPGAVEALKKLRDKGHEIVIITARPPEFPDHSAEEKREWLERH--FP--FIPYDNLIFTGD---K-T---LVGGD 138 (191)
T ss_dssp TT--B-TTHHHHHHHHHTSTTEEEEEEE-SSSSGCCCHHHHHHHHHHH--HT--HHHHCCEEEESS---G-G---GC--S
T ss_pred cCCCccHHHHHHHHHHHHcCCcEEEEEecCccccchHHHHHHHHHHHH--cC--CCchheEEEecC---C-C---eEecc
Confidence 35677899999999999996 55555555444 1 233334455553 22 555688999843 2 2 45789
Q ss_pred eeecCCHHHHHHHH-hhccceeeec
Q 025704 202 WHIDTNPEIVSQLA-RFIKYQLHIS 225 (249)
Q Consensus 202 lHIDtd~~vv~~L~-rfVp~lv~I~ 225 (249)
+.||-++..+..+. .-+|-+|+=.
T Consensus 139 vlIDD~~~n~~~~~~~g~~~iLfd~ 163 (191)
T PF06941_consen 139 VLIDDRPHNLEQFANAGIPVILFDQ 163 (191)
T ss_dssp EEEESSSHHHSS-SSESSEEEEE--
T ss_pred EEecCChHHHHhccCCCceEEEEcC
Confidence 99999999998875 4455555543
No 7
>COG0144 Sun tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]
Probab=63.45 E-value=7.9 Score=36.69 Aligned_cols=96 Identities=24% Similarity=0.222 Sum_probs=67.2
Q ss_pred Eeeccee------eccCChhhhhccceeehhHHHHHHHHhhcC--ceEEEEEeeChhhHHHHHHHHHHcCCcCC--CCcc
Q 025704 109 CRLLGVI------LEESCPEELQKQVTVKSSVLEALLEITKFC--DLYLMERVLDNESEKKVLLALETAGVFTS--GGLV 178 (249)
Q Consensus 109 is~~gvv------l~e~sp~el~~~a~v~esa~e~LleLak~~--DvYLm~~V~dD~eE~~Vl~lLe~~GlF~~--gGL~ 178 (249)
||-.|++ .|+.+++++.+-+.++.+.++.-..+.|-. =||--|.+.-.|.|++|..+|++...|.- .++.
T Consensus 239 CSg~G~irr~Pd~~~~~~~~~i~~l~~lQ~~iL~~a~~~lk~GG~LVYSTCS~~~eENE~vV~~~L~~~~~~~~~~~~~~ 318 (355)
T COG0144 239 CSGTGVIRRDPDVKWRRTPEDIAELAKLQKEILAAALKLLKPGGVLVYSTCSLTPEENEEVVERFLERHPDFELEPVRLP 318 (355)
T ss_pred CCCCcccccCccccccCCHHHHHHHHHHHHHHHHHHHHhcCCCCEEEEEccCCchhcCHHHHHHHHHhCCCceeeccccc
Confidence 7888887 677788888888888888888888888775 47888999999999999999998655431 0111
Q ss_pred cceEEeeccccCcchheeecccceeecCC
Q 025704 179 KDKVLFCSTEIGRTSFVRQLEPDWHIDTN 207 (249)
Q Consensus 179 rhKVLFCST~~Gr~sfVRQLeP~lHIDtd 207 (249)
-.. ++.-.......++++-|..| ++|
T Consensus 319 ~~~--~~~~~~~~~~~~~r~~p~~~-~~d 344 (355)
T COG0144 319 WGP--LFEGLGSELGKTRRLYPHVH-GTD 344 (355)
T ss_pred ccc--cccccccccCCeEEECCCCC-CCC
Confidence 000 22221123445789999998 444
No 8
>PF01644 Chitin_synth_1: Chitin synthase; InterPro: IPR004834 This region is found commonly in chitin synthases classes I, II and III 2.4.1.16 from EC. Chitin a linear homopolymer of GlcNAc residues, it is an important component of the cell wall of fungi and is synthesised on the cytoplasmic surface of the cell membrane by membrane bound chitin synthases []. ; GO: 0004100 chitin synthase activity, 0006031 chitin biosynthetic process
Probab=60.58 E-value=20 Score=31.38 Aligned_cols=29 Identities=31% Similarity=0.678 Sum_probs=22.3
Q ss_pred CcccceEEeeccccCc----------chheeecccceee
Q 025704 176 GLVKDKVLFCSTEIGR----------TSFVRQLEPDWHI 204 (249)
Q Consensus 176 GL~rhKVLFCST~~Gr----------~sfVRQLeP~lHI 204 (249)
|..+=.+|||-.++=+ -+|+|||+|.+.|
T Consensus 105 ~~~PvQ~ifclKe~N~kKinSHrWfFnaf~~~l~P~vcv 143 (163)
T PF01644_consen 105 NIVPVQIIFCLKEKNAKKINSHRWFFNAFCRQLQPNVCV 143 (163)
T ss_pred CCCCEEEEEEeccccccccchhhHHHHHHHhhcCCcEEE
Confidence 6677789999877643 3799999998754
No 9
>cd08563 GDPD_TtGDE_like Glycerophosphodiester phosphodiesterase domain of Thermoanaerobacter tengcongensis and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermoanaerobacter tengcongensis glycerophosphodiester phosphodiesterase (TtGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. Despite the fact that most of GDPD family members exist as the monomer, TtGDE can function as a dimeric unit. Its catalytic mechanism is based on the general base-acid catalysis, which is similar to that of phosphoinositide-specific phospholipases C (PI-PLCs, EC 3.1.4.11). A divalent metal cation is required for the enzyme activity of TtGDE.
Probab=55.36 E-value=20 Score=30.88 Aligned_cols=58 Identities=26% Similarity=0.356 Sum_probs=43.5
Q ss_pred HHhhcCceEEEEEeeChhh-----HHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccceee
Q 025704 140 EITKFCDLYLMERVLDNES-----EKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDWHI 204 (249)
Q Consensus 140 eLak~~DvYLm~~V~dD~e-----E~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~lHI 204 (249)
++.+.-+++++.-++++.. ++.+.++++++| ..+++++.|-..-....+|++.|.+.+
T Consensus 96 ~~~~~~~~~l~leiK~~~~~~~~~~~~l~~~l~~~~-------~~~~v~~~Sf~~~~l~~~~~~~p~~~~ 158 (230)
T cd08563 96 DLLKDKDLLLNIEIKTDVIHYPGIEKKVLELVKEYN-------LEDRVIFSSFNHESLKRLKKLDPKIKL 158 (230)
T ss_pred HHHHhcCcEEEEEECCCCCcChhHHHHHHHHHHHcC-------CCCCEEEEcCCHHHHHHHHHHCCCCcE
Confidence 4444457888888887643 467888888865 236899999888888889999997543
No 10
>cd08579 GDPD_memb_like Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in uncharacterized bacterial glycerophosphodiester phosphodiesterases. In addition to a C-terminal GDPD domain, most members in this family have an N-terminus that functions as a membrane anchor.
Probab=54.36 E-value=24 Score=30.18 Aligned_cols=60 Identities=13% Similarity=0.086 Sum_probs=41.8
Q ss_pred HHHHhhcCceEEEEEeeChh-----hHHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccceee
Q 025704 138 LLEITKFCDLYLMERVLDNE-----SEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDWHI 204 (249)
Q Consensus 138 LleLak~~DvYLm~~V~dD~-----eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~lHI 204 (249)
++++.+..++.++.-++++. -.+.+++++++.|+. ++++|+|-......-+|++.|.+.+
T Consensus 88 vl~~~~~~~~~l~iEiK~~~~~~~~~~~~v~~~l~~~~~~-------~~v~v~Sf~~~~l~~~~~~~p~~~~ 152 (220)
T cd08579 88 YLALAKGLKQKLLIELKPHGHDSPDLVEKFVKLYKQNLIE-------NQHQVHSLDYRVIEKVKKLDPKIKT 152 (220)
T ss_pred HHHHhhccCCeEEEEECCCCCCCHHHHHHHHHHHHHcCCC-------cCeEEEeCCHHHHHHHHHHCCCCeE
Confidence 33444445777888888765 246677888886532 4799999877777788888887655
No 11
>cd08567 GDPD_SpGDE_like Glycerophosphodiester phosphodiesterase domain of putative Silicibacter pomeroyi glycerophosphodiester phosphodiesterase and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46) and similar proteins. The prototype of this CD is a putative GP-GDE from Silicibacter pomeroyi (SpGDE). It shows high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=53.61 E-value=19 Score=31.21 Aligned_cols=66 Identities=20% Similarity=0.266 Sum_probs=44.1
Q ss_pred ehhHHHHHHHHhhcC---ceEEEEEeeChhh-----------HHHHHHHHHHcCCcCCCCcccceEEeeccccCcchhee
Q 025704 131 KSSVLEALLEITKFC---DLYLMERVLDNES-----------EKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVR 196 (249)
Q Consensus 131 ~esa~e~LleLak~~---DvYLm~~V~dD~e-----------E~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVR 196 (249)
.+.--|+| ++.+.. +++|..-++++.. .+.+++++++.|. .+||+|.|...-....+|
T Consensus 109 iptL~evl-~~~~~~~~~~~~l~iEiK~~~~~~~~~~~~~~~~~~v~~~l~~~~~-------~~~v~~~Sf~~~~l~~~~ 180 (263)
T cd08567 109 IPTLEEVF-ALVEKYGNQKVRFNIETKSDPDRDILHPPPEEFVDAVLAVIRKAGL-------EDRVVLQSFDWRTLQEVR 180 (263)
T ss_pred CCCHHHHH-HHHHHhccCCceEEEEEcCCCCccccCccHHHHHHHHHHHHHHcCC-------CCceEEEeCCHHHHHHHH
Confidence 34444444 444443 5777777875432 2678888888643 368999998877788889
Q ss_pred ecccceee
Q 025704 197 QLEPDWHI 204 (249)
Q Consensus 197 QLeP~lHI 204 (249)
++.|.+.+
T Consensus 181 ~~~p~~~~ 188 (263)
T cd08567 181 RLAPDIPT 188 (263)
T ss_pred HHCCCccE
Confidence 98887644
No 12
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=52.22 E-value=14 Score=29.91 Aligned_cols=28 Identities=21% Similarity=0.171 Sum_probs=21.2
Q ss_pred CCchhhHHHHHHHHHHHHHHhhcCCCCC
Q 025704 13 DSRSVGAIAGLALAIVFTWRMFRSPGAP 40 (249)
Q Consensus 13 ~~~s~~~~ag~a~a~v~~w~~lr~~~~~ 40 (249)
...-+++++|+++++++.|++-|.-...
T Consensus 97 ~~~~l~~l~~l~~~~~~~~~~~~~~~~~ 124 (135)
T PF04246_consen 97 LWAILGGLLGLALGFLILRLFDRRLKKK 124 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhccC
Confidence 3445788999999999999888865544
No 13
>TIGR03510 XapX XapX domain. This model describes an uncharacterized small, hydrophobic protein of about 50 amino acids, found between the xapB and xapR genes of the E. coli xanthosine utilization system, and homologous regions in other small proteins, such as the N-terminal region of DUF1427 (Pfam model pfam07235). We name this domain XapX, as it comprises the full length of the protein encoded between the genes for the well-studied XapB and XapR proteins.
Probab=51.20 E-value=18 Score=26.09 Aligned_cols=23 Identities=22% Similarity=0.345 Sum_probs=19.5
Q ss_pred hhHHHHHHHHHHHHHHhhcCCCC
Q 025704 17 VGAIAGLALAIVFTWRMFRSPGA 39 (249)
Q Consensus 17 ~~~~ag~a~a~v~~w~~lr~~~~ 39 (249)
++-.+||++.++|+|--+++|-+
T Consensus 4 lsl~~G~~vG~~~~~l~vp~PAP 26 (49)
T TIGR03510 4 LSLGAGLLVGALYSLLKVPSPAP 26 (49)
T ss_pred HHHHHHHHHHHHHHHhCCCCCCC
Confidence 46689999999999999988753
No 14
>TIGR03778 VPDSG_CTERM VPDSG-CTERM exosortase interaction domain. Through in silico analysis, we previously described the PEP-CTERM/exosortase system (PubMed:16930487). This model describes a PEP-CTERM-like variant C-terminal protein sorting signal, as found at the C-terminus of twenty otherwise unrelated proteins in Verrucomicrobiae bacterium DG1235. The variant motif, VPDSG, seems an intermediate between the VPEP motif (TIGR02595) of typical exosortase systems and the classical LPXTG of sortase in Gram-positive bacteria.
Probab=50.66 E-value=20 Score=23.08 Aligned_cols=21 Identities=38% Similarity=0.376 Sum_probs=18.7
Q ss_pred CCCchhhHHHHHHHHHHHHHH
Q 025704 12 QDSRSVGAIAGLALAIVFTWR 32 (249)
Q Consensus 12 ~~~~s~~~~ag~a~a~v~~w~ 32 (249)
.|++|-.+++|++++.++++|
T Consensus 2 PDsGST~~Ll~~~l~~l~~~r 22 (26)
T TIGR03778 2 PDSGSTLALLGLGLLGLLGLR 22 (26)
T ss_pred CCchhHHHHHHHHHHHHHHHh
Confidence 478899999999999999886
No 15
>cd08601 GDPD_SaGlpQ_like Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in uncharacterized glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46) from Staphylococcus aureus, Bacillus subtilis and similar proteins. Members in this family show very high sequence similarity to Escherichia coli periplasmic phosphodiesterase GlpQ, which catalyzes the Ca2+-dependent degradation of periplasmic glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=48.29 E-value=38 Score=29.74 Aligned_cols=44 Identities=27% Similarity=0.382 Sum_probs=34.7
Q ss_pred hHHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccce
Q 025704 158 SEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDW 202 (249)
Q Consensus 158 eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~l 202 (249)
-++.+.++++++|+.+. .+.+++|+|+|-..--...+|++.|.+
T Consensus 127 ~~~~v~~~l~~~~~~~~-~~~~~~v~i~Sf~~~~l~~~~~~~p~~ 170 (256)
T cd08601 127 MEEKLLATLDKYGLLTD-NLKNGQVIIQSFSKESLKKLHQLNPNI 170 (256)
T ss_pred HHHHHHHHHHHcCCCcc-cCCCCCEEEecCCHHHHHHHHHhCCCC
Confidence 35789999999887642 445689999998888778888888864
No 16
>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general b
Probab=47.82 E-value=1.2e+02 Score=24.84 Aligned_cols=95 Identities=25% Similarity=0.281 Sum_probs=59.1
Q ss_pred CCCchhHHHHHHhcCc-----------eeEEEeecceeeccCChhhhhcc--------------cee---ehhHHHHHHH
Q 025704 89 VKPTLGQVVRQKLSEG-----------RKVTCRLLGVILEESCPEELQKQ--------------VTV---KSSVLEALLE 140 (249)
Q Consensus 89 ~~~~~~qiv~~kl~~g-----------RkvTis~~gvvl~e~sp~el~~~--------------a~v---~esa~e~Lle 140 (249)
+||+.++-..+=|+++ .-+.+++.|=+++=..|++-.+. ... ....++.|.+
T Consensus 7 EKPs~a~~ia~~L~~~~~~~~~~~~~~~~~v~~~~GHl~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~ 86 (142)
T cd01028 7 EKPSKAKTIAKILGKGSKKKGFYGEGGGYVVTASVGHLLELPFPEEYVDWDKDWPLELFPFEPKYVVIPDKKKQLKALKK 86 (142)
T ss_pred eCHHHHHHHHHHhCCCcccCCceecCCCEEEEEEccccccCCCcccccccccCCchhhCCCCceEEeCCcHHHHHHHHHH
Confidence 4555555555555543 33666777877776555543321 111 3456778889
Q ss_pred HhhcCceEEEEEeeChhhHHHHHHHHHHcCCcCCCCcccceEEeec
Q 025704 141 ITKFCDLYLMERVLDNESEKKVLLALETAGVFTSGGLVKDKVLFCS 186 (249)
Q Consensus 141 Lak~~DvYLm~~V~dD~eE~~Vl~lLe~~GlF~~gGL~rhKVLFCS 186 (249)
+++.+|.++++.=-|.|.|.-...+++-.|. . -.+-.|+.|-|
T Consensus 87 l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~-~--~~~v~R~~fss 129 (142)
T cd01028 87 LAKKADEIVLATDPDREGELIAWEILEVLKC-D--NKPVKRAWFSE 129 (142)
T ss_pred HHhcCCEEEEcCCCCcchHHHHHHHHHHhCC-C--CCCeEEEEEcc
Confidence 9999998888876666666666667776543 1 23456777766
No 17
>cd08564 GDPD_GsGDE_like Glycerophosphodiester phosphodiesterase domain of putative Galdieria sulphuraria glycerophosphodiester phosphodiesterase and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in putative Galdieria sulphuraria glycerophosphodiester phosphodiesterase (GsGDE, EC 3.1.4.46) and its uncharacterized eukaryotic homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=47.75 E-value=41 Score=29.90 Aligned_cols=49 Identities=22% Similarity=0.270 Sum_probs=38.1
Q ss_pred ceEEEEEeeCh--hhHHHHHHHHHHcCCcCCCCcccceEEeecccc-Ccchheeecccc
Q 025704 146 DLYLMERVLDN--ESEKKVLLALETAGVFTSGGLVKDKVLFCSTEI-GRTSFVRQLEPD 201 (249)
Q Consensus 146 DvYLm~~V~dD--~eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~-Gr~sfVRQLeP~ 201 (249)
++.+..-++++ .-++.++++|++.|.. ++|+|||-.- .-...+|++.|.
T Consensus 120 ~~~l~iEiK~~~~~~~~~v~~~l~~~~~~-------~~v~i~SF~~~~~l~~~~~~~~~ 171 (265)
T cd08564 120 KLKYNIELKGREVGLGERVLNLVEKYGMI-------LQVHFSSFLHYDRLDLLKALRPN 171 (265)
T ss_pred CcEEEEEeCCCchhHHHHHHHHHHHcCCC-------CCEEEEecCchhHHHHHHHhCcC
Confidence 67777778866 3457889999986532 6899999888 777788998886
No 18
>cd08573 GDPD_GDE1 Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE1 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE1 (also known as MIR16, membrane interacting protein of RGS16) and their metazoan homologs. GDE1 is widely expressed in mammalian tissues, including the heart, brain, liver, and kidney. It shows sequence homology to bacterial glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), which catalyzes the hydrolysis of various glycerophosphodiesters, and produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. GDE1 has been characterized as GPI-GDE (EC 3.1.4.44) that selectively hydrolyzes extracellular glycerophosphoinositol (GPI) to generate glycerol phosphate and inositol. It functions as an integral membrane-bound glycoprotein interacting with regulator of G protein signaling protein RGS16, and is modulated by G
Probab=46.36 E-value=37 Score=30.40 Aligned_cols=63 Identities=21% Similarity=0.124 Sum_probs=45.4
Q ss_pred HHHHHHhhcCceEEEEEeeChhh--HHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccceee
Q 025704 136 EALLEITKFCDLYLMERVLDNES--EKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDWHI 204 (249)
Q Consensus 136 e~LleLak~~DvYLm~~V~dD~e--E~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~lHI 204 (249)
+-++++.+..++.++.-++++.+ ++.+.+++++.|. + .++++++|-......-+|++.|.+.+
T Consensus 92 ~evl~~~~~~~~~l~iEiK~~~~~~~~~v~~~l~~~~~-----~-~~~v~v~SF~~~~l~~~~~~~p~~~~ 156 (258)
T cd08573 92 EEAVKECLENNLRMIFDVKSNSSKLVDALKNLFKKYPG-----L-YDKAIVCSFNPIVIYKVRKADPKILT 156 (258)
T ss_pred HHHHHHHHhcCCEEEEEeCCCcHHHHHHHHHHHHHCCC-----c-cCCEEEEECCHHHHHHHHHhCCCceE
Confidence 33345555557777778886643 4678888888542 2 36899999998888899999998654
No 19
>TIGR02250 FCP1_euk FCP1-like phosphatase, phosphatase domain. This domain is related to domains found in the human NLI interacting factor-like phosphatases, and together both are detected by the Pfam model pfam03031.
Probab=44.30 E-value=1.4e+02 Score=25.06 Aligned_cols=55 Identities=13% Similarity=0.221 Sum_probs=34.0
Q ss_pred ccceeehhHHHHHHHHhhcCceEEEEEeeChhhHHHHHHHHHHcC-CcCCCCcccceEEeecc
Q 025704 126 KQVTVKSSVLEALLEITKFCDLYLMERVLDNESEKKVLLALETAG-VFTSGGLVKDKVLFCST 187 (249)
Q Consensus 126 ~~a~v~esa~e~LleLak~~DvYLm~~V~dD~eE~~Vl~lLe~~G-lF~~gGL~rhKVLFCST 187 (249)
.....+|.+.+.|-++++.+++++.+ -...+--+.|++.|.-.+ +| .++|++-+.
T Consensus 55 ~~v~~rPgv~efL~~l~~~yel~I~T-~~~~~yA~~vl~~ldp~~~~F------~~ri~~rd~ 110 (156)
T TIGR02250 55 YLTKLRPFLHEFLKEASKLYEMHVYT-MGTRAYAQAIAKLIDPDGKYF------GDRIISRDE 110 (156)
T ss_pred EEEEECCCHHHHHHHHHhhcEEEEEe-CCcHHHHHHHHHHhCcCCCee------ccEEEEecc
Confidence 45678999999999999988887754 222222344455554322 33 367775443
No 20
>PF13419 HAD_2: Haloacid dehalogenase-like hydrolase; PDB: 2FI1_A 2I6X_A 3SD7_A 4F71_A 4DFD_B 4F72_B 4DCC_A 3DDH_A 3KZX_A 2B0C_A ....
Probab=44.12 E-value=1.3e+02 Score=23.06 Aligned_cols=58 Identities=21% Similarity=0.283 Sum_probs=39.7
Q ss_pred hccceeehhHHHHHHHHh-hcCceEEEEEeeChhhHHHHHHHHHHcCCcCCCCcccceEEeeccccCc
Q 025704 125 QKQVTVKSSVLEALLEIT-KFCDLYLMERVLDNESEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGR 191 (249)
Q Consensus 125 ~~~a~v~esa~e~LleLa-k~~DvYLm~~V~dD~eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr 191 (249)
....+..+.+.+.|.+|. +...+++++. .+...+...|+..|+-+ + -+. ++|+.+.|.
T Consensus 73 ~~~~~~~~~~~~~L~~l~~~~~~~~i~Sn----~~~~~~~~~l~~~~~~~---~-f~~-i~~~~~~~~ 131 (176)
T PF13419_consen 73 ESKLQPYPGVRELLERLKAKGIPLVIVSN----GSRERIERVLERLGLDD---Y-FDE-IISSDDVGS 131 (176)
T ss_dssp HGGEEESTTHHHHHHHHHHTTSEEEEEES----SEHHHHHHHHHHTTHGG---G-CSE-EEEGGGSSS
T ss_pred hhccchhhhhhhhhhhcccccceeEEeec----CCccccccccccccccc---c-ccc-ccccchhhh
Confidence 368899999999999998 6677777643 25677778888865442 1 233 456655553
No 21
>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase. This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins []. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase 2.7.7.6 from EC is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division []. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases []. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.; PDB: 2ZJT_A 3IG0_A 3M4I_A 3NUH_B 1GKU_B 1GL9_C 3PWT_A 1CY4_A 1ECL_A 1CY7_A ....
Probab=40.95 E-value=1.2e+02 Score=22.91 Aligned_cols=76 Identities=21% Similarity=0.253 Sum_probs=52.2
Q ss_pred CCchhHHHHHHhcCceeEEEeecceeeccCChhhhhccceeehhHHHHHHHHhhcCceEEEEEeeChhhHHHHHHHHH
Q 025704 90 KPTLGQVVRQKLSEGRKVTCRLLGVILEESCPEELQKQVTVKSSVLEALLEITKFCDLYLMERVLDNESEKKVLLALE 167 (249)
Q Consensus 90 ~~~~~qiv~~kl~~gRkvTis~~gvvl~e~sp~el~~~a~v~esa~e~LleLak~~DvYLm~~V~dD~eE~~Vl~lLe 167 (249)
+++-..-+++=|++.....+++.|-+++-..|++-.+ .-....++.|.++.+.+|-.+++.=.|.+.|.-...+++
T Consensus 7 ~ps~a~~i~~~l~~~~~~v~~~~Ghl~~~~~~~~~~~--~~~~~~i~~l~~~~~~~~~iiiatD~D~EGe~Ia~~i~~ 82 (100)
T PF01751_consen 7 KPSDAKAIAKALGGEEYIVIATSGHLLELAKPEDYDP--KDKKKQIKNLKKLLKKADEIIIATDPDREGELIAWEIIE 82 (100)
T ss_dssp SHHHHHHHHHHSSTTTEEEEEESSSSEESTTSSHHHC--HTTHHHHHHHHHHHHSCSEEEEEC-SSHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCCEEEEEeCCccccccccccccc--ccccccchhhHHHhhhccEeeecCCCChHHHHHHHHHHH
Confidence 4455555655566666888999999999888776544 344566788888888888888787666666654444444
No 22
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=40.93 E-value=24 Score=29.53 Aligned_cols=19 Identities=26% Similarity=0.369 Sum_probs=14.9
Q ss_pred hhHHHHHHHHHHHHHHhhc
Q 025704 17 VGAIAGLALAIVFTWRMFR 35 (249)
Q Consensus 17 ~~~~ag~a~a~v~~w~~lr 35 (249)
+|.+||++..+++.++++|
T Consensus 71 ~gv~aGvIg~Illi~y~ir 89 (122)
T PF01102_consen 71 FGVMAGVIGIILLISYCIR 89 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 6778888887788888874
No 23
>PRK07066 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=40.27 E-value=95 Score=29.35 Aligned_cols=73 Identities=16% Similarity=0.124 Sum_probs=49.1
Q ss_pred HHhhcCceEEEEEeeChhhHHHHHHHHHHcCCcCCCCcccceEEeeccccCcch--hee-----------------eccc
Q 025704 140 EITKFCDLYLMERVLDNESEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTS--FVR-----------------QLEP 200 (249)
Q Consensus 140 eLak~~DvYLm~~V~dD~eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~s--fVR-----------------QLeP 200 (249)
+..+.||+.+-+-..+-+-|..+..-+++ ..+++-||-+||+ |-.. |.. ++-|
T Consensus 79 ~av~~aDlViEavpE~l~vK~~lf~~l~~-------~~~~~aIlaSnTS-~l~~s~la~~~~~p~R~~g~HffnP~~~~p 150 (321)
T PRK07066 79 ACVADADFIQESAPEREALKLELHERISR-------AAKPDAIIASSTS-GLLPTDFYARATHPERCVVGHPFNPVYLLP 150 (321)
T ss_pred HHhcCCCEEEECCcCCHHHHHHHHHHHHH-------hCCCCeEEEECCC-ccCHHHHHHhcCCcccEEEEecCCccccCc
Confidence 55578998876666666667777777765 4566778888887 5321 321 2233
Q ss_pred ceee----cCCHHHHHHHHhhccc
Q 025704 201 DWHI----DTNPEIVSQLARFIKY 220 (249)
Q Consensus 201 ~lHI----Dtd~~vv~~L~rfVp~ 220 (249)
.+=| +|+++++..+..|...
T Consensus 151 LVEVv~g~~T~~e~~~~~~~f~~~ 174 (321)
T PRK07066 151 LVEVLGGERTAPEAVDAAMGIYRA 174 (321)
T ss_pred eEEEeCCCCCCHHHHHHHHHHHHH
Confidence 4333 8999999999998765
No 24
>TIGR03190 benz_CoA_bzdN benzoyl-CoA reductase, bzd-type, N subunit. Members of this family are the N subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=38.91 E-value=9 Score=36.36 Aligned_cols=70 Identities=17% Similarity=0.130 Sum_probs=46.6
Q ss_pred HHHHHHhhcCceEEEEEeeC-hh--hHHHHHHHHHHcCCcCCCCcccceEEeeccccCcchhe-eecc----cceeecCC
Q 025704 136 EALLEITKFCDLYLMERVLD-NE--SEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFV-RQLE----PDWHIDTN 207 (249)
Q Consensus 136 e~LleLak~~DvYLm~~V~d-D~--eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfV-RQLe----P~lHIDtd 207 (249)
+++..||+.+--...|.... +. --+.+.++.+++ ...|+.-|-.-||.+..+-...+ ++|+ |.++||+|
T Consensus 276 dpl~alA~~yl~~~~C~~~~~p~~~R~~~i~~lv~~~---~~DGVI~~~~kfC~~~~~e~~~lk~~l~e~GIP~L~iE~D 352 (377)
T TIGR03190 276 DVIKAIAERYCDRPACPTKDYPVHTRYDHVLGLAKEY---NVQGAIFLQQKFCDPHEGDYPDLKRHLEANGIPTLFLEFD 352 (377)
T ss_pred cHHHHHHHHhcCCCCCCCcCCCHHHHHHHHHHHHHHh---CCCEEEEecccCCCcchhhhHHHHHHHHHCCCCEEEEecC
Confidence 45666776652123344432 22 225566666664 34599999999999999988665 6787 99999988
Q ss_pred H
Q 025704 208 P 208 (249)
Q Consensus 208 ~ 208 (249)
-
T Consensus 353 ~ 353 (377)
T TIGR03190 353 I 353 (377)
T ss_pred C
Confidence 3
No 25
>PF01171 ATP_bind_3: PP-loop family; InterPro: IPR011063 This entry represents the PP-loop motif superfamily [,]. The PP-loop motif appears to be a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding []. Named PP-motif, since it appears to be a part of a previously uncharacterised ATP pyrophophatase domain. ATP sulfurylases, Escherichia coli NtrL, and Bacillus subtilis OutB consist of this domain alone. In other proteins, the pyrophosphatase domain is associated with amidotransferase domains (type I or type II), a putative citrulline-aspartate ligase domain or a nitrilase/amidase domain.; PDB: 3A2K_A 2E89_B 2E21_D 1WY5_B 1NI5_A.
Probab=38.76 E-value=68 Score=26.82 Aligned_cols=67 Identities=19% Similarity=0.299 Sum_probs=42.7
Q ss_pred eehhHHHHHHHHhhc--CceEEEEEeeChhhHHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccceeec
Q 025704 130 VKSSVLEALLEITKF--CDLYLMERVLDNESEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDWHID 205 (249)
Q Consensus 130 v~esa~e~LleLak~--~DvYLm~~V~dD~eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~lHID 205 (249)
.|.--.+.|.++|+. |+..++.|-.||+-|.-+++++...|+.+-.|+.+.+-. .| ++=+.|.+.+.
T Consensus 80 aR~~Ry~~l~~~a~~~g~~~i~~GHh~dD~~ET~l~~l~rg~~~~~l~~~~~~~~~-----~~----~~~iRPLl~~~ 148 (182)
T PF01171_consen 80 ARELRYQFLREIAKEEGCNKIALGHHLDDQAETFLMNLLRGSGLRGLAGMPPVSPF-----KG----IKLIRPLLYVS 148 (182)
T ss_dssp HHHHHHHHHHHHHHTTT-CEEE---BHHHHHHHHHHHHHHT--CCCCC-S-SEEEE-----TT----CEEE-GGGCS-
T ss_pred HHHHHHHHHHHhhhcccccceeecCcCCccHHHHHHHHHHhccchhhccccccccc-----cC----cccCCcchhCC
Confidence 344555788888876 699999999999999999999999888665566653322 23 66677887765
No 26
>cd08561 GDPD_cytoplasmic_ScUgpQ2_like Glycerophosphodiester phosphodiesterase domain of Streptomyces coelicolor cytoplasmic phosphodiesterases UgpQ2 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized cytoplasmic phosphodiesterases which predominantly exist in bacteria. The prototype of this family is a putative cytoplasmic phosphodiesterase encoded by gene ulpQ2 (SCO1419) in the Streptomyces coelicolor genome. It is distantly related to the Escherichia coli cytoplasmic phosphodiesterases UgpQ that catalyzes the hydrolysis of glycerophosphodiesters at the inner side of the cytoplasmic membrane to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=38.64 E-value=93 Score=27.18 Aligned_cols=57 Identities=21% Similarity=0.206 Sum_probs=45.6
Q ss_pred ceEEEEEeeCh--hhHHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccceeecCCHH
Q 025704 146 DLYLMERVLDN--ESEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDWHIDTNPE 209 (249)
Q Consensus 146 DvYLm~~V~dD--~eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~lHIDtd~~ 209 (249)
++++..-+++. .-++.++++++++|+ .++++|.|-...-...++++.|.+.+....+
T Consensus 106 ~~~~~ieiK~~~~~~~~~~~~~l~~~~~-------~~~~~~~Sf~~~~l~~~~~~~p~~~~~~~~~ 164 (249)
T cd08561 106 DVRLNIEIKDDGPAAAAALADLIERYGA-------QDRVLVASFSDRVLRRFRRLCPRVATSAGEG 164 (249)
T ss_pred CCcEEEEECCCchhHHHHHHHHHHHcCC-------CCcEEEEECCHHHHHHHHHHCCCcceeccHH
Confidence 47888888886 446788999998652 3689999999999999999999888765543
No 27
>cd01427 HAD_like Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.
Probab=35.00 E-value=1.2e+02 Score=21.79 Aligned_cols=60 Identities=28% Similarity=0.305 Sum_probs=43.7
Q ss_pred EEeecceeeccCChhhhhccceeehhHHHHHHHHhhc-CceEEEEEeeChhhHHHHHHHHHHcCC
Q 025704 108 TCRLLGVILEESCPEELQKQVTVKSSVLEALLEITKF-CDLYLMERVLDNESEKKVLLALETAGV 171 (249)
Q Consensus 108 Tis~~gvvl~e~sp~el~~~a~v~esa~e~LleLak~-~DvYLm~~V~dD~eE~~Vl~lLe~~Gl 171 (249)
.+-+.|++..+.+..+........+.+++.|-+|... ..+|+++ ......+...++..|+
T Consensus 3 vfD~D~tl~~~~~~~~~~~~~~~~~~~~~~l~~l~~~g~~i~ivS----~~~~~~~~~~~~~~~~ 63 (139)
T cd01427 3 LFDLDGTLLDSEPGIAEIEELELYPGVKEALKELKEKGIKLALAT----NKSRREVLELLEELGL 63 (139)
T ss_pred EEccCCceEccCccccccccCCcCcCHHHHHHHHHHCCCeEEEEe----CchHHHHHHHHHHcCC
Confidence 4567788877777766667788999999999999986 4555544 3336677777777654
No 28
>PF10389 CoatB: Bacteriophage coat protein B ; InterPro: IPR008020 The major coat protein in the capsid of filamentous bacteriophage forms a helical assembly of about 7000 identical protomers, with each protomer comprised of 46 amino acids, after the cleavage of the signal peptide. Each protomer forms a slightly curved helix that combines to form a tubular structure that encapsulates the viral DNA [].; PDB: 2IFO_A.
Probab=34.76 E-value=29 Score=24.85 Aligned_cols=11 Identities=9% Similarity=0.241 Sum_probs=8.7
Q ss_pred HHHHHHhhcCC
Q 025704 27 IVFTWRMFRSP 37 (249)
Q Consensus 27 ~v~~w~~lr~~ 37 (249)
.+..||++|.+
T Consensus 35 ~i~v~kwiRra 45 (46)
T PF10389_consen 35 GIAVYKWIRRA 45 (46)
T ss_dssp HHHHHHHHHHT
T ss_pred HHHHHHHHHhh
Confidence 57889999854
No 29
>PRK11009 aphA acid phosphatase/phosphotransferase; Provisional
Probab=34.75 E-value=2.4e+02 Score=25.55 Aligned_cols=110 Identities=10% Similarity=0.078 Sum_probs=65.0
Q ss_pred CCchhHHHHHHhcCce--eEEEeecceeeccCCh------------------hh--------hhccceeehhHHHHHHHH
Q 025704 90 KPTLGQVVRQKLSEGR--KVTCRLLGVILEESCP------------------EE--------LQKQVTVKSSVLEALLEI 141 (249)
Q Consensus 90 ~~~~~qiv~~kl~~gR--kvTis~~gvvl~e~sp------------------~e--------l~~~a~v~esa~e~LleL 141 (249)
-++..||-+. |.|.+ .|.+-+.++||-++.+ ++ .+......+.++|.|-.+
T Consensus 48 ~~~~~~~~~~-~~~~~p~av~~DIDeTvldnsp~~~~~~~~f~~~~~~y~~~~~fw~~y~~~~~~~a~p~~Ga~elL~~L 126 (237)
T PRK11009 48 WVSVAQIEKS-LEGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPGSEDYLKNQKFWEKMNNGWDEFSIPKEVARQLIDMH 126 (237)
T ss_pred EEEHHHhhhh-ccCCCCcEEEEECcCccccCCchheeeeeccCCCcccccChHHHHHHHHhcccccCcchHHHHHHHHHH
Confidence 3678888754 33332 5777788898864321 00 012334455589999998
Q ss_pred -hhcCceEEEEEeeChhhHHHHHHHHHHcCC--cCCCCcccceEEeeccc---cCcchheeecccceeec
Q 025704 142 -TKFCDLYLMERVLDNESEKKVLLALETAGV--FTSGGLVKDKVLFCSTE---IGRTSFVRQLEPDWHID 205 (249)
Q Consensus 142 -ak~~DvYLm~~V~dD~eE~~Vl~lLe~~Gl--F~~gGL~rhKVLFCST~---~Gr~sfVRQLeP~lHID 205 (249)
.+-..||+++-=.....+..+..+++..|+ -. -..+++|.+. ..+...+++++-.++|.
T Consensus 127 ~~~G~~I~iVTnR~~~k~~~t~~~Llk~~gip~~~-----~f~vil~gd~~~K~~K~~~l~~~~i~I~IG 191 (237)
T PRK11009 127 VKRGDSIYFITGRTATKTETVSKTLADDFHIPADN-----MNPVIFAGDKPGQYTKTQWLKKKNIRIFYG 191 (237)
T ss_pred HHCCCeEEEEeCCCCcccHHHHHHHHHHcCCCccc-----ceeEEEcCCCCCCCCHHHHHHhcCCeEEEc
Confidence 555678876632223445566666776554 22 2367787663 34555666666677775
No 30
>cd08568 GDPD_TmGDE_like Glycerophosphodiester phosphodiesterase domain of Thermotoga maritime and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermotoga maritime glycerophosphodiester phosphodiesterase (TmGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. TmGDE exists as a monomer that might be the biologically relevant form.
Probab=34.60 E-value=71 Score=27.57 Aligned_cols=52 Identities=25% Similarity=0.369 Sum_probs=40.4
Q ss_pred ceEEEEEeeChhhHHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccceee
Q 025704 146 DLYLMERVLDNESEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDWHI 204 (249)
Q Consensus 146 DvYLm~~V~dD~eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~lHI 204 (249)
.++|+.-+++....+.+.++++++|.. .++++-|-..-....+|++.|.+.+
T Consensus 92 ~~~l~iEiK~~~~~~~~~~~l~~~~~~-------~~v~i~SF~~~~l~~~~~~~p~~~~ 143 (226)
T cd08568 92 DAIINVEIKDIDAVEPVLEIVEKFNAL-------DRVIFSSFNHDALRELRKLDPDAKV 143 (226)
T ss_pred CcEEEEEECCccHHHHHHHHHHHcCCC-------CcEEEEECCHHHHHHHHHhCCCCcE
Confidence 467888899887788899999986542 5788888777777778888887543
No 31
>cd08565 GDPD_pAtGDE_like Glycerophosphodiester phosphodiesterase domain of putative Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in putative Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase (pAtGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=33.82 E-value=78 Score=27.89 Aligned_cols=60 Identities=18% Similarity=0.211 Sum_probs=41.6
Q ss_pred HHHHHHHhhcCceEEEEEeeChh-------hHHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccce
Q 025704 135 LEALLEITKFCDLYLMERVLDNE-------SEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDW 202 (249)
Q Consensus 135 ~e~LleLak~~DvYLm~~V~dD~-------eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~l 202 (249)
++-++++.+..+++|..-++++. -++.+.+++++.|+ .++++|.|-......-+|++ |.+
T Consensus 84 L~evl~~~~~~~~~l~iEiK~~~~~~~~~~~~~~v~~~i~~~~~-------~~~v~~~Sf~~~~l~~~~~~-p~~ 150 (235)
T cd08565 84 LEEVLALFAPSGLELHVEIKTDADGTPYPGAAALAAATLRRHGL-------LERSVLTSFDPAVLTEVRKH-PGV 150 (235)
T ss_pred HHHHHHHhhccCcEEEEEECCCCCCCccHHHHHHHHHHHHhCCC-------cCCEEEEECCHHHHHHHHhC-CCC
Confidence 33444555557788888888653 23667888888653 25889998887777888888 764
No 32
>COG4317 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.44 E-value=47 Score=26.93 Aligned_cols=20 Identities=35% Similarity=0.534 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHhhcCCC
Q 025704 19 AIAGLALAIVFTWRMFRSPG 38 (249)
Q Consensus 19 ~~ag~a~a~v~~w~~lr~~~ 38 (249)
-.||+++.++|+...+|+|-
T Consensus 8 lgAGllVGiiyaLl~vrsPA 27 (93)
T COG4317 8 LGAGLLVGIIYALLKVRSPA 27 (93)
T ss_pred HhhhHHHHHHHHHHhCCCCC
Confidence 34799999999999999875
No 33
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=31.62 E-value=55 Score=24.92 Aligned_cols=19 Identities=26% Similarity=0.504 Sum_probs=13.9
Q ss_pred hhHHHHHHHHHHHHHHhhc
Q 025704 17 VGAIAGLALAIVFTWRMFR 35 (249)
Q Consensus 17 ~~~~ag~a~a~v~~w~~lr 35 (249)
+|+++||.+|--+-=|+|+
T Consensus 9 ~G~~~Gff~ar~~~~k~l~ 27 (64)
T PF03672_consen 9 VGAVIGFFIARKYMEKQLK 27 (64)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 6777777777777777776
No 34
>PRK06129 3-hydroxyacyl-CoA dehydrogenase; Validated
Probab=30.48 E-value=1.6e+02 Score=26.78 Aligned_cols=88 Identities=10% Similarity=0.111 Sum_probs=50.8
Q ss_pred HHhhcCceEEEEEeeChhhHHHHHHHHHHcCCcCCCCcccceEEeeccccCcch--heee-----------------ccc
Q 025704 140 EITKFCDLYLMERVLDNESEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTS--FVRQ-----------------LEP 200 (249)
Q Consensus 140 eLak~~DvYLm~~V~dD~eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~s--fVRQ-----------------LeP 200 (249)
+..+.||+.+.|--.+.+-+..++..+++. .+.+++++||..+... +... +.|
T Consensus 78 ~a~~~ad~Vi~avpe~~~~k~~~~~~l~~~--------~~~~~ii~ssts~~~~~~la~~~~~~~~~~~~hp~~p~~~~~ 149 (308)
T PRK06129 78 DAVADADYVQESAPENLELKRALFAELDAL--------APPHAILASSTSALLASAFTEHLAGRERCLVAHPINPPYLIP 149 (308)
T ss_pred HhhCCCCEEEECCcCCHHHHHHHHHHHHHh--------CCCcceEEEeCCCCCHHHHHHhcCCcccEEEEecCCCcccCc
Confidence 334578988776554445566666655442 2234555666666432 2222 222
Q ss_pred ceee----cCCHHHHHHHHhhc----cceeeecCCCCCCCccc
Q 025704 201 DWHI----DTNPEIVSQLARFI----KYQLHISPNRPERSAAN 235 (249)
Q Consensus 201 ~lHI----Dtd~~vv~~L~rfV----p~lv~I~~~~~~~~~~N 235 (249)
.+-| .++++.+..+..|+ ++.+++.+..+|-..-|
T Consensus 150 lveiv~~~~t~~~~~~~~~~~~~~lG~~~v~v~~~~~G~i~nr 192 (308)
T PRK06129 150 VVEVVPAPWTAPATLARAEALYRAAGQSPVRLRREIDGFVLNR 192 (308)
T ss_pred eEEEeCCCCCCHHHHHHHHHHHHHcCCEEEEecCCCccHHHHH
Confidence 2223 38888888887776 67788887777754433
No 35
>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.
Probab=29.67 E-value=38 Score=25.03 Aligned_cols=14 Identities=43% Similarity=0.714 Sum_probs=8.7
Q ss_pred hhHHHHHHHHHHHH
Q 025704 17 VGAIAGLALAIVFT 30 (249)
Q Consensus 17 ~~~~ag~a~a~v~~ 30 (249)
+|+++|.++++.|+
T Consensus 7 ~Ga~~Ga~~glL~a 20 (74)
T PF12732_consen 7 AGAAAGAAAGLLFA 20 (74)
T ss_pred HHHHHHHHHHHHhC
Confidence 56666666666553
No 36
>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=29.58 E-value=89 Score=22.16 Aligned_cols=30 Identities=20% Similarity=0.131 Sum_probs=25.8
Q ss_pred hhcCceEEEEEeeChhhHHHHHHHHHHcCC
Q 025704 142 TKFCDLYLMERVLDNESEKKVLLALETAGV 171 (249)
Q Consensus 142 ak~~DvYLm~~V~dD~eE~~Vl~lLe~~Gl 171 (249)
.+.+.+.+...+.+.++-+.+++.|++.|.
T Consensus 35 ~~~~~v~v~ie~~~~~~~~~i~~~L~~~G~ 64 (68)
T cd04885 35 GDEARVLVGIQVPDREDLAELKERLEALGY 64 (68)
T ss_pred CCceEEEEEEEeCCHHHHHHHHHHHHHcCC
Confidence 456888898999998999999999999764
No 37
>TIGR02245 HAD_IIID1 HAD-superfamily subfamily IIID hydrolase, TIGR02245. This family of sequences appears to belong to the Haloacid Dehalogenase (HAD) superfamily of enzymes by virtue of the presence of three catalytic domains, in this case: LLVLD(ILV)D(YH)T, I(VMG)IWS, and (DN)(VC)K(PA)Lx{15-17}T(IL)(MH)(FV)DD(IL)(GRS)(RK)N. Since this family has no large "cap" domain between motifs 1 and 2 or between 2 and 3, it is formally a "class III" HAD.
Probab=29.22 E-value=4e+02 Score=23.62 Aligned_cols=76 Identities=16% Similarity=0.187 Sum_probs=53.8
Q ss_pred CceeEEEeecceeeccCChhhhhccceeehhHHHHHHHHhhcCceEEEEEeeChhhHHHHHHHHHHcCCcCCCCcccceE
Q 025704 103 EGRKVTCRLLGVILEESCPEELQKQVTVKSSVLEALLEITKFCDLYLMERVLDNESEKKVLLALETAGVFTSGGLVKDKV 182 (249)
Q Consensus 103 ~gRkvTis~~gvvl~e~sp~el~~~a~v~esa~e~LleLak~~DvYLm~~V~dD~eE~~Vl~lLe~~GlF~~gGL~rhKV 182 (249)
|.+.+.+-+.++++--.++.+ ......|+-+-|-|-.++..+||++.+ ...++.+...+++-|+.++ ...|+
T Consensus 20 ~kklLVLDLDeTLvh~~~~~~-~~~~~kRP~l~eFL~~~~~~feIvVwT----Aa~~~ya~~~l~~l~~~~~---~~~~i 91 (195)
T TIGR02245 20 GKKLLVLDIDYTLFDHRSPAE-TGEELMRPYLHEFLTSAYEDYDIVIWS----ATSMKWIEIKMTELGVLTN---PNYKI 91 (195)
T ss_pred CCcEEEEeCCCceEcccccCC-CceEEeCCCHHHHHHHHHhCCEEEEEe----cCCHHHHHHHHHHhcccCC---ccceE
Confidence 445677888888885333333 246788999999999999999999876 4446788888888666543 23456
Q ss_pred Eeec
Q 025704 183 LFCS 186 (249)
Q Consensus 183 LFCS 186 (249)
.||=
T Consensus 92 ~~~l 95 (195)
T TIGR02245 92 TFLL 95 (195)
T ss_pred EEEe
Confidence 6654
No 38
>PF13844 Glyco_transf_41: Glycosyl transferase family 41; PDB: 3PE4_C 3PE3_D 3TAX_C 2XGO_A 2JLB_B 2XGM_A 2VSY_B 2XGS_B 2VSN_A.
Probab=28.26 E-value=1.3e+02 Score=30.35 Aligned_cols=99 Identities=15% Similarity=0.180 Sum_probs=61.9
Q ss_pred ccceeehhHHHHHHHHhhc---CceEEEEEeeChhhHHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccce
Q 025704 126 KQVTVKSSVLEALLEITKF---CDLYLMERVLDNESEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDW 202 (249)
Q Consensus 126 ~~a~v~esa~e~LleLak~---~DvYLm~~V~dD~eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~l 202 (249)
..+++.++.+++..+|.+. +-+.|+. .....++.+...+++ .|+.++||+|.-...-..++-|.-.-|+
T Consensus 293 ~~~KI~p~~l~~W~~IL~~vP~S~L~L~~--~~~~~~~~l~~~~~~------~Gv~~~Ri~f~~~~~~~ehl~~~~~~DI 364 (468)
T PF13844_consen 293 NLFKISPETLDLWARILKAVPNSRLWLLR--FPASGEARLRRRFAA------HGVDPDRIIFSPVAPREEHLRRYQLADI 364 (468)
T ss_dssp -GGG--HHHHHHHHHHHHHSTTEEEEEEE--TSTTHHHHHHHHHHH------TTS-GGGEEEEE---HHHHHHHGGG-SE
T ss_pred ccccCCHHHHHHHHHHHHhCCCcEEEEee--CCHHHHHHHHHHHHH------cCCChhhEEEcCCCCHHHHHHHhhhCCE
Confidence 4677889999999998887 3444443 345567888888877 3788899999887665667767677888
Q ss_pred eecCC-----HHHHHHHHhhccceeeecCCCCCCC
Q 025704 203 HIDTN-----PEIVSQLARFIKYQLHISPNRPERS 232 (249)
Q Consensus 203 HIDtd-----~~vv~~L~rfVp~lv~I~~~~~~~~ 232 (249)
..|+- -...+.|--=||-+-+.+..-.++.
T Consensus 365 ~LDT~p~nG~TTt~dALwmGVPvVTl~G~~~~sR~ 399 (468)
T PF13844_consen 365 CLDTFPYNGGTTTLDALWMGVPVVTLPGETMASRV 399 (468)
T ss_dssp EE--SSS--SHHHHHHHHHT--EEB---SSGGGSH
T ss_pred EeeCCCCCCcHHHHHHHHcCCCEEeccCCCchhHH
Confidence 88864 5677888888888888776655543
No 39
>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=28.26 E-value=3.1e+02 Score=22.59 Aligned_cols=79 Identities=25% Similarity=0.223 Sum_probs=50.3
Q ss_pred EEEeecceeeccCChhhhhc--------------cc--ee---ehhHHHHHHHHhhcCceEEEEEeeChhhHHHHHHHHH
Q 025704 107 VTCRLLGVILEESCPEELQK--------------QV--TV---KSSVLEALLEITKFCDLYLMERVLDNESEKKVLLALE 167 (249)
Q Consensus 107 vTis~~gvvl~e~sp~el~~--------------~a--~v---~esa~e~LleLak~~DvYLm~~V~dD~eE~~Vl~lLe 167 (249)
+.++.-|=|++=.-|++..+ .+ .. ..+.++.|.++++.||.++++.=-|-|.|.-...+++
T Consensus 42 ~vt~~~GHl~~l~~p~~y~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~ik~l~~~ad~ii~atD~DrEGE~I~~~i~~ 121 (151)
T cd03362 42 VVTWASGHLLELDFPEEYDPWDKVWPLEDPLFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILE 121 (151)
T ss_pred EEEEEhhHhhcccChHHhccCCCCCccccCCcCCceEEEECccHHHHHHHHHHHHhCCCeEEEccCCCccccHHHHHHHH
Confidence 55667777776665654321 11 11 3466788999999999877776666677766666777
Q ss_pred HcCCcCCCCcccceEEeecc
Q 025704 168 TAGVFTSGGLVKDKVLFCST 187 (249)
Q Consensus 168 ~~GlF~~gGL~rhKVLFCST 187 (249)
..|.-. ..+-.|+.|.+-
T Consensus 122 ~~~~~~--~~~v~R~~fssl 139 (151)
T cd03362 122 YAKCVK--RKPVKRAWFSSL 139 (151)
T ss_pred HhCCCC--CCcEEEEEEccC
Confidence 654321 234578888763
No 40
>cd08566 GDPD_AtGDE_like Glycerophosphodiester phosphodiesterase domain of Agrobacterium tumefaciens and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase (AtGDE, EC 3.1.4.46) and its uncharacterized eukaryotic homolgoues. Members in this family shows high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. AtGDE exists as a hexamer that is a trimer of dimers, which is unique among current known GDPD family members. However, it remains unclear if the hexamer plays a physiological role in AtGDE enzymatic function.
Probab=27.48 E-value=1.2e+02 Score=26.66 Aligned_cols=48 Identities=23% Similarity=0.318 Sum_probs=38.0
Q ss_pred eEEEEEeeChhhHHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccce
Q 025704 147 LYLMERVLDNESEKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDW 202 (249)
Q Consensus 147 vYLm~~V~dD~eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~l 202 (249)
+.|..-+++. ..+.+.+++++.|. ..||+|.|-.......+|++.|.+
T Consensus 101 ~~l~iEiK~~-~~~~~~~~~~~~~~-------~~~v~~~sf~~~~l~~~~~~~p~~ 148 (240)
T cd08566 101 ILLNLDLKDA-DLDEVIALVKKHGA-------LDQVIFKSYSEEQAKELRALAPEV 148 (240)
T ss_pred cEEEEEECch-HHHHHHHHHHHcCC-------cccEEEEECCHHHHHHHHHhCCCC
Confidence 7788888865 56778899988654 258999999888888888888876
No 41
>PF05729 NACHT: NACHT domain
Probab=27.01 E-value=1.1e+02 Score=23.55 Aligned_cols=44 Identities=14% Similarity=0.226 Sum_probs=33.5
Q ss_pred cccceEEeeccccCcchheeecccc--eeec--CCHHHHHHHHhhccc
Q 025704 177 LVKDKVLFCSTEIGRTSFVRQLEPD--WHID--TNPEIVSQLARFIKY 220 (249)
Q Consensus 177 L~rhKVLFCST~~Gr~sfVRQLeP~--lHID--td~~vv~~L~rfVp~ 220 (249)
....|++.++++.+...+.+.++.. ++|+ +++++-+++..+.++
T Consensus 118 ~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~f~~ 165 (166)
T PF05729_consen 118 PPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSEEDIKQYLRKYFSN 165 (166)
T ss_pred CCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCHHHHHHHHHHHhhc
Confidence 4468899988898888888888888 7777 566777777766654
No 42
>TIGR03593 yidC_nterm membrane protein insertase, YidC/Oxa1 family, N-terminal domain. Essentially all bacteria have a member of the YidC family, whose C-terminal domain is modeled by TIGR03592. The two copies are found in endospore-forming bacteria such as Bacillus subtilis appear redundant during vegetative growth, although the member designated spoIIIJ (stage III sporulation protein J) has a distinct role in spore formation. YidC, its mitochondrial homolog Oxa1, and its chloroplast homolog direct insertion into the bacterial/organellar inner (or only) membrane. This model describes an N-terminal sequence region, including a large periplasmic domain lacking in YidC members from Gram-positive species. The multifunctional YidC protein acts both with and independently of the Sec system.
Probab=26.66 E-value=1.3e+02 Score=27.95 Aligned_cols=19 Identities=26% Similarity=0.712 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHhhcCCCCC
Q 025704 22 GLALAIVFTWRMFRSPGAP 40 (249)
Q Consensus 22 g~a~a~v~~w~~lr~~~~~ 40 (249)
.|.+++++.|.++..+..+
T Consensus 9 ~ls~~~~~~w~~~~~~~~~ 27 (366)
T TIGR03593 9 ALSFVIFLLWQAWQSDPGP 27 (366)
T ss_pred HHHHHHHHHHHHHHhhccC
Confidence 3566688999999866543
No 43
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=26.62 E-value=1e+02 Score=22.96 Aligned_cols=29 Identities=24% Similarity=0.311 Sum_probs=25.0
Q ss_pred hcCceEEEEEeeC-hhhHHHHHHHHHHcCC
Q 025704 143 KFCDLYLMERVLD-NESEKKVLLALETAGV 171 (249)
Q Consensus 143 k~~DvYLm~~V~d-D~eE~~Vl~lLe~~Gl 171 (249)
..+++.+..++.+ .++-+.+++.|++.|.
T Consensus 38 ~~~~v~i~ie~~~~~~~~~~i~~~L~~~G~ 67 (85)
T cd04906 38 KDAHIFVGVSVANGAEELAELLEDLKSAGY 67 (85)
T ss_pred CeeEEEEEEEeCCcHHHHHHHHHHHHHCCC
Confidence 4678888899998 8899999999999765
No 44
>cd08559 GDPD_periplasmic_GlpQ_like Periplasmic glycerophosphodiester phosphodiesterase domain (GlpQ) and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in bacterial and eukaryotic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46) similar to Escherichia coli periplasmic phosphodiesterase GlpQ. GP-GDEs are involved in glycerol metabolism and catalyze the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols, which are major sources of carbon and phosphate. In E. coli, there are two major G3P uptake systems: Glp and Ugp, which contain genes coding for two different GP-GDEs. GlpQ gene from the glp operon codes for a periplasmic phosphodiesterase GlpQ. GlpQ is a dimeric enzyme that hydrolyzes periplasmic glycerophosphodiesters, such as glycerophosphocholine (GPC), glycerophosphoethanolanmine (GPE), glycerophosphoglycerol (GPG), glycerophosphoinositol (GPI),
Probab=26.21 E-value=1.3e+02 Score=27.48 Aligned_cols=53 Identities=23% Similarity=0.197 Sum_probs=39.9
Q ss_pred ceEEEEEeeChhh--------HHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccce
Q 025704 146 DLYLMERVLDNES--------EKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDW 202 (249)
Q Consensus 146 DvYLm~~V~dD~e--------E~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~l 202 (249)
.+.|..-++++.. ++.++++++++|+-+ ..++|++.|=...-..-+|++.|.+
T Consensus 128 ~~~l~IEiK~~~~~~~~~~~~~~~v~~~l~~~~~~~----~~~~v~i~SF~~~~L~~~r~~~p~~ 188 (296)
T cd08559 128 NVGIYPETKHPTFHKQEGPDIEEKLLEVLKKYGYTG----KNDPVFIQSFEPESLKRLRNETPDI 188 (296)
T ss_pred cceEEEEecChhhhhhcCCCHHHHHHHHHHHcCCCC----CCCCEEEecCCHHHHHHHHHhCCCC
Confidence 6777777886543 478899999865431 2479999998888888889988864
No 45
>PRK09260 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=25.80 E-value=1.5e+02 Score=26.46 Aligned_cols=43 Identities=14% Similarity=0.006 Sum_probs=28.2
Q ss_pred HHHhhcCceEEEEEeeChhhHHHHHHHHHHcCCcCCCCcccceEEeeccc
Q 025704 139 LEITKFCDLYLMERVLDNESEKKVLLALETAGVFTSGGLVKDKVLFCSTE 188 (249)
Q Consensus 139 leLak~~DvYLm~~V~dD~eE~~Vl~lLe~~GlF~~gGL~rhKVLFCST~ 188 (249)
-+..+.||+.+.|--.+.+-++.+..-+++ .+.++.|+...|+
T Consensus 76 ~~~~~~aD~Vi~avpe~~~~k~~~~~~l~~-------~~~~~~il~~~tS 118 (288)
T PRK09260 76 KAAVADADLVIEAVPEKLELKKAVFETADA-------HAPAECYIATNTS 118 (288)
T ss_pred HHhhcCCCEEEEeccCCHHHHHHHHHHHHh-------hCCCCcEEEEcCC
Confidence 356678999998877666667777665654 3455666643333
No 46
>PF00891 Methyltransf_2: O-methyltransferase; InterPro: IPR001077 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. This domain includes a range of O-methyltransferases some of which utilise S-adenosyl methionine as substrate []. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. In eukaryotes, DNA methylation has been implicated in the control of several cellular processes, including differentiation, gene regulation, and embryonic development. O-methyltransferases have a common catalytic domain structure, which might be universal among S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases []. Comparative analysis of the predicted amino acid sequences of a number of plant O-methyltransferase cDNA clones show that they share some 32-71% sequence identity, and can be grouped according to the different compounds they utilise as substrates [].; GO: 0008171 O-methyltransferase activity; PDB: 1FPQ_A 1FP1_D 3P9K_B 3P9I_D 3P9C_A 3I53_A 3I5U_A 3I64_A 3I58_A 1ZG3_A ....
Probab=25.67 E-value=49 Score=28.57 Aligned_cols=27 Identities=26% Similarity=0.494 Sum_probs=22.5
Q ss_pred HhhcCceEEEEEeeChhhHHHHHHHHHH
Q 025704 141 ITKFCDLYLMERVLDNESEKKVLLALET 168 (249)
Q Consensus 141 Lak~~DvYLm~~V~dD~eE~~Vl~lLe~ 168 (249)
+-. +|+|+|.+|..|=.++.+..+|++
T Consensus 156 ~P~-~D~~~l~~vLh~~~d~~~~~iL~~ 182 (241)
T PF00891_consen 156 LPV-ADVYLLRHVLHDWSDEDCVKILRN 182 (241)
T ss_dssp CSS-ESEEEEESSGGGS-HHHHHHHHHH
T ss_pred hcc-ccceeeehhhhhcchHHHHHHHHH
Confidence 444 899999999999999999999985
No 47
>cd08570 GDPD_YPL206cp_fungi Glycerophosphodiester phosphodiesterase domain of Saccharomyces cerevisiae YPL206cp and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Saccharomyces cerevisiae YPL206cp and uncharacterized hypothetical homologs existing in fungi. The product of S. cerevisiae ORF YPL206c (PGC1), YPL206cp (Pgc1p), displays homology to bacterial and mammalian glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. S. cerevisiae YPL206cp is an integral membrane protein with a single GDPD domain following by a short hydrophobic C-terminal tail that may function as a membrane anchor. This protein plays an essential role in the regulation of the cardiolipin (CL) biosynthetic pathway in yeast by removing the excess phosphatidylglycerol (PG) content of membranes via a phospholip
Probab=25.31 E-value=1.4e+02 Score=25.96 Aligned_cols=65 Identities=14% Similarity=0.197 Sum_probs=43.9
Q ss_pred HHHHHHHhhcC---ceEEEEEeeChhh----HHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccce
Q 025704 135 LEALLEITKFC---DLYLMERVLDNES----EKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDW 202 (249)
Q Consensus 135 ~e~LleLak~~---DvYLm~~V~dD~e----E~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~l 202 (249)
++-++++.+.. ++++..-++++.. ++.+..++++++..+ -..++|+|.|-...-..-.|++.|.+
T Consensus 85 L~evl~~~~~~~~~~~~l~iEiK~~~~~~~~~~~v~~~i~~~~~~~---~~~~~v~i~Sf~~~~l~~l~~~~p~~ 156 (234)
T cd08570 85 LKDVLEWLVEHELPDVKLMLDIKRDNDPEILFKLIAEMLAVKPDLD---FWRERIILGLWHLDFLKYGKEVLPGF 156 (234)
T ss_pred HHHHHHHHHhcCCCCeEEEEEECCCCCHHHHHHHHHHHHHhcCCcc---cccCCEEEEeCCHHHHHHHHHhCCCC
Confidence 44455565554 8999999997643 356677777754322 13479999987777777778887763
No 48
>cd03363 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=25.09 E-value=3.7e+02 Score=21.74 Aligned_cols=93 Identities=17% Similarity=0.136 Sum_probs=54.9
Q ss_pred CCCchhHHHHHHhcCceeEEEeecceeeccCChhhhh--------cccee---ehhHHHHHHHHhhcCceEEEEEeeChh
Q 025704 89 VKPTLGQVVRQKLSEGRKVTCRLLGVILEESCPEELQ--------KQVTV---KSSVLEALLEITKFCDLYLMERVLDNE 157 (249)
Q Consensus 89 ~~~~~~qiv~~kl~~gRkvTis~~gvvl~e~sp~el~--------~~a~v---~esa~e~LleLak~~DvYLm~~V~dD~ 157 (249)
+||+.++-.++-|+++- +.+.+.|=+++=..|++-- ..+.+ .....+.|.++++.+|-++++.=.|-|
T Consensus 7 EKp~~a~~ia~~Lg~~~-~v~~~~GHl~~l~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~l~~~~~eiiiAtD~drE 85 (123)
T cd03363 7 ESPAKAKTIKKYLGKEY-EVLASVGHIRDLPKKGLGVDGEDDGFEPKYVVIPGKKKVVKELKKLAKKADEIYLATDPDRE 85 (123)
T ss_pred eCHHHHHHHHHHhCCCc-EEEeccCccccCCCcccCCChhccCcCceEEECccHHHHHHHHHHHHhcCCEEEEcCCCCcc
Confidence 56777777777776533 3445667776654443321 11222 345678889999999966666555555
Q ss_pred hHHHHHHHHHHcCCcCCCCcccceEEeec
Q 025704 158 SEKKVLLALETAGVFTSGGLVKDKVLFCS 186 (249)
Q Consensus 158 eE~~Vl~lLe~~GlF~~gGL~rhKVLFCS 186 (249)
.|.-...+++..|. +.+-.|+-|.|
T Consensus 86 Ge~i~~~i~~~~~~----~~~v~Rl~~ss 110 (123)
T cd03363 86 GEAIAWHLAEVLKL----KKNVKRVVFNE 110 (123)
T ss_pred hHHHHHHHHHHcCC----CCCeEEEEEcc
Confidence 55544455565442 34556777765
No 49
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=25.04 E-value=65 Score=26.55 Aligned_cols=16 Identities=25% Similarity=0.530 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHHHhhc
Q 025704 20 IAGLALAIVFTWRMFR 35 (249)
Q Consensus 20 ~ag~a~a~v~~w~~lr 35 (249)
++||.|+++.+|...|
T Consensus 3 ~i~lvvG~iiG~~~~r 18 (128)
T PF06295_consen 3 IIGLVVGLIIGFLIGR 18 (128)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4444444444444555
No 50
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=24.12 E-value=49 Score=27.26 Aligned_cols=21 Identities=14% Similarity=0.332 Sum_probs=17.2
Q ss_pred hhHHHHHHHHHHHHHHhhcCC
Q 025704 17 VGAIAGLALAIVFTWRMFRSP 37 (249)
Q Consensus 17 ~~~~ag~a~a~v~~w~~lr~~ 37 (249)
||.|+|++|+++..+..-++-
T Consensus 4 i~lvvG~iiG~~~~r~~~~~~ 24 (128)
T PF06295_consen 4 IGLVVGLIIGFLIGRLTSSNQ 24 (128)
T ss_pred HHHHHHHHHHHHHHHHhccch
Confidence 789999999988887777653
No 51
>COG4218 MtrF Tetrahydromethanopterin S-methyltransferase, subunit F [Coenzyme metabolism]
Probab=22.94 E-value=71 Score=25.02 Aligned_cols=18 Identities=39% Similarity=0.536 Sum_probs=14.9
Q ss_pred hhHHHHHHHHHHHHHHhh
Q 025704 17 VGAIAGLALAIVFTWRMF 34 (249)
Q Consensus 17 ~~~~ag~a~a~v~~w~~l 34 (249)
.+.++||||.+||+-.++
T Consensus 48 st~i~GlaiGfvfA~vLv 65 (73)
T COG4218 48 STRIAGLAIGFVFAGVLV 65 (73)
T ss_pred hhhhHHHHHHHHHHHHHH
Confidence 467899999999987665
No 52
>TIGR00550 nadA quinolinate synthetase complex, A subunit. This protein, termed NadA, plays a role in the synthesis of pyridine, a precursor to NAD. The quinolinate synthetase complex consists of A protein (this protein) and B protein. B protein converts L-aspartate to iminoaspartate, an unstable reaction product which in the absence of A protein is spontaneously hydrolyzed to form oxaloacetate. The A protein, NadA, converts iminoaspartate to quinolate.
Probab=22.94 E-value=49 Score=31.37 Aligned_cols=94 Identities=12% Similarity=0.160 Sum_probs=56.5
Q ss_pred hhHHHHHHHHhhcCceEEEEEeeChhhHHHHHHHH-HHcCCcCCC-CcccceEEeecccc----------Ccchhe--ee
Q 025704 132 SSVLEALLEITKFCDLYLMERVLDNESEKKVLLAL-ETAGVFTSG-GLVKDKVLFCSTEI----------GRTSFV--RQ 197 (249)
Q Consensus 132 esa~e~LleLak~~DvYLm~~V~dD~eE~~Vl~lL-e~~GlF~~g-GL~rhKVLFCST~~----------Gr~sfV--RQ 197 (249)
++..+-+.+|-+.-|..+++|++...|=+.+-+.. .++++...+ -+..+.|+||-=.. ||.=.. -.
T Consensus 4 ~~~~~~I~~lk~e~~~~ivah~y~~~Evk~~aD~~gdS~~l~~~a~~~~~~~IvF~gv~fMae~a~~l~p~k~vilp~~~ 83 (310)
T TIGR00550 4 DNLVEAILRLKKELNAVILAHYYQKDEIQQIADYTGDSLELAQIAAKTDADIIVFCGVHFMGETAKILNPEKTVLMPDLG 83 (310)
T ss_pred HHHHHHHHHHHHHcCCEEEEEcCCCHHHHHhhcceeeHHHHHHHHHhCCCCEEEEeCCchHHHHHHHhCCCCEEEccCCC
Confidence 34566677777777999999999999887776544 333333322 35668899993211 111111 11
Q ss_pred cccceeecCCHHHHHHHHhhccceeeec
Q 025704 198 LEPDWHIDTNPEIVSQLARFIKYQLHIS 225 (249)
Q Consensus 198 LeP~lHIDtd~~vv~~L~rfVp~lv~I~ 225 (249)
=.-.+|---+++.+..|+.-.|+-+.|.
T Consensus 84 a~C~~a~~~~~~~i~~lk~~~Pda~vva 111 (310)
T TIGR00550 84 AGCSMADMCPPEEFKKLKERHPDAFVVT 111 (310)
T ss_pred CCCccccccCHHHHHHHHHHCCCCEEEE
Confidence 1223444456777888888776654443
No 53
>COG0241 HisB Histidinol phosphatase and related phosphatases [Amino acid transport and metabolism]
Probab=22.86 E-value=2.1e+02 Score=25.36 Aligned_cols=84 Identities=20% Similarity=0.269 Sum_probs=53.6
Q ss_pred eEEEeecceeeccCCh-hhhhccceeehhHHHHHHHHhhcCceEEEEEeeC--------------hhhHHHHHHHHHHcC
Q 025704 106 KVTCRLLGVILEESCP-EELQKQVTVKSSVLEALLEITKFCDLYLMERVLD--------------NESEKKVLLALETAG 170 (249)
Q Consensus 106 kvTis~~gvvl~e~sp-~el~~~a~v~esa~e~LleLak~~DvYLm~~V~d--------------D~eE~~Vl~lLe~~G 170 (249)
.+=+--.|||..|..+ =.-.+.+.+.+.++++|.++.+.- |.+..|.+ ++--+.+++.|++.|
T Consensus 7 ~lflDRDGtin~d~~~yv~~~~~~~~~~g~i~al~~l~~~g--y~lVvvTNQsGi~rgyf~~~~f~~~~~~m~~~l~~~g 84 (181)
T COG0241 7 ALFLDRDGTINIDKGDYVDSLDDFQFIPGVIPALLKLQRAG--YKLVVVTNQSGIGRGYFTEADFDKLHNKMLKILASQG 84 (181)
T ss_pred EEEEcCCCceecCCCcccCcHHHhccCccHHHHHHHHHhCC--CeEEEEECCCCccccCccHHHHHHHHHHHHHHHHHcC
Confidence 3455567888887773 232368999999999999998653 33333333 233366888888855
Q ss_pred CcCCCCcccceEEeeccccCcchheee
Q 025704 171 VFTSGGLVKDKVLFCSTEIGRTSFVRQ 197 (249)
Q Consensus 171 lF~~gGL~rhKVLFCST~~Gr~sfVRQ 197 (249)
. +=.-|+||--..-....+|-
T Consensus 85 v------~id~i~~Cph~p~~~c~cRK 105 (181)
T COG0241 85 V------KIDGILYCPHHPEDNCDCRK 105 (181)
T ss_pred C------ccceEEECCCCCCCCCcccC
Confidence 4 33677887654443344443
No 54
>cd06660 Aldo_ket_red Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others.
Probab=22.66 E-value=1.6e+02 Score=25.69 Aligned_cols=86 Identities=20% Similarity=0.212 Sum_probs=50.5
Q ss_pred CCchhHHHHHHhcCceeEEEeecceeeccCChhhhhccceeehhHHHHHHHH-hhcCceEEEEEeeChhh-HHHHHHHHH
Q 025704 90 KPTLGQVVRQKLSEGRKVTCRLLGVILEESCPEELQKQVTVKSSVLEALLEI-TKFCDLYLMERVLDNES-EKKVLLALE 167 (249)
Q Consensus 90 ~~~~~qiv~~kl~~gRkvTis~~gvvl~e~sp~el~~~a~v~esa~e~LleL-ak~~DvYLm~~V~dD~e-E~~Vl~lLe 167 (249)
...++++.++.. .-.++.|++..-...... .......++.++.+.|-+| ...-|+|++-....+.. ...+.++|+
T Consensus 58 E~~lG~al~~~~-~R~~~~i~tK~~~~~~~~--~~~~~~~~~~~l~~sL~~L~~~~iDl~~lh~~~~~~~~~~~~~~~l~ 134 (285)
T cd06660 58 EELLGEALKERG-PREEVFIATKVGPRPGDG--RDLSPEHIRRAVEESLKRLGTDYIDLYLLHWPDPDTPDIEETLRALE 134 (285)
T ss_pred HHHHHHHHhccC-CcCcEEEEeeecCCCCCC--CCCCHHHHHHHHHHHHHHhCCCceeEEEecCCCCCCCCHHHHHHHHH
Confidence 344566665422 234788888854322110 0112334777888888888 56789999998876554 455555554
Q ss_pred ---HcCCcCCCCcc
Q 025704 168 ---TAGVFTSGGLV 178 (249)
Q Consensus 168 ---~~GlF~~gGL~ 178 (249)
+.|.+..-|+-
T Consensus 135 ~l~~~G~ir~iGvS 148 (285)
T cd06660 135 ELVKEGKIRAIGVS 148 (285)
T ss_pred HHHHcCCccEEEee
Confidence 66665533443
No 55
>PF09527 ATPase_gene1: Putative F0F1-ATPase subunit (ATPase_gene1)
Probab=22.58 E-value=96 Score=21.55 Aligned_cols=19 Identities=21% Similarity=0.569 Sum_probs=12.5
Q ss_pred hhHHHHHHHHHHHHHHhhc
Q 025704 17 VGAIAGLALAIVFTWRMFR 35 (249)
Q Consensus 17 ~~~~ag~a~a~v~~w~~lr 35 (249)
+|.+.|++.++.-.||++|
T Consensus 37 ~g~llG~~~g~~~~~~~~k 55 (55)
T PF09527_consen 37 IGLLLGIAAGFYNVYRLVK 55 (55)
T ss_pred HHHHHHHHHHHHHHHHHhC
Confidence 4556666677777777765
No 56
>COG4980 GvpP Gas vesicle protein [General function prediction only]
Probab=22.51 E-value=57 Score=27.27 Aligned_cols=14 Identities=43% Similarity=0.824 Sum_probs=10.9
Q ss_pred hhHHHHHHHHHHHH
Q 025704 17 VGAIAGLALAIVFT 30 (249)
Q Consensus 17 ~~~~ag~a~a~v~~ 30 (249)
+|+|+|.+.|+.|+
T Consensus 13 iGgiiGa~aaLL~A 26 (115)
T COG4980 13 IGGIIGAAAALLFA 26 (115)
T ss_pred HHHHHHHHHHHHhC
Confidence 68888888887774
No 57
>PRK08942 D,D-heptose 1,7-bisphosphate phosphatase; Validated
Probab=22.25 E-value=2.6e+02 Score=23.00 Aligned_cols=72 Identities=15% Similarity=0.184 Sum_probs=45.7
Q ss_pred eEEEeecceeeccC-ChhhhhccceeehhHHHHHHHHhhc-CceEEEEEeeChhh--------------HHHHHHHHHHc
Q 025704 106 KVTCRLLGVILEES-CPEELQKQVTVKSSVLEALLEITKF-CDLYLMERVLDNES--------------EKKVLLALETA 169 (249)
Q Consensus 106 kvTis~~gvvl~e~-sp~el~~~a~v~esa~e~LleLak~-~DvYLm~~V~dD~e--------------E~~Vl~lLe~~ 169 (249)
-+-+-+.|+|.++. .+.+..++....+.+.+.|.+|.+. ..+++ +.+... ++.+...|+..
T Consensus 5 ~~~~d~~~t~~~~~~~~~~~~~~~~~~pgv~e~L~~Lk~~g~~l~I---~Tn~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 81 (181)
T PRK08942 5 AIFLDRDGVINVDSDGYVKSPDEWIPIPGSIEAIARLKQAGYRVVV---ATNQSGIARGLFTEAQLNALHEKMDWSLADR 81 (181)
T ss_pred EEEEECCCCcccCCccccCCHHHeEECCCHHHHHHHHHHCCCEEEE---EeCCccccCCcCCHHHHHHHHHHHHHHHHHc
Confidence 35566788887776 3444456889999999999999875 34443 444321 24455567765
Q ss_pred CCcCCCCcccceEEeec
Q 025704 170 GVFTSGGLVKDKVLFCS 186 (249)
Q Consensus 170 GlF~~gGL~rhKVLFCS 186 (249)
|+ .-..+.+|.
T Consensus 82 g~------~f~~i~~~~ 92 (181)
T PRK08942 82 GG------RLDGIYYCP 92 (181)
T ss_pred CC------ccceEEECC
Confidence 54 234566664
No 58
>TIGR01261 hisB_Nterm histidinol-phosphatase. This model describes histidinol phosphatase. All known examples in the scope of this model are bifunctional proteins with a histidinol phosphatase domain followed by an imidazoleglycerol-phosphate dehydratase domain. These enzymatic domains catalyze the ninth and seventh steps, respectively, of histidine biosynthesis.
Probab=22.12 E-value=2.9e+02 Score=23.11 Aligned_cols=69 Identities=20% Similarity=0.378 Sum_probs=42.7
Q ss_pred ecceeeccCC---hhhhhccceeehhHHHHHHHHhhc-CceEEEEEeeC-----------hhhHHHHHHHHHHcCCcCCC
Q 025704 111 LLGVILEESC---PEELQKQVTVKSSVLEALLEITKF-CDLYLMERVLD-----------NESEKKVLLALETAGVFTSG 175 (249)
Q Consensus 111 ~~gvvl~e~s---p~el~~~a~v~esa~e~LleLak~-~DvYLm~~V~d-----------D~eE~~Vl~lLe~~GlF~~g 175 (249)
..|++.++.+ +.+..+..++.+.+.+.|..|... ..+++++--.. ...+..+..+|++.|+
T Consensus 8 ~dg~l~~~~~~~~~~~~~~~~~~~pgv~e~L~~L~~~g~~l~IvSN~~g~~~~~~~~~~~~~~~~~~~~~l~~~gl---- 83 (161)
T TIGR01261 8 RDGTLIEEPPSDFQVDALEKLRFEKGVIPALLKLKKAGYKFVMVTNQDGLGTPSFPQADFDGPHNLMLQIFRSQGI---- 83 (161)
T ss_pred CCCCccccCCCccccCCHHHeeECCCHHHHHHHHHHCCCeEEEEeCCccccCCcCCHHHHHHHHHHHHHHHHHCCC----
Confidence 4566655433 233445678889999999999764 55555442110 0245678888888655
Q ss_pred CcccceEEee
Q 025704 176 GLVKDKVLFC 185 (249)
Q Consensus 176 GL~rhKVLFC 185 (249)
.=+.+++|
T Consensus 84 --~fd~ii~~ 91 (161)
T TIGR01261 84 --IFDDVLIC 91 (161)
T ss_pred --ceeEEEEC
Confidence 22567777
No 59
>PF08370 PDR_assoc: Plant PDR ABC transporter associated; InterPro: IPR013581 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This domain is found on the C terminus of ABC-2 type transporter domains (IPR013525 from INTERPRO). It seems to be associated with the plant pleiotropic drug resistance (PDR) protein family of ABC transporters. Like in yeast, plant PDR ABC transporters may also play a role in the transport of antifungal agents [] (see also IPR010929 from INTERPRO). The PDR family is characterised by a configuration in which the ABC domain is nearer the N terminus of the protein than the transmembrane domain [].
Probab=22.08 E-value=1.2e+02 Score=22.85 Aligned_cols=26 Identities=19% Similarity=0.385 Sum_probs=17.9
Q ss_pred chhhHHHHHHH----HHHHHHHhhcCCCCC
Q 025704 15 RSVGAIAGLAL----AIVFTWRMFRSPGAP 40 (249)
Q Consensus 15 ~s~~~~ag~a~----a~v~~w~~lr~~~~~ 40 (249)
.++||++|+++ ...++..+|..++.+
T Consensus 31 IgvgaL~G~~vlFNil~~laL~yL~p~~k~ 60 (65)
T PF08370_consen 31 IGVGALLGFIVLFNILFTLALTYLNPLGKS 60 (65)
T ss_pred ehHHHHHHHHHHHHHHHHHHHHhcCCcCCC
Confidence 36899999886 345566777766543
No 60
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=22.05 E-value=1.1e+02 Score=26.77 Aligned_cols=55 Identities=20% Similarity=0.280 Sum_probs=44.6
Q ss_pred eehhHHHHHHHHhhcCceEEEEEeeChhhHHHHHHHHHHcCCcCCC--CcccceEEee
Q 025704 130 VKSSVLEALLEITKFCDLYLMERVLDNESEKKVLLALETAGVFTSG--GLVKDKVLFC 185 (249)
Q Consensus 130 v~esa~e~LleLak~~DvYLm~~V~dD~eE~~Vl~lLe~~GlF~~g--GL~rhKVLFC 185 (249)
++-+..|-|-.+-+.|.||+ .-+.--..|++|-.+....|-...- ||++.+--+|
T Consensus 22 f~gt~~e~~~a~r~S~tvyV-gNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpC 78 (153)
T KOG0121|consen 22 FRGTDEEQLEALRKSCTVYV-GNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPC 78 (153)
T ss_pred hcCchHHHHHHHhhcceEEE-eeeeeeecHHHHHHHHHhccchheeEeccccCCcCcc
Confidence 34456677777888999998 7788888899999999999988743 9999887666
No 61
>PF13940 Ldr_toxin: Toxin Ldr, type I toxin-antitoxin system
Probab=22.01 E-value=49 Score=22.64 Aligned_cols=26 Identities=23% Similarity=0.520 Sum_probs=19.5
Q ss_pred eeehhhcCCCchhhHHHHHHHHHHHHHH
Q 025704 5 LTLLSWYQDSRSVGAIAGLALAIVFTWR 32 (249)
Q Consensus 5 ~~~~~~~~~~~s~~~~ag~a~a~v~~w~ 32 (249)
+++.|||-=+- -.|||++.+++..|.
T Consensus 6 lg~~~WhDLAA--P~iagIi~s~iv~w~ 31 (35)
T PF13940_consen 6 LGIAFWHDLAA--PIIAGIIASLIVGWL 31 (35)
T ss_pred HHHHHHHHhHh--HHHHHHHHHHHHHHH
Confidence 45678886444 358899999999985
No 62
>PF14155 DUF4307: Domain of unknown function (DUF4307)
Probab=21.68 E-value=87 Score=25.34 Aligned_cols=27 Identities=15% Similarity=0.191 Sum_probs=19.7
Q ss_pred cCCCchhhHHHHHHHHHHHHHHhhcCC
Q 025704 11 YQDSRSVGAIAGLALAIVFTWRMFRSP 37 (249)
Q Consensus 11 ~~~~~s~~~~ag~a~a~v~~w~~lr~~ 37 (249)
++...-++++++++.+.+++|..+...
T Consensus 3 rr~~~~~~~v~~vv~~~~~~w~~~~~~ 29 (112)
T PF14155_consen 3 RRKLVIAGAVLVVVAGAVVAWFGYSQF 29 (112)
T ss_pred cceeEehHHHHHHHHHHHHhHhhhhhc
Confidence 344556778888888888888888743
No 63
>PRK06049 rpl30p 50S ribosomal protein L30P; Reviewed
Probab=21.45 E-value=1.7e+02 Score=25.35 Aligned_cols=67 Identities=7% Similarity=0.159 Sum_probs=53.7
Q ss_pred eEEEEEeeChhhH-HHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccceeecC-CHHHHHHHHhhc
Q 025704 147 LYLMERVLDNESE-KKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDWHIDT-NPEIVSQLARFI 218 (249)
Q Consensus 147 vYLm~~V~dD~eE-~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~lHIDt-d~~vv~~L~rfV 218 (249)
+|++.+|.+...- ..+.+.|+..||=.. |+..|-.-.....-|++..+|.+-+.. |.+.++.|-..=
T Consensus 2 ~~~ViriRg~ig~~~~~r~tL~~LgL~ki-----~~~V~v~~tp~~~GML~kV~~~V~~ge~~~~tv~~Li~kR 70 (154)
T PRK06049 2 MYAVIRIRGRVNVPRDIADTLKMLRLHRV-----NHCVLVPETPSYKGMLQKVKDYVTWGEIDADTLAELLRKR 70 (154)
T ss_pred cEEEEEecCCCCCCHHHHHHHHHcCCCcC-----CCEEEEeCCHHHHHHHHhhhceeEEeeCchHHHHHHHHHh
Confidence 6888999887433 678888888655554 788888777889999999999999985 899999997653
No 64
>PF12263 DUF3611: Protein of unknown function (DUF3611); InterPro: IPR022051 This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 180 and 205 amino acids in length. There are two completely conserved residues (W and G) that may be functionally important.
Probab=20.74 E-value=1.1e+02 Score=27.08 Aligned_cols=21 Identities=19% Similarity=0.455 Sum_probs=16.4
Q ss_pred hhhHHHHHHHHHHHHHHhhcC
Q 025704 16 SVGAIAGLALAIVFTWRMFRS 36 (249)
Q Consensus 16 s~~~~ag~a~a~v~~w~~lr~ 36 (249)
.+++++-+.+.+.|.|+|.|-
T Consensus 62 a~~gl~~l~~si~~~fry~Rl 82 (183)
T PF12263_consen 62 AICGLVALFFSIFWSFRYTRL 82 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 456777777888999999884
No 65
>PRK01294 lipase chaperone; Provisional
Probab=20.36 E-value=5.7e+02 Score=24.57 Aligned_cols=21 Identities=10% Similarity=0.023 Sum_probs=12.9
Q ss_pred HHHhhhhc-CCCCCchhHHHHH
Q 025704 79 TQIADALF-QPVKPTLGQVVRQ 99 (249)
Q Consensus 79 ~~~~~~~~-~~~~~~~~qiv~~ 99 (249)
++..|-|+ .-+..++.+|..+
T Consensus 89 Rd~FDYfLs~~gE~~l~~i~~~ 110 (336)
T PRK01294 89 RDFFDYFLSALGELDLAAIDAL 110 (336)
T ss_pred HHHHHHHhhccCCCCHHHHHHH
Confidence 45556666 4566677777644
No 66
>PRK11677 hypothetical protein; Provisional
Probab=20.27 E-value=56 Score=27.79 Aligned_cols=19 Identities=26% Similarity=0.310 Sum_probs=13.6
Q ss_pred hHHHHHHHHHHHHHHhhcC
Q 025704 18 GAIAGLALAIVFTWRMFRS 36 (249)
Q Consensus 18 ~~~ag~a~a~v~~w~~lr~ 36 (249)
-+++||.|+++.+|...|-
T Consensus 5 ~a~i~livG~iiG~~~~R~ 23 (134)
T PRK11677 5 YALIGLVVGIIIGAVAMRF 23 (134)
T ss_pred HHHHHHHHHHHHHHHHHhh
Confidence 3567777777778878884
No 67
>cd01657 Ribosomal_L7_archeal_euk Ribosomal protein L7, which is found in archaea and eukaryotes but not in prokaryotes, binds domain II of the 23S rRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. The eukaryotic L7 members have an N-terminal extension not found in the archeal L7 orthologs. L7 is closely related to the ribosomal L30 protein found in eukaryotes and prokaryotes.
Probab=20.12 E-value=1.6e+02 Score=25.36 Aligned_cols=66 Identities=17% Similarity=0.202 Sum_probs=53.3
Q ss_pred eEEEEEeeChhh-HHHHHHHHHHcCCcCCCCcccceEEeeccccCcchheeecccceeecC-CHHHHHHHHhh
Q 025704 147 LYLMERVLDNES-EKKVLLALETAGVFTSGGLVKDKVLFCSTEIGRTSFVRQLEPDWHIDT-NPEIVSQLARF 217 (249)
Q Consensus 147 vYLm~~V~dD~e-E~~Vl~lLe~~GlF~~gGL~rhKVLFCST~~Gr~sfVRQLeP~lHIDt-d~~vv~~L~rf 217 (249)
+|++.++.+... ...+.+.|+..||=.. |...|..-.....-|++.++|.+-+.. +.+.++.|-..
T Consensus 1 l~~Virirg~~g~~~~~r~tL~~LgL~k~-----~~~v~~~~t~~~~gmL~kV~~~V~~ge~~~~tv~~Li~k 68 (159)
T cd01657 1 LYAVVRIRGIVGVPPKIRKTLQLLRLRRI-----NNAVFVKLTKATIGMLKKVEPYVTWGEPNLETLRELIYK 68 (159)
T ss_pred CEEEEEecCcCCCCHHHHHHHHHcCCCcC-----CCEEEEeCCHHHHHHHHHhhhheEeccCcHHHHHHHHHH
Confidence 477888888763 3678888888665554 888998888999999999999999985 88888888644
Done!