Query psy9632
Match_columns 83
No_of_seqs 112 out of 1030
Neff 4.1
Searched_HMMs 46136
Date Sat Aug 17 00:41:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9632.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9632hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14681 UPRTase: Uracil phosp 99.9 1.6E-24 3.5E-29 157.1 3.3 52 1-52 156-207 (207)
2 PLN02541 uracil phosphoribosyl 99.9 4.6E-24 1E-28 160.5 5.7 52 1-52 192-243 (244)
3 COG0035 Upp Uracil phosphoribo 99.9 5E-24 1.1E-28 158.9 5.3 53 1-53 158-210 (210)
4 TIGR01091 upp uracil phosphori 99.9 2.3E-22 5E-27 145.7 5.5 53 1-53 155-207 (207)
5 PRK00129 upp uracil phosphorib 99.9 3.1E-22 6.7E-27 145.1 5.3 53 1-53 157-209 (209)
6 KOG4203|consensus 99.2 5.7E-12 1.2E-16 102.3 1.1 53 1-53 421-473 (473)
7 KOG1017|consensus 97.2 0.00037 8.1E-09 53.8 3.4 44 1-53 224-267 (267)
8 PF09960 DUF2194: Uncharacteri 76.0 4.9 0.00011 34.3 4.5 33 5-37 404-436 (585)
9 PF00984 UDPG_MGDP_dh: UDP-glu 63.4 2.1 4.5E-05 28.1 -0.3 9 66-74 59-67 (96)
10 COG2159 Predicted metal-depend 51.7 13 0.00029 28.4 2.4 23 7-29 179-201 (293)
11 PF15608 PELOTA_1: PELOTA RNA 49.7 6.6 0.00014 26.7 0.4 16 31-46 33-48 (100)
12 PF03452 Anp1: Anp1; InterPro 46.6 13 0.00028 29.0 1.7 40 31-72 207-252 (269)
13 PRK01211 dihydroorotase; Provi 46.5 5.7 0.00012 31.7 -0.3 43 29-71 35-79 (409)
14 COG0118 HisH Glutamine amidotr 45.4 9.5 0.00021 28.9 0.7 40 11-50 14-56 (204)
15 smart00785 AARP2CN AARP2CN (NU 44.5 10 0.00022 24.4 0.6 10 37-46 63-72 (83)
16 PF08142 AARP2CN: AARP2CN (NUC 43.6 10 0.00023 24.4 0.6 15 32-46 59-74 (85)
17 PF09550 DUF2376: Conserved hy 43.5 23 0.0005 20.6 2.0 14 7-20 30-43 (43)
18 PF01819 Levi_coat: Levivirus 42.6 9.1 0.0002 27.3 0.2 16 62-77 68-83 (129)
19 PF04909 Amidohydro_2: Amidohy 38.8 16 0.00035 25.4 1.0 22 7-28 151-172 (273)
20 PRK15057 UDP-glucose 6-dehydro 36.3 13 0.00029 29.5 0.3 8 67-74 249-256 (388)
21 PF01148 CTP_transf_1: Cytidyl 34.9 16 0.00036 25.7 0.5 21 30-50 223-243 (259)
22 PRK00125 pyrF orotidine 5'-pho 34.8 59 0.0013 25.2 3.6 30 4-47 194-225 (278)
23 TIGR02127 pyrF_sub2 orotidine 34.8 68 0.0015 24.4 3.9 29 4-46 191-222 (261)
24 PF14492 EFG_II: Elongation Fa 34.2 57 0.0012 20.0 2.9 32 9-45 23-54 (75)
25 TIGR02216 phage_TIGR02216 phag 33.4 40 0.00086 21.1 2.0 14 7-20 46-59 (60)
26 PRK11064 wecC UDP-N-acetyl-D-m 31.9 19 0.0004 28.7 0.5 8 67-74 262-269 (415)
27 COG0031 CysK Cysteine synthase 31.3 64 0.0014 25.6 3.4 35 9-45 184-225 (300)
28 PF02550 AcetylCoA_hydro: Acet 30.2 37 0.00081 24.2 1.8 34 14-48 118-151 (198)
29 PF02991 Atg8: Autophagy prote 30.1 1.1E+02 0.0023 20.5 3.9 65 11-76 6-76 (104)
30 KOG4388|consensus 28.7 39 0.00085 30.3 1.9 25 12-36 781-805 (880)
31 KOG1593|consensus 28.6 60 0.0013 26.4 2.8 37 5-52 287-323 (349)
32 cd03144 GATase1_ScBLP_like Typ 28.5 41 0.00089 22.9 1.6 43 7-50 11-60 (114)
33 COG1004 Ugd Predicted UDP-gluc 28.4 21 0.00047 29.7 0.3 8 67-74 258-265 (414)
34 COG4878 Uncharacterized protei 28.2 88 0.0019 25.3 3.7 25 4-28 115-139 (309)
35 PRK15182 Vi polysaccharide bio 26.5 25 0.00054 28.3 0.3 8 67-74 257-264 (425)
36 PRK05426 peptidyl-tRNA hydrola 25.1 34 0.00074 25.0 0.8 20 37-56 3-22 (189)
37 smart00546 CUE Domain that may 25.0 65 0.0014 17.5 1.8 15 8-22 3-17 (43)
38 PLN02353 probable UDP-glucose 24.9 26 0.00057 28.8 0.2 8 67-74 268-275 (473)
39 cd05311 NAD_bind_2_malic_enz N 24.5 25 0.00053 25.8 -0.0 26 20-45 143-170 (226)
40 KOG2255|consensus 24.5 63 0.0014 25.0 2.2 32 25-56 28-59 (224)
41 cd08436 PBP2_LTTR_like_3 The C 24.5 84 0.0018 19.5 2.4 19 8-26 16-34 (194)
42 cd08472 PBP2_CrgA_like_3 The C 24.4 84 0.0018 19.8 2.5 19 8-26 17-35 (202)
43 PRK07627 dihydroorotase; Provi 24.4 26 0.00056 27.9 0.1 40 32-71 46-88 (425)
44 KOG0907|consensus 24.0 1.1E+02 0.0023 20.2 3.0 20 11-30 43-62 (106)
45 cd08464 PBP2_DntR_like_2 The C 23.7 88 0.0019 19.6 2.5 19 8-26 16-34 (200)
46 KOG1654|consensus 22.7 1.3E+02 0.0029 21.1 3.4 31 11-41 18-53 (116)
47 cd01316 CAD_DHOase The eukaryo 22.6 31 0.00068 26.9 0.2 36 36-71 2-39 (344)
48 PRK13384 delta-aminolevulinic 22.6 93 0.002 25.2 2.9 23 8-30 102-125 (322)
49 cd08461 PBP2_DntR_like_3 The C 22.3 98 0.0021 19.5 2.5 18 8-25 16-33 (198)
50 cd08470 PBP2_CrgA_like_1 The C 22.1 97 0.0021 19.5 2.4 19 8-26 17-35 (197)
51 cd08450 PBP2_HcaR The C-termin 22.0 97 0.0021 19.4 2.4 19 8-26 16-34 (196)
52 cd04823 ALAD_PBGS_aspartate_ri 21.9 97 0.0021 25.1 2.8 24 8-31 97-121 (320)
53 cd00384 ALAD_PBGS Porphobilino 21.8 99 0.0022 24.9 2.9 23 8-30 92-115 (314)
54 cd04824 eu_ALAD_PBGS_cysteine_ 21.7 1E+02 0.0022 25.0 2.9 23 8-30 95-118 (320)
55 cd08441 PBP2_MetR The C-termin 20.9 1E+02 0.0022 19.4 2.4 18 8-25 16-33 (198)
56 cd08451 PBP2_BudR The C-termin 20.9 1.1E+02 0.0023 19.1 2.4 19 7-25 16-34 (199)
57 PF01887 SAM_adeno_trans: S-ad 20.9 1.7E+02 0.0036 22.3 3.9 25 11-35 50-74 (258)
58 cd08471 PBP2_CrgA_like_2 The C 20.6 1.1E+02 0.0024 19.2 2.5 18 9-26 18-35 (201)
59 COG0284 PyrF Orotidine-5'-phos 20.3 1.5E+02 0.0033 22.5 3.5 28 3-44 159-187 (240)
60 cd06533 Glyco_transf_WecG_TagA 20.3 1.3E+02 0.0027 21.0 2.9 50 3-53 50-118 (171)
61 PF00490 ALAD: Delta-aminolevu 20.2 1.2E+02 0.0026 24.6 3.1 24 8-31 100-124 (324)
No 1
>PF14681 UPRTase: Uracil phosphoribosyltransferase; PDB: 1V9S_B 1UPF_A 1UPU_D 1JLR_B 1BD4_A 1BD3_C 1JLS_D 1XTV_C 1XTU_H 3G6W_C ....
Probab=99.90 E-value=1.6e-24 Score=157.05 Aligned_cols=52 Identities=48% Similarity=0.949 Sum_probs=48.0
Q ss_pred CeeeeeCHHHHHHHHHhCCCcEEEEEeecCCCCCCCeEecCCCCccccccCC
Q psy9632 1 MTTPAITISGIHSIAYAFPNVKIVTSAVDPEINENFYVIPGIGNFGDRYFGT 52 (83)
Q Consensus 1 ~lSliaS~~Gi~~v~~~fP~v~I~ta~ID~~Lde~~yIvPGlGD~GDR~fgt 52 (83)
++|+|+|++||+++.++||+++|||++||++||+++||+|||||||||||||
T Consensus 156 ~v~~ias~~Gl~~l~~~~P~v~I~ta~iD~~L~~~~~i~PGlGD~GdR~fgT 207 (207)
T PF14681_consen 156 IVSVIASPEGLERLLKAFPDVRIYTAAIDPELNENGYIVPGLGDAGDRYFGT 207 (207)
T ss_dssp EEEEEEEHHHHHHHHHHSTTSEEEEEEEESEEETTSEEESS-S-HHHHHHT-
T ss_pred EEEEEecHHHHHHHHHhCCCeEEEEEEEccccCCCCCccCCCCChHhcccCc
Confidence 4799999999999999999999999999999999999999999999999997
No 2
>PLN02541 uracil phosphoribosyltransferase
Probab=99.90 E-value=4.6e-24 Score=160.54 Aligned_cols=52 Identities=31% Similarity=0.694 Sum_probs=51.0
Q ss_pred CeeeeeCHHHHHHHHHhCCCcEEEEEeecCCCCCCCeEecCCCCccccccCC
Q psy9632 1 MTTPAITISGIHSIAYAFPNVKIVTSAVDPEINENFYVIPGIGNFGDRYFGT 52 (83)
Q Consensus 1 ~lSliaS~~Gi~~v~~~fP~v~I~ta~ID~~Lde~~yIvPGlGD~GDR~fgt 52 (83)
++|+||||+||+++.++||+++|||++||++||+++||+|||||||||||||
T Consensus 192 ~v~~ias~~Gl~~i~~~fP~v~I~ta~ID~~Lne~~yIvPGlGDaGDR~fGt 243 (244)
T PLN02541 192 VVCAVAAPPALKKLSEKFPGLHVYAGIIDEEVNEKGYIVPGLGDAGDRSFGT 243 (244)
T ss_pred EEEEEECHHHHHHHHHHCcCCEEEEEEECccccCCCcCcCCCCCccccccCC
Confidence 5899999999999999999999999999999999999999999999999998
No 3
>COG0035 Upp Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=99.89 E-value=5e-24 Score=158.89 Aligned_cols=53 Identities=40% Similarity=0.757 Sum_probs=51.5
Q ss_pred CeeeeeCHHHHHHHHHhCCCcEEEEEeecCCCCCCCeEecCCCCccccccCCC
Q psy9632 1 MTTPAITISGIHSIAYAFPNVKIVTSAVDPEINENFYVIPGIGNFGDRYFGTE 53 (83)
Q Consensus 1 ~lSliaS~~Gi~~v~~~fP~v~I~ta~ID~~Lde~~yIvPGlGD~GDR~fgt~ 53 (83)
++++||||+||+++.++||+|+||||+||++|||++||+|||||||||+|||+
T Consensus 158 ~v~~vAapeGi~~v~~~~p~v~I~ta~iD~~Lne~gYIvPGLGDaGDR~fGt~ 210 (210)
T COG0035 158 VVSLVAAPEGIKAVEKAHPDVEIYTAAIDEGLNEKGYIVPGLGDAGDRLFGTK 210 (210)
T ss_pred EEEEEecHHHHHHHHHhCCCCeEEEEEeccccccCCCCccCCCcccccccCCC
Confidence 58999999999999999999999999999999999999999999999999985
No 4
>TIGR01091 upp uracil phosphoribosyltransferase. that includes uracil phosphoribosyltransferase, uridine kinases, and other, uncharacterized proteins.
Probab=99.86 E-value=2.3e-22 Score=145.75 Aligned_cols=53 Identities=40% Similarity=0.753 Sum_probs=50.9
Q ss_pred CeeeeeCHHHHHHHHHhCCCcEEEEEeecCCCCCCCeEecCCCCccccccCCC
Q psy9632 1 MTTPAITISGIHSIAYAFPNVKIVTSAVDPEINENFYVIPGIGNFGDRYFGTE 53 (83)
Q Consensus 1 ~lSliaS~~Gi~~v~~~fP~v~I~ta~ID~~Lde~~yIvPGlGD~GDR~fgt~ 53 (83)
+++++++++|++++.++||+++|||++||++||+++||+||+||||||||||.
T Consensus 155 v~~ll~~~~gl~~l~~~~p~v~i~~~~id~~l~~~~yivPGlGd~Gdr~fgt~ 207 (207)
T TIGR01091 155 VLSIVAAPEGIEAVEKAHPDVDIYTAAIDEKLNDNGYIVPGLGDAGDRAFGTK 207 (207)
T ss_pred EEEEecCHHHHHHHHHHCCCCEEEEEEECCCccCCccCcCCCCCccccccCCC
Confidence 36889999999999999999999999999999999999999999999999983
No 5
>PRK00129 upp uracil phosphoribosyltransferase; Reviewed
Probab=99.86 E-value=3.1e-22 Score=145.06 Aligned_cols=53 Identities=40% Similarity=0.745 Sum_probs=50.8
Q ss_pred CeeeeeCHHHHHHHHHhCCCcEEEEEeecCCCCCCCeEecCCCCccccccCCC
Q psy9632 1 MTTPAITISGIHSIAYAFPNVKIVTSAVDPEINENFYVIPGIGNFGDRYFGTE 53 (83)
Q Consensus 1 ~lSliaS~~Gi~~v~~~fP~v~I~ta~ID~~Lde~~yIvPGlGD~GDR~fgt~ 53 (83)
+++++++++|++++.++||+++|||++||++||+++||+||+||||||||||.
T Consensus 157 ~~~ll~~~~gl~~l~~~~p~v~i~~~~iD~~l~~~~yi~PGlGd~Gdr~fgt~ 209 (209)
T PRK00129 157 VLCLVAAPEGIKALEEAHPDVEIYTAAIDEKLNEHGYIVPGLGDAGDRLFGTK 209 (209)
T ss_pred EEEEecCHHHHHHHHHHCCCcEEEEEeecCCcCCCCcCCCCCCCccccccCCC
Confidence 36889999999999999999999999999999999999999999999999983
No 6
>KOG4203|consensus
Probab=99.18 E-value=5.7e-12 Score=102.25 Aligned_cols=53 Identities=58% Similarity=1.034 Sum_probs=50.3
Q ss_pred CeeeeeCHHHHHHHHHhCCCcEEEEEeecCCCCCCCeEecCCCCccccccCCC
Q psy9632 1 MTTPAITISGIHSIAYAFPNVKIVTSAVDPEINENFYVIPGIGNFGDRYFGTE 53 (83)
Q Consensus 1 ~lSliaS~~Gi~~v~~~fP~v~I~ta~ID~~Lde~~yIvPGlGD~GDR~fgt~ 53 (83)
+++++++++|++.++.+||.++++++++|+.+|+++|++||+|||||||||+.
T Consensus 421 ~~~ll~~~~~~~~~~~~f~~v~~v~~~~d~~~~~~~~~~pg~g~~~dryfg~~ 473 (473)
T KOG4203|consen 421 FLNLLAAPQGIHEVAYAFPKVKIVTSQIDKLLNEKRYVVPGLGNFGDRYFGTD 473 (473)
T ss_pred HHHHHhhhhhhhHHHHhcccceeehhhhcccccccceECcccccchhhccCCC
Confidence 35789999999999999999999999999999999999999999999999973
No 7
>KOG1017|consensus
Probab=97.18 E-value=0.00037 Score=53.77 Aligned_cols=44 Identities=36% Similarity=0.720 Sum_probs=39.6
Q ss_pred CeeeeeCHHHHHHHHHhCCCcEEEEEeecCCCCCCCeEecCCCCccccccCCC
Q psy9632 1 MTTPAITISGIHSIAYAFPNVKIVTSAVDPEINENFYVIPGIGNFGDRYFGTE 53 (83)
Q Consensus 1 ~lSliaS~~Gi~~v~~~fP~v~I~ta~ID~~Lde~~yIvPGlGD~GDR~fgt~ 53 (83)
++|++.+|-|++.+.++||.++|+|+.|.|--.++ ||..||||.
T Consensus 224 L~sLF~tP~gak~i~~~fP~itiltseihpvaPnH---------FgqkYFGtd 267 (267)
T KOG1017|consen 224 LVSLFITPTGAKNITRKFPYITILTSEIHPVAPNH---------FGQKYFGTD 267 (267)
T ss_pred EEEeeecchhhHHHHHhCCeEEEEeecceecCccc---------ccchhcCCC
Confidence 57999999999999999999999999999987764 788999974
No 8
>PF09960 DUF2194: Uncharacterized protein conserved in bacteria (DUF2194); InterPro: IPR018695 This family of prokaryotic proteins has no known function; however it may be a membrane protein.
Probab=76.02 E-value=4.9 Score=34.33 Aligned_cols=33 Identities=24% Similarity=0.363 Sum_probs=26.5
Q ss_pred eeCHHHHHHHHHhCCCcEEEEEeecCCCCCCCe
Q psy9632 5 AITISGIHSIAYAFPNVKIVTSAVDPEINENFY 37 (83)
Q Consensus 5 iaS~~Gi~~v~~~fP~v~I~ta~ID~~Lde~~y 37 (83)
|-+++|++.|.+.||+++++.+.-..+-.+..|
T Consensus 404 ils~eG~e~L~~~~P~ik~IaS~Y~~~~~~~~y 436 (585)
T PF09960_consen 404 ILSEEGREALKKAFPEIKTIASLYFGDDEEGEY 436 (585)
T ss_pred ccCHHHHHHHHHhCCCeEEEEEeeecCCcCCcc
Confidence 568999999999999999999876665554433
No 9
>PF00984 UDPG_MGDP_dh: UDP-glucose/GDP-mannose dehydrogenase family, central domain; InterPro: IPR014026 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [, ]. The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin [], which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation []. In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence []. GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyses the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response [], while in A. vinelandii it is essential for the encystment process []. This entry represents an alpha helical region that serves as the dimerisation interface for these enzymes [, ].; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 2O3J_A 3OJO_A 3OJL_A 3PLR_A 3PJG_A 3PID_A 3PLN_A 3PHL_A 3TDK_B 2Q3E_A ....
Probab=63.36 E-value=2.1 Score=28.06 Aligned_cols=9 Identities=67% Similarity=1.398 Sum_probs=5.9
Q ss_pred ccCcccccc
Q psy9632 66 TAGGSCLPR 74 (83)
Q Consensus 66 ~~~~~~~~~ 74 (83)
-+||+|||+
T Consensus 59 g~GG~Clpk 67 (96)
T PF00984_consen 59 GFGGSCLPK 67 (96)
T ss_dssp S--SSCHHH
T ss_pred CCCCcchhh
Confidence 479999996
No 10
>COG2159 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]
Probab=51.72 E-value=13 Score=28.37 Aligned_cols=23 Identities=26% Similarity=0.381 Sum_probs=19.3
Q ss_pred CHHHHHHHHHhCCCcEEEEEeec
Q psy9632 7 TISGIHSIAYAFPNVKIVTSAVD 29 (83)
Q Consensus 7 S~~Gi~~v~~~fP~v~I~ta~ID 29 (83)
.+-=++.++++||+++|+.+.+=
T Consensus 179 ~p~~~~~va~~fP~l~IVl~H~G 201 (293)
T COG2159 179 DPLYLDDVARKFPELKIVLGHMG 201 (293)
T ss_pred CchHHHHHHHHCCCCcEEEEecC
Confidence 44568899999999999999874
No 11
>PF15608 PELOTA_1: PELOTA RNA binding domain
Probab=49.71 E-value=6.6 Score=26.70 Aligned_cols=16 Identities=31% Similarity=0.505 Sum_probs=13.4
Q ss_pred CCCCCCeEecCCCCcc
Q psy9632 31 EINENFYVIPGIGNFG 46 (83)
Q Consensus 31 ~Lde~~yIvPGlGD~G 46 (83)
++++-.+|.||+|.+-
T Consensus 33 gI~diN~IKPGIgEaT 48 (100)
T PF15608_consen 33 GISDINLIKPGIGEAT 48 (100)
T ss_pred CCCCcccccCChhHHH
Confidence 5677789999999875
No 12
>PF03452 Anp1: Anp1; InterPro: IPR005109 The members of this family (Anp1, Van1 and Mnn9) are membrane proteins required for proper Golgi function. These proteins colocalize within the cis Golgi, where they are physically associated in two distinct complexes [].
Probab=46.58 E-value=13 Score=28.98 Aligned_cols=40 Identities=18% Similarity=0.270 Sum_probs=27.3
Q ss_pred CCCCCCeEecCCCCcc------ccccCCCCCccccccccccccCcccc
Q psy9632 31 EINENFYVIPGIGNFG------DRYFGTEPTITVTGGSIKATAGGSCL 72 (83)
Q Consensus 31 ~Lde~~yIvPGlGD~G------DR~fgt~~~~~~~~~~~~~~~~~~~~ 72 (83)
.++++-+|++|-..+- ..... .....++.+-+-.|||.||
T Consensus 207 ~~~~d~iiveGy~~~~T~r~~m~~~~d--~~~~~~~~v~LDgVGG~~l 252 (269)
T PF03452_consen 207 KLDEDDIIVEGYAEFPTYRPLMAYMRD--PNGDPDEEVPLDGVGGTAL 252 (269)
T ss_pred hcCCCcEEecCcccccchhHHHHhccC--CCCCCCcEEeccccCceeE
Confidence 4666778999988653 22332 2234477888889999997
No 13
>PRK01211 dihydroorotase; Provisional
Probab=46.50 E-value=5.7 Score=31.74 Aligned_cols=43 Identities=16% Similarity=0.186 Sum_probs=31.8
Q ss_pred cCCCCCCCeEecCCCCccc--cccCCCCCccccccccccccCccc
Q psy9632 29 DPEINENFYVIPGIGNFGD--RYFGTEPTITVTGGSIKATAGGSC 71 (83)
Q Consensus 29 D~~Lde~~yIvPGlGD~GD--R~fgt~~~~~~~~~~~~~~~~~~~ 71 (83)
++.+|-+++++||+=|.=- |..|....+++..+...|++||+.
T Consensus 35 ~~~ida~g~vlPG~ID~HvH~r~pg~~~ked~~s~s~AAaaGGvT 79 (409)
T PRK01211 35 IGKKELKGAILPAATDIHVHFRTPGETEKEDFSTGTLSAIFGGTT 79 (409)
T ss_pred ceEEEeccEEcCCeEEeeeccCCCCCcccCcHHHHHHHHHcCCcE
Confidence 3446667799999988643 333445677888899999999985
No 14
>COG0118 HisH Glutamine amidotransferase [Amino acid transport and metabolism]
Probab=45.42 E-value=9.5 Score=28.91 Aligned_cols=40 Identities=20% Similarity=0.483 Sum_probs=25.3
Q ss_pred HHHHHHhCCCc---EEEEEeecCCCCCCCeEecCCCCcccccc
Q psy9632 11 IHSIAYAFPNV---KIVTSAVDPEINENFYVIPGIGNFGDRYF 50 (83)
Q Consensus 11 i~~v~~~fP~v---~I~ta~ID~~Lde~~yIvPGlGD~GDR~f 50 (83)
|..+.+++-.+ .++|..-+.-...++-|+||.|.|.|=.-
T Consensus 14 L~Sv~~Aler~G~~~~vs~d~~~i~~AD~liLPGVGaf~~am~ 56 (204)
T COG0118 14 LRSVKKALERLGAEVVVSRDPEEILKADKLILPGVGAFGAAMA 56 (204)
T ss_pred HHHHHHHHHHcCCeeEEecCHHHHhhCCEEEecCCCCHHHHHH
Confidence 44444444332 34555555556788999999999986443
No 15
>smart00785 AARP2CN AARP2CN (NUC121) domain. This domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU PUBMED:15112237.
Probab=44.50 E-value=10 Score=24.41 Aligned_cols=10 Identities=50% Similarity=1.089 Sum_probs=8.0
Q ss_pred eEecCCCCcc
Q psy9632 37 YVIPGIGNFG 46 (83)
Q Consensus 37 yIvPGlGD~G 46 (83)
-=+||+|||-
T Consensus 63 VHIpG~GDfq 72 (83)
T smart00785 63 VHIPGLGDFQ 72 (83)
T ss_pred EEeCCcCCeE
Confidence 3489999985
No 16
>PF08142 AARP2CN: AARP2CN (NUC121) domain; InterPro: IPR012948 This domain is the central domain of AARP2 (asparagine and aspartate rich protein 2). It is weakly similar to the GTP-binding domain of elongation factor TU []. PfAARP2 is an antigen from Plasmodium falciparum of 150 kDa, which is encoded by a unique gene on chromosome 1 []. The central region of Pfaarp2 contains blocks of repetitions encoding asparagine and aspartate residues. ; GO: 0042254 ribosome biogenesis, 0005634 nucleus
Probab=43.63 E-value=10 Score=24.35 Aligned_cols=15 Identities=47% Similarity=0.944 Sum_probs=10.0
Q ss_pred CCCCCeE-ecCCCCcc
Q psy9632 32 INENFYV-IPGIGNFG 46 (83)
Q Consensus 32 Lde~~yI-vPGlGD~G 46 (83)
|+.+.-| +||+|||-
T Consensus 59 l~~n~lVHIpG~GDFq 74 (85)
T PF08142_consen 59 LSVNQLVHIPGVGDFQ 74 (85)
T ss_pred ccCCCEEEeCCcCCeE
Confidence 4444433 79999985
No 17
>PF09550 DUF2376: Conserved hypothetical phage protein (DUF2376); InterPro: IPR019056 Gene transfer agents belong to a group of unusual genetic exchange elements []. GTAs are unusual in the sense they have the structure of a small tailed phage, which do not possess typical phage traits such as host cell lysis and infectious transmission of the GTA genes. In the Rhodobacter capsulatus GTA the GTA particles contain random 4.5 kb DNA fragments of the R.capsulatus genome. These DNA fragments can be transmitted to other cells where allelic conversion may occur via homologous recombination. The genes coding for the GTA particles are of two distinct types: the first is a cluster of genes reminiscent of a cryptyic prophage, where a number of the genes have similarity to known phage structural genes; the second type consists of two genes coding for a cellular two-component signal transduction system, which regulates the transcription of the GTA structural gene cluster in a growth phase dependent manner []. This entry is represented by ORFg10.1 (RCAP_rcc01693) of the Gene Transfer Agent (GTA) of Rhodobacter capsulatus [see Fig.1, in ]. The function is not known.
Probab=43.55 E-value=23 Score=20.62 Aligned_cols=14 Identities=14% Similarity=0.446 Sum_probs=12.6
Q ss_pred CHHHHHHHHHhCCC
Q psy9632 7 TISGIHSIAYAFPN 20 (83)
Q Consensus 7 S~~Gi~~v~~~fP~ 20 (83)
+..+++.++++|||
T Consensus 30 ~R~~L~~Lm~~~PD 43 (43)
T PF09550_consen 30 DRAELDALMRRFPD 43 (43)
T ss_pred CHHHHHHHHHHCcC
Confidence 57889999999997
No 18
>PF01819 Levi_coat: Levivirus coat protein; InterPro: IPR002703 This entry represents the coat proteins of the leviviruses (phage MS2) and alloleviruses (phage Qbeta and phage F1). The Levivirus coat protein forms the bacteriophage coat that encapsidates the viral RNA. 180 copies of this protein form the virion shell. The Bacteriophage MS2 coat protein controls two distinct processes: sequence-specific RNA encapsidation and repression of replicase translation-by binding to an RNA stem-loop structure of 19 nucleotides containing the initiation codon of the replicase gene. The binding of a coat protein dimer to this hairpin shuts off synthesis of the viral replicase, switching the viral replication cycle to virion assembly rather than continued replication [].; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 2VF9_A 6MSF_A 2MS2_A 1ZDI_B 2BS1_C 1MST_C 2C4Y_A 1ZDK_B 1ZDJ_A 1ZSE_B ....
Probab=42.65 E-value=9.1 Score=27.33 Aligned_cols=16 Identities=31% Similarity=0.349 Sum_probs=12.5
Q ss_pred ccccccCcccccceec
Q psy9632 62 SIKATAGGSCLPRVET 77 (83)
Q Consensus 62 ~~~~~~~~~~~~~~~~ 77 (83)
.-.|+++|+|+|-+--
T Consensus 68 ~~tqt~~Gve~Pvv~r 83 (129)
T PF01819_consen 68 VTTQTVNGVELPVVAR 83 (129)
T ss_dssp EEEEEETTEEEEEEEE
T ss_pred ceeEeeCcEecchHhh
Confidence 3468999999997643
No 19
>PF04909 Amidohydro_2: Amidohydrolase; InterPro: IPR006992 These proteins are related to the metal-dependent hydrolase superfamily []. The family includes 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase which converts alpha-amino-beta-carboxymuconate-epsilon- semialdehyde (ACMS) to alpha-aminomuconate semialdehyde (AMS). ACMS can be converted non-enzymatically to quinolate, a potent endogenous excitoxin of neuronal cells which is implicated in the pathogenesis of various neurodegenerative disorders. In the presence of AMCSD, ACMS is converted to AMS, a benign catabolite. 2-amino-3-(3-oxoprop-2-enyl)-but-2-enedioate = 2-aminomuconate semialdehyde + CO2. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2QPX_A 4D8L_A 3K4W_I 3IRS_B 4DZI_B 3S4T_G 2GWG_B 3IJ6_A 2DVX_C 2DVT_C ....
Probab=38.79 E-value=16 Score=25.36 Aligned_cols=22 Identities=14% Similarity=0.421 Sum_probs=16.9
Q ss_pred CHHHHHHHHHhCCCcEEEEEee
Q psy9632 7 TISGIHSIAYAFPNVKIVTSAV 28 (83)
Q Consensus 7 S~~Gi~~v~~~fP~v~I~ta~I 28 (83)
.+.=+..+..+||+++|+.+..
T Consensus 151 ~~~~~~~~~~~~P~l~ii~~H~ 172 (273)
T PF04909_consen 151 DPEELEELLERFPDLRIILAHL 172 (273)
T ss_dssp HHHHHTTHHHHSTTSEEEESGG
T ss_pred HHHHHHHHHHHhcCCeEEEecC
Confidence 3445778899999999987654
No 20
>PRK15057 UDP-glucose 6-dehydrogenase; Provisional
Probab=36.33 E-value=13 Score=29.51 Aligned_cols=8 Identities=63% Similarity=1.452 Sum_probs=6.8
Q ss_pred cCcccccc
Q psy9632 67 AGGSCLPR 74 (83)
Q Consensus 67 ~~~~~~~~ 74 (83)
+||+|+|+
T Consensus 249 ~GG~Clpk 256 (388)
T PRK15057 249 YGGYCLPK 256 (388)
T ss_pred CCCcChhh
Confidence 78999986
No 21
>PF01148 CTP_transf_1: Cytidylyltransferase family; InterPro: IPR000374 Phosphatidate cytidylyltransferase (2.7.7.41 from EC) [, , ] (also known as CDP- diacylglycerol synthase) (CDS) is the enzyme that catalyzes the synthesis of CDP-diacylglycerol from CTP and phosphatidate (PA): CTP + phosphatidate = diphosphate + CDP-diacylglycerol CDP-diacylglycerol is an important branch point intermediate in both prokaryotic and eukaryotic organisms. CDS is a membrane-bound enzyme.; GO: 0016772 transferase activity, transferring phosphorus-containing groups, 0016020 membrane
Probab=34.89 E-value=16 Score=25.72 Aligned_cols=21 Identities=33% Similarity=0.520 Sum_probs=17.4
Q ss_pred CCCCCCCeEecCCCCcccccc
Q psy9632 30 PEINENFYVIPGIGNFGDRYF 50 (83)
Q Consensus 30 ~~Lde~~yIvPGlGD~GDR~f 50 (83)
-++-|-+.++||-|..-||+-
T Consensus 223 ~~iKD~g~lipghGg~lDr~d 243 (259)
T PF01148_consen 223 AGIKDSGNLIPGHGGILDRFD 243 (259)
T ss_pred hhcccccccccCcCCcccchH
Confidence 345677999999999999974
No 22
>PRK00125 pyrF orotidine 5'-phosphate decarboxylase; Reviewed
Probab=34.82 E-value=59 Score=25.17 Aligned_cols=30 Identities=20% Similarity=0.369 Sum_probs=21.8
Q ss_pred eeeC--HHHHHHHHHhCCCcEEEEEeecCCCCCCCeEecCCCCccc
Q psy9632 4 PAIT--ISGIHSIAYAFPNVKIVTSAVDPEINENFYVIPGIGNFGD 47 (83)
Q Consensus 4 liaS--~~Gi~~v~~~fP~v~I~ta~ID~~Lde~~yIvPGlGD~GD 47 (83)
+++| |+=+.++.+.+|+..| ++||+|-.|.
T Consensus 194 VVgaT~p~e~~~iR~~~~~~~i--------------L~PGigaQGg 225 (278)
T PRK00125 194 VVGATFPPELAAVRKILGGMPL--------------LIPGIGAQGG 225 (278)
T ss_pred EECCCCHHHHHHHHHhCCCCeE--------------EeCCcCCCCc
Confidence 5666 6667778777777544 8999997663
No 23
>TIGR02127 pyrF_sub2 orotidine 5'-phosphate decarboxylase, subfamily 2. This model represents orotidine 5'-monophosphate decarboxylase, the PyrF protein of pyrimidine nucleotide biosynthesis. See TIGR01740 for a related but distinct subfamily of the same enzyme.
Probab=34.79 E-value=68 Score=24.45 Aligned_cols=29 Identities=17% Similarity=0.526 Sum_probs=21.8
Q ss_pred eee---CHHHHHHHHHhCCCcEEEEEeecCCCCCCCeEecCCCCcc
Q psy9632 4 PAI---TISGIHSIAYAFPNVKIVTSAVDPEINENFYVIPGIGNFG 46 (83)
Q Consensus 4 lia---S~~Gi~~v~~~fP~v~I~ta~ID~~Lde~~yIvPGlGD~G 46 (83)
+++ +|+=+.++.+.+|+..| +.||+|-.|
T Consensus 191 vV~gAT~p~e~~~iR~~~~~~~i--------------l~PGigaqG 222 (261)
T TIGR02127 191 AVVGATSPGDLLRLRIEMPTAPF--------------LVPGFGAQG 222 (261)
T ss_pred EEECCCCHHHHHHHHHhCCCCeE--------------EeCCcCCCC
Confidence 455 77778888887777665 899999655
No 24
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=34.16 E-value=57 Score=19.97 Aligned_cols=32 Identities=19% Similarity=0.539 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCCcEEEEEeecCCCCCCCeEecCCCCc
Q psy9632 9 SGIHSIAYAFPNVKIVTSAVDPEINENFYVIPGIGNF 45 (83)
Q Consensus 9 ~Gi~~v~~~fP~v~I~ta~ID~~Lde~~yIvPGlGD~ 45 (83)
++|+++.++-|-+++ ..|++-.+ +++-|+|+.
T Consensus 23 ~aL~~l~~eDP~l~~---~~d~et~e--~~l~g~Gel 54 (75)
T PF14492_consen 23 EALQKLSEEDPSLRV---ERDEETGE--LILSGMGEL 54 (75)
T ss_dssp HHHHHHHHH-TTSEE---EEETTTSE--EEEEESSHH
T ss_pred HHHHHHHhcCCeEEE---EEcchhce--EEEEECCHH
Confidence 689999999999998 66666444 889999874
No 25
>TIGR02216 phage_TIGR02216 phage conserved hypothetical protein. This model describes a family of proteins found exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA.
Probab=33.42 E-value=40 Score=21.10 Aligned_cols=14 Identities=14% Similarity=0.446 Sum_probs=12.7
Q ss_pred CHHHHHHHHHhCCC
Q psy9632 7 TISGIHSIAYAFPN 20 (83)
Q Consensus 7 S~~Gi~~v~~~fP~ 20 (83)
+..+++.++++|||
T Consensus 46 ~Ra~Ld~Lm~~fPD 59 (60)
T TIGR02216 46 DRAALDALLAAWPD 59 (60)
T ss_pred CHHHHHHHHHHCcC
Confidence 57899999999997
No 26
>PRK11064 wecC UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional
Probab=31.89 E-value=19 Score=28.74 Aligned_cols=8 Identities=38% Similarity=1.070 Sum_probs=5.5
Q ss_pred cCcccccc
Q psy9632 67 AGGSCLPR 74 (83)
Q Consensus 67 ~~~~~~~~ 74 (83)
+||+|+|+
T Consensus 262 ~GG~Clpk 269 (415)
T PRK11064 262 VGGHCIAV 269 (415)
T ss_pred CCCccccc
Confidence 56777775
No 27
>COG0031 CysK Cysteine synthase [Amino acid transport and metabolism]
Probab=31.28 E-value=64 Score=25.56 Aligned_cols=35 Identities=40% Similarity=0.452 Sum_probs=23.4
Q ss_pred HH-HHHHHHhCCCcEEEEEeecCCC---CC---CCeEecCCCCc
Q psy9632 9 SG-IHSIAYAFPNVKIVTSAVDPEI---NE---NFYVIPGIGNF 45 (83)
Q Consensus 9 ~G-i~~v~~~fP~v~I~ta~ID~~L---de---~~yIvPGlGD~ 45 (83)
.| -+.+.+++|+++|+. +||.= -. ..+.++|||.-
T Consensus 184 tGvar~Lk~~~p~i~iv~--vdP~~S~~~~~G~g~~~i~GIG~~ 225 (300)
T COG0031 184 TGVARYLKERNPNVRIVA--VDPEGSVLLSGGEGPHKIEGIGAG 225 (300)
T ss_pred HHHHHHHHhhCCCcEEEE--ECCCCCcccCCCCCCcccCCCCCC
Confidence 45 356777899999875 45542 11 35788998864
No 28
>PF02550 AcetylCoA_hydro: Acetyl-CoA hydrolase/transferase N-terminal domain; InterPro: IPR003702 This family contains several enzymes which take part in pathways involving acetyl-CoA. Acetyl-CoA hydrolase 3.1.2.1 from EC from yeast catalyses the formation of acetate from acetyl-CoA, CoA transferase (CAT1) 2.8.3 from EC produces succinyl-CoA, and acetate-CoA transferase 2.8.3.8 from EC utilises acyl-CoA and acetate to form acetyl-CoA.; GO: 0003824 catalytic activity, 0006084 acetyl-CoA metabolic process; PDB: 2NVV_C 2G39_A 3D3U_A 3S8D_B 3QLI_B 3QLK_B 3GK7_B 3QDQ_A 3EH7_A 2OAS_A ....
Probab=30.22 E-value=37 Score=24.16 Aligned_cols=34 Identities=15% Similarity=0.165 Sum_probs=19.9
Q ss_pred HHHhCCCcEEEEEeecCCCCCCCeEecCCCCcccc
Q psy9632 14 IAYAFPNVKIVTSAVDPEINENFYVIPGIGNFGDR 48 (83)
Q Consensus 14 v~~~fP~v~I~ta~ID~~Lde~~yIvPGlGD~GDR 48 (83)
+.+.+..+.+...++ ..+|++||+.+|++.--.|
T Consensus 118 ~~~~~~~~Dvaii~v-Sp~De~Gy~slG~s~~~~~ 151 (198)
T PF02550_consen 118 FRRGFIPIDVAIIQV-SPMDEHGYFSLGTSVDYTK 151 (198)
T ss_dssp HHTTSSH-SEEEEEE-CEE-TTSEEECTTBHBTHH
T ss_pred HHcCCCCCCEEEEEe-cCcCCCCCEeecHHHHhHH
Confidence 333444344444444 6789999999999854443
No 29
>PF02991 Atg8: Autophagy protein Atg8 ubiquitin like; InterPro: IPR004241 Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N terminus and the C terminus of Atg19. Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [] Related proteins that belong to this group include the human ganglioside expression factor and a symbiosis-related fungal protein.; PDB: 3ECI_A 3D32_B 1GNU_A 1KM7_A 1KLV_A 1KOT_A 3DOW_A 1KJT_A 1V49_A 2ZJD_C ....
Probab=30.07 E-value=1.1e+02 Score=20.51 Aligned_cols=65 Identities=11% Similarity=0.298 Sum_probs=33.3
Q ss_pred HHHHHHhCCC-cEEEEEeec----CCCCCCCeEecCCCCccccccCCCCCccc-cccccccccCccccccee
Q psy9632 11 IHSIAYAFPN-VKIVTSAVD----PEINENFYVIPGIGNFGDRYFGTEPTITV-TGGSIKATAGGSCLPRVE 76 (83)
Q Consensus 11 i~~v~~~fP~-v~I~ta~ID----~~Lde~~yIvPGlGD~GDR~fgt~~~~~~-~~~~~~~~~~~~~~~~~~ 76 (83)
.+++.++||+ |-|++=-.. +.||...|++|.=--.++=.+-....... .+..+--.|++ ++|...
T Consensus 6 ~~~ir~kyP~~IPVIvEr~~~s~lp~ldk~KfLvp~~~tv~qf~~~ir~rl~l~~~~alfl~Vn~-~lp~~s 76 (104)
T PF02991_consen 6 SERIREKYPDKIPVIVERYPKSKLPDLDKKKFLVPKDLTVGQFVYIIRKRLQLSPEQALFLFVNN-TLPSTS 76 (104)
T ss_dssp HHHHHHHSTTEEEEEEEE-TTSSS---SSSEEEEETTSBHHHHHHHHHHHTT--TTS-EEEEBTT-BESSTT
T ss_pred HHHHHHHCCCccEEEEEEccCCChhhcCccEEEEcCCCchhhHHHHhhhhhcCCCCceEEEEEcC-cccchh
Confidence 5678999999 666654433 35788899999744333222211111111 12334445677 677543
No 30
>KOG4388|consensus
Probab=28.73 E-value=39 Score=30.33 Aligned_cols=25 Identities=28% Similarity=0.579 Sum_probs=21.7
Q ss_pred HHHHHhCCCcEEEEEeecCCCCCCC
Q psy9632 12 HSIAYAFPNVKIVTSAVDPEINENF 36 (83)
Q Consensus 12 ~~v~~~fP~v~I~ta~ID~~Lde~~ 36 (83)
+...++.|.++|++.++||-||+-=
T Consensus 781 de~l~qLPp~~i~ac~mDP~LDD~v 805 (880)
T KOG4388|consen 781 DEMLKQLPPVHIVACAMDPMLDDSV 805 (880)
T ss_pred hHHHhcCCCceEEEeccCcchhHHH
Confidence 4567889999999999999999853
No 31
>KOG1593|consensus
Probab=28.56 E-value=60 Score=26.39 Aligned_cols=37 Identities=22% Similarity=0.428 Sum_probs=27.3
Q ss_pred eeCHHHHHHHHHhCCCcEEEEEeecCCCCCCCeEecCCCCccccccCC
Q psy9632 5 AITISGIHSIAYAFPNVKIVTSAVDPEINENFYVIPGIGNFGDRYFGT 52 (83)
Q Consensus 5 iaS~~Gi~~v~~~fP~v~I~ta~ID~~Lde~~yIvPGlGD~GDR~fgt 52 (83)
.|++.+|.+|.+.||+..--.-++|. +|.+|-+.||.
T Consensus 287 eAa~~~i~RI~khfp~F~gAvia~n~-----------~G~ygaaC~g~ 323 (349)
T KOG1593|consen 287 EAAQKAISRILKHFPDFSGAVIAANV-----------LGSYGAACYGI 323 (349)
T ss_pred HHHHHHHHHHHHhCccceeeEEEEec-----------cCchhhhhccc
Confidence 46789999999999997644444443 67777777775
No 32
>cd03144 GATase1_ScBLP_like Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP). Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP). Biotin-apoprotein ligase modifies proteins by covalently attaching biotin. ScBLP is known to biotinylate acety-CoA carboxylase and pyruvate carboxylase. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, the Cys residue found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow in a typical GATase1 domain is conserved.
Probab=28.48 E-value=41 Score=22.91 Aligned_cols=43 Identities=19% Similarity=0.133 Sum_probs=25.4
Q ss_pred CHHHHHHHHHhCCC---cEEEEEeecCC----CCCCCeEecCCCCcccccc
Q psy9632 7 TISGIHSIAYAFPN---VKIVTSAVDPE----INENFYVIPGIGNFGDRYF 50 (83)
Q Consensus 7 S~~Gi~~v~~~fP~---v~I~ta~ID~~----Lde~~yIvPGlGD~GDR~f 50 (83)
++.-++++.+.+.. +..++++.-.. .+-+..|+|| |.|++-.-
T Consensus 11 ~~~~~~~~~~~L~~~~~v~~~~~~~I~~~~~~~~ad~lVlPG-Ga~~~~~~ 60 (114)
T cd03144 11 SPGSLKHLAELLRLYLAVSTVTADELAVGPWESKTALLVVPG-GADLPYCR 60 (114)
T ss_pred CHHHHHHHHHHHhhccceeeecHHHHhcCchhhCCCEEEECC-CChHHHHH
Confidence 44456666666554 44444433222 2456899999 99986544
No 33
>COG1004 Ugd Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]
Probab=28.40 E-value=21 Score=29.67 Aligned_cols=8 Identities=63% Similarity=1.539 Sum_probs=6.5
Q ss_pred cCcccccc
Q psy9632 67 AGGSCLPR 74 (83)
Q Consensus 67 ~~~~~~~~ 74 (83)
-||||+|.
T Consensus 258 yGGsCfPK 265 (414)
T COG1004 258 YGGSCFPK 265 (414)
T ss_pred CCCcCCcH
Confidence 48999995
No 34
>COG4878 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.21 E-value=88 Score=25.26 Aligned_cols=25 Identities=16% Similarity=0.263 Sum_probs=20.4
Q ss_pred eeeCHHHHHHHHHhCCCcEEEEEee
Q psy9632 4 PAITISGIHSIAYAFPNVKIVTSAV 28 (83)
Q Consensus 4 liaS~~Gi~~v~~~fP~v~I~ta~I 28 (83)
-+-.|+|...+.+++|+++.+.+..
T Consensus 115 nil~q~gk~alvk~~p~lktissiy 139 (309)
T COG4878 115 NILLQKGKFALVKQAPSLKTISSIY 139 (309)
T ss_pred cccchhHHHHHHHhCCCcceeeeEe
Confidence 4668999999999999998766543
No 35
>PRK15182 Vi polysaccharide biosynthesis protein TviB; Provisional
Probab=26.51 E-value=25 Score=28.33 Aligned_cols=8 Identities=38% Similarity=0.991 Sum_probs=5.5
Q ss_pred cCcccccc
Q psy9632 67 AGGSCLPR 74 (83)
Q Consensus 67 ~~~~~~~~ 74 (83)
+||+|+|.
T Consensus 257 vGG~Clpk 264 (425)
T PRK15182 257 VGGHCIGV 264 (425)
T ss_pred cccccccc
Confidence 67777774
No 36
>PRK05426 peptidyl-tRNA hydrolase; Provisional
Probab=25.09 E-value=34 Score=25.00 Aligned_cols=20 Identities=40% Similarity=0.607 Sum_probs=17.1
Q ss_pred eEecCCCCccccccCCCCCc
Q psy9632 37 YVIPGIGNFGDRYFGTEPTI 56 (83)
Q Consensus 37 yIvPGlGD~GDR~fgt~~~~ 56 (83)
+++=|||+.|.+|-+|.++-
T Consensus 3 ~LivGLGNPG~~Y~~TRHNv 22 (189)
T PRK05426 3 KLIVGLGNPGPEYANTRHNI 22 (189)
T ss_pred EEEEEeCCCchhhCcCchHH
Confidence 46779999999999998764
No 37
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=25.02 E-value=65 Score=17.54 Aligned_cols=15 Identities=27% Similarity=0.574 Sum_probs=12.4
Q ss_pred HHHHHHHHHhCCCcE
Q psy9632 8 ISGIHSIAYAFPNVK 22 (83)
Q Consensus 8 ~~Gi~~v~~~fP~v~ 22 (83)
.+.++.+.+.||++.
T Consensus 3 ~~~v~~L~~mFP~l~ 17 (43)
T smart00546 3 DEALHDLKDMFPNLD 17 (43)
T ss_pred HHHHHHHHHHCCCCC
Confidence 467899999999874
No 38
>PLN02353 probable UDP-glucose 6-dehydrogenase
Probab=24.89 E-value=26 Score=28.85 Aligned_cols=8 Identities=50% Similarity=1.211 Sum_probs=6.5
Q ss_pred cCcccccc
Q psy9632 67 AGGSCLPR 74 (83)
Q Consensus 67 ~~~~~~~~ 74 (83)
+||+|+|+
T Consensus 268 ~GG~Clpk 275 (473)
T PLN02353 268 FGGSCFQK 275 (473)
T ss_pred CCCcchhh
Confidence 68888885
No 39
>cd05311 NAD_bind_2_malic_enz NAD(P) binding domain of malic enzyme (ME), subgroup 2. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists primarily of archaeal and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydroph
Probab=24.55 E-value=25 Score=25.84 Aligned_cols=26 Identities=23% Similarity=0.210 Sum_probs=15.1
Q ss_pred CcEEEEEeecC--CCCCCCeEecCCCCc
Q psy9632 20 NVKIVTSAVDP--EINENFYVIPGIGNF 45 (83)
Q Consensus 20 ~v~I~ta~ID~--~Lde~~yIvPGlGD~ 45 (83)
..+|+.....- .=-++.||.||||-.
T Consensus 143 ga~i~a~G~~~~~~Q~nn~~~fPg~~~g 170 (226)
T cd05311 143 GADIVATGRSDFPNQVNNVLGFPGIFRG 170 (226)
T ss_pred CCcEEEeCCCCCccccceeeecchhhHH
Confidence 55544433222 223567999999853
No 40
>KOG2255|consensus
Probab=24.52 E-value=63 Score=25.00 Aligned_cols=32 Identities=28% Similarity=0.645 Sum_probs=25.3
Q ss_pred EEeecCCCCCCCeEecCCCCccccccCCCCCc
Q psy9632 25 TSAVDPEINENFYVIPGIGNFGDRYFGTEPTI 56 (83)
Q Consensus 25 ta~ID~~Lde~~yIvPGlGD~GDR~fgt~~~~ 56 (83)
.+..-+....+-.|+=||||.|..|.||..+-
T Consensus 28 ~c~l~~~~~~k~wli~GLGNPg~~y~gTRHnv 59 (224)
T KOG2255|consen 28 HCDLKPRVSIKPWLIVGLGNPGSKYVGTRHNV 59 (224)
T ss_pred eeecccCCCCCceEEEecCCCcccccccchhh
Confidence 34455666666789999999999999998764
No 41
>cd08436 PBP2_LTTR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=24.51 E-value=84 Score=19.46 Aligned_cols=19 Identities=16% Similarity=0.092 Sum_probs=14.7
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q psy9632 8 ISGIHSIAYAFPNVKIVTS 26 (83)
Q Consensus 8 ~~Gi~~v~~~fP~v~I~ta 26 (83)
++-+.++.++||+++|-..
T Consensus 16 ~~~l~~~~~~~P~v~i~i~ 34 (194)
T cd08436 16 PELLARFHRRHPGVDIRLR 34 (194)
T ss_pred HHHHHHHHHHCCCcEEEEe
Confidence 5668999999999776543
No 42
>cd08472 PBP2_CrgA_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=24.45 E-value=84 Score=19.76 Aligned_cols=19 Identities=11% Similarity=0.392 Sum_probs=15.0
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q psy9632 8 ISGIHSIAYAFPNVKIVTS 26 (83)
Q Consensus 8 ~~Gi~~v~~~fP~v~I~ta 26 (83)
++-+.++.++||+++|-..
T Consensus 17 ~~~l~~~~~~~P~i~v~~~ 35 (202)
T cd08472 17 IPALPDFLARYPDIELDLG 35 (202)
T ss_pred HHHHHHHHHHCCCcEEEEE
Confidence 4568899999999877654
No 43
>PRK07627 dihydroorotase; Provisional
Probab=24.41 E-value=26 Score=27.92 Aligned_cols=40 Identities=30% Similarity=0.433 Sum_probs=27.7
Q ss_pred CCCC-CeEecCCCCccccc--cCCCCCccccccccccccCccc
Q psy9632 32 INEN-FYVIPGIGNFGDRY--FGTEPTITVTGGSIKATAGGSC 71 (83)
Q Consensus 32 Lde~-~yIvPGlGD~GDR~--fgt~~~~~~~~~~~~~~~~~~~ 71 (83)
+|.+ .+++||+-|.=--+ .|....+++......+..||+.
T Consensus 46 iDa~g~~vlPG~iD~H~H~~~~g~~~~e~~~t~s~aa~~gGvT 88 (425)
T PRK07627 46 IDASGLIVCPGLVDLSARLREPGYEYKATLESEMAAAVAGGVT 88 (425)
T ss_pred EECCCCEEeccEEeccccccCCCccccCcHHHHHHHHHhCCee
Confidence 4433 59999999875332 3434456667788899999985
No 44
>KOG0907|consensus
Probab=24.02 E-value=1.1e+02 Score=20.22 Aligned_cols=20 Identities=25% Similarity=0.491 Sum_probs=18.5
Q ss_pred HHHHHHhCCCcEEEEEeecC
Q psy9632 11 IHSIAYAFPNVKIVTSAVDP 30 (83)
Q Consensus 11 i~~v~~~fP~v~I~ta~ID~ 30 (83)
++.++++||++.++.--+|+
T Consensus 43 ~~~La~~y~~v~Flkvdvde 62 (106)
T KOG0907|consen 43 FEKLAEKYPDVVFLKVDVDE 62 (106)
T ss_pred HHHHHHHCCCCEEEEEeccc
Confidence 68899999999999999997
No 45
>cd08464 PBP2_DntR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=23.70 E-value=88 Score=19.63 Aligned_cols=19 Identities=16% Similarity=0.214 Sum_probs=14.3
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q psy9632 8 ISGIHSIAYAFPNVKIVTS 26 (83)
Q Consensus 8 ~~Gi~~v~~~fP~v~I~ta 26 (83)
+.-+.++.++||+++|-..
T Consensus 16 ~~~l~~~~~~~P~v~l~i~ 34 (200)
T cd08464 16 PPLLAALRAEAPGVRLVFR 34 (200)
T ss_pred HHHHHHHHHHCCCcEEEEe
Confidence 4557899999999776443
No 46
>KOG1654|consensus
Probab=22.67 E-value=1.3e+02 Score=21.08 Aligned_cols=31 Identities=16% Similarity=0.665 Sum_probs=22.8
Q ss_pred HHHHHHhCCC-cEEEEEeec----CCCCCCCeEecC
Q psy9632 11 IHSIAYAFPN-VKIVTSAVD----PEINENFYVIPG 41 (83)
Q Consensus 11 i~~v~~~fP~-v~I~ta~ID----~~Lde~~yIvPG 41 (83)
.++|.++||+ +-+++=--. |.||.+.|++|-
T Consensus 18 ~~~Ir~kyP~riPVIvEk~~~~~lp~lDK~KyLVP~ 53 (116)
T KOG1654|consen 18 VRRIREKYPDRIPVIVEKAGKSQLPDLDKKKYLVPD 53 (116)
T ss_pred HHHHHHHCCCCCcEEEEecccccCcccccceeeccc
Confidence 5679999998 766654222 368889999994
No 47
>cd01316 CAD_DHOase The eukaryotic CAD protein is a trifunctional enzyme of carbamoylphosphate synthetase-aspartate transcarbamoylase-dihydroorotase, which catalyzes the first three steps of de novo pyrimidine nucleotide biosynthesis. Dihydroorotase (DHOase) catalyzes the third step, the reversible interconversion of carbamoyl aspartate to dihydroorotate.
Probab=22.61 E-value=31 Score=26.86 Aligned_cols=36 Identities=22% Similarity=0.242 Sum_probs=26.0
Q ss_pred CeEecCCCCcccc--ccCCCCCccccccccccccCccc
Q psy9632 36 FYVIPGIGNFGDR--YFGTEPTITVTGGSIKATAGGSC 71 (83)
Q Consensus 36 ~yIvPGlGD~GDR--~fgt~~~~~~~~~~~~~~~~~~~ 71 (83)
..++||+=|.=-. ..|....+++..+...|++||++
T Consensus 2 ~~vlPG~ID~HvH~r~pg~~~~ed~~sgs~AAa~GGvT 39 (344)
T cd01316 2 TIRLPGLIDVHVHLREPGATHKEDFASGTKAALAGGFT 39 (344)
T ss_pred eEEeCCeEEeeeccCCCCcCCcChHHHHHHHHHhCCCe
Confidence 4678888776532 23455667888889999999985
No 48
>PRK13384 delta-aminolevulinic acid dehydratase; Provisional
Probab=22.56 E-value=93 Score=25.22 Aligned_cols=23 Identities=13% Similarity=0.215 Sum_probs=18.5
Q ss_pred HHHHHHHHHhCCCcEEEE-EeecC
Q psy9632 8 ISGIHSIAYAFPNVKIVT-SAVDP 30 (83)
Q Consensus 8 ~~Gi~~v~~~fP~v~I~t-a~ID~ 30 (83)
++.|+.+.++||++-|+| .++|+
T Consensus 102 ~~air~iK~~~pdl~vi~DVcLc~ 125 (322)
T PRK13384 102 ARMVRTIKAAVPEMMVIPDICFCE 125 (322)
T ss_pred HHHHHHHHHHCCCeEEEeeeeccc
Confidence 688999999999988877 34454
No 49
>cd08461 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=22.32 E-value=98 Score=19.46 Aligned_cols=18 Identities=11% Similarity=0.213 Sum_probs=13.5
Q ss_pred HHHHHHHHHhCCCcEEEE
Q psy9632 8 ISGIHSIAYAFPNVKIVT 25 (83)
Q Consensus 8 ~~Gi~~v~~~fP~v~I~t 25 (83)
++-+..+.++||+++|-.
T Consensus 16 ~~~l~~f~~~~P~v~i~i 33 (198)
T cd08461 16 PPLLAALRQEAPGVRVAI 33 (198)
T ss_pred HHHHHHHHHHCCCcEEEE
Confidence 456788999999866533
No 50
>cd08470 PBP2_CrgA_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene
Probab=22.09 E-value=97 Score=19.45 Aligned_cols=19 Identities=5% Similarity=0.252 Sum_probs=14.9
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q psy9632 8 ISGIHSIAYAFPNVKIVTS 26 (83)
Q Consensus 8 ~~Gi~~v~~~fP~v~I~ta 26 (83)
++=|.++.++||+++|-..
T Consensus 17 ~~~l~~f~~~~P~v~l~i~ 35 (197)
T cd08470 17 APLVNDFMQRYPKLEVDIE 35 (197)
T ss_pred HHHHHHHHHHCCCeEEEEE
Confidence 4558899999999876554
No 51
>cd08450 PBP2_HcaR The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold. HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=22.02 E-value=97 Score=19.36 Aligned_cols=19 Identities=11% Similarity=0.139 Sum_probs=14.2
Q ss_pred HHHHHHHHHhCCCcEEEEE
Q psy9632 8 ISGIHSIAYAFPNVKIVTS 26 (83)
Q Consensus 8 ~~Gi~~v~~~fP~v~I~ta 26 (83)
++=+..+.++||+++|-.-
T Consensus 16 ~~~l~~~~~~~P~i~l~i~ 34 (196)
T cd08450 16 PEVLPILREEHPDLDVELS 34 (196)
T ss_pred HHHHHHHHhhCCCcEEEEE
Confidence 4557889999999876543
No 52
>cd04823 ALAD_PBGS_aspartate_rich Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. All of PBGS_aspartate_rich contain an aspartate rich metal binding site with the general sequence DXALDX(Y/F)X3G(H/Q)DG. They also contain an allosteric magnesiu
Probab=21.93 E-value=97 Score=25.08 Aligned_cols=24 Identities=42% Similarity=0.650 Sum_probs=19.0
Q ss_pred HHHHHHHHHhCCCcEEEE-EeecCC
Q psy9632 8 ISGIHSIAYAFPNVKIVT-SAVDPE 31 (83)
Q Consensus 8 ~~Gi~~v~~~fP~v~I~t-a~ID~~ 31 (83)
++.|+.+.++||++-|+| .++|+=
T Consensus 97 ~~air~iK~~~p~l~vi~DVclc~Y 121 (320)
T cd04823 97 CRAIRAIKEAFPELGIITDVALDPY 121 (320)
T ss_pred HHHHHHHHHhCCCcEEEEeeeccCC
Confidence 678999999999998877 345543
No 53
>cd00384 ALAD_PBGS Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. They either contain a cysteine-rich zinc binding site (consensus DXCXCX(Y/F)X3G(H/Q)CG) or an aspartate-rich magnesium binding site (consensus DXALDX(Y/F)X3G(H/Q)DG). The cyste
Probab=21.81 E-value=99 Score=24.95 Aligned_cols=23 Identities=22% Similarity=0.326 Sum_probs=18.6
Q ss_pred HHHHHHHHHhCCCcEEEE-EeecC
Q psy9632 8 ISGIHSIAYAFPNVKIVT-SAVDP 30 (83)
Q Consensus 8 ~~Gi~~v~~~fP~v~I~t-a~ID~ 30 (83)
++.|+.+.++||++-|+| .++|+
T Consensus 92 ~~air~iK~~~p~l~vi~DvcLc~ 115 (314)
T cd00384 92 QRAIRAIKEAVPELVVITDVCLCE 115 (314)
T ss_pred HHHHHHHHHhCCCcEEEEeeeccC
Confidence 678999999999988877 34554
No 54
>cd04824 eu_ALAD_PBGS_cysteine_rich Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. The eukaryotic PBGSs represented by this model, which contain a cysteine-rich zinc binding motif (DXCXCX(Y/F)X3G(H/Q)CG), require zinc for their activity, they
Probab=21.73 E-value=1e+02 Score=25.03 Aligned_cols=23 Identities=26% Similarity=0.353 Sum_probs=18.4
Q ss_pred HHHHHHHHHhCCCcEEEE-EeecC
Q psy9632 8 ISGIHSIAYAFPNVKIVT-SAVDP 30 (83)
Q Consensus 8 ~~Gi~~v~~~fP~v~I~t-a~ID~ 30 (83)
++.|+.+.++||++-|+| .++|+
T Consensus 95 ~~air~iK~~~pdl~vi~Dvclc~ 118 (320)
T cd04824 95 IQAIKLIREEFPELLIACDVCLCE 118 (320)
T ss_pred HHHHHHHHHhCCCcEEEEeeeccC
Confidence 688999999999988877 34444
No 55
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=20.94 E-value=1e+02 Score=19.41 Aligned_cols=18 Identities=11% Similarity=0.311 Sum_probs=14.3
Q ss_pred HHHHHHHHHhCCCcEEEE
Q psy9632 8 ISGIHSIAYAFPNVKIVT 25 (83)
Q Consensus 8 ~~Gi~~v~~~fP~v~I~t 25 (83)
++-+..+.++||+++|-.
T Consensus 16 ~~~l~~~~~~~P~i~i~i 33 (198)
T cd08441 16 MPVLDQFRERWPDVELDL 33 (198)
T ss_pred HHHHHHHHHhCCCeEEEE
Confidence 567899999999876543
No 56
>cd08451 PBP2_BudR The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substra
Probab=20.94 E-value=1.1e+02 Score=19.14 Aligned_cols=19 Identities=21% Similarity=0.333 Sum_probs=14.8
Q ss_pred CHHHHHHHHHhCCCcEEEE
Q psy9632 7 TISGIHSIAYAFPNVKIVT 25 (83)
Q Consensus 7 S~~Gi~~v~~~fP~v~I~t 25 (83)
-++-++++.++||+++|-.
T Consensus 16 l~~~l~~~~~~~P~i~l~i 34 (199)
T cd08451 16 VPGLIRRFREAYPDVELTL 34 (199)
T ss_pred cHHHHHHHHHHCCCcEEEE
Confidence 3677999999999866543
No 57
>PF01887 SAM_adeno_trans: S-adenosyl-l-methionine hydroxide adenosyltransferase; InterPro: IPR002747 The S-adenosyl-L-methionine (SAM) hydroxide adenosyltransferase family groups several fluorinase and chlorinase enzymes whose common feature is that they mediate nucleophilic reactions of their respective halide ions to the C-5' carbon of SAM []. These enzymes utilise a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. Structural studies indicate that the protein is a homotrimer, with each monomer being composed of N- and C-terminal domains [, ]. The N-terminal domain has a central seven-stranded beta-sheet, which combines parallel and antiparallel strands sandwiched between alpha helices. The C-terminal domain forms a beta-barrel with a greek-key topology. SAM is bound at the interface between the C-terminal domain of one monomer and the N-terminal domain of the neighbouring monomer, with a total of three molecules bound by the trimer.; PDB: 2CW5_C 1WU8_C 2WR8_A 2Q6O_B 2Q6L_A 2Q6K_A 2Q6I_A 2V7T_B 2C4U_F 1RQP_C ....
Probab=20.89 E-value=1.7e+02 Score=22.34 Aligned_cols=25 Identities=20% Similarity=0.352 Sum_probs=18.3
Q ss_pred HHHHHHhCCCcEEEEEeecCCCCCC
Q psy9632 11 IHSIAYAFPNVKIVTSAVDPEINEN 35 (83)
Q Consensus 11 i~~v~~~fP~v~I~ta~ID~~Lde~ 35 (83)
|....+.||+=+|+.+-|||++..+
T Consensus 50 L~~a~~~fP~gtvhl~vVDPgVGt~ 74 (258)
T PF01887_consen 50 LAQAYPYFPKGTVHLAVVDPGVGTE 74 (258)
T ss_dssp HHHHHGGS-TTEEEEEE--TTTTSS
T ss_pred HHHHHhhCCCCCEEEEEECCCCCCC
Confidence 5667788999999999999987664
No 58
>cd08471 PBP2_CrgA_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=20.59 E-value=1.1e+02 Score=19.16 Aligned_cols=18 Identities=22% Similarity=0.266 Sum_probs=13.7
Q ss_pred HHHHHHHHhCCCcEEEEE
Q psy9632 9 SGIHSIAYAFPNVKIVTS 26 (83)
Q Consensus 9 ~Gi~~v~~~fP~v~I~ta 26 (83)
.=+.++.++||+++|-..
T Consensus 18 ~~l~~~~~~~P~v~i~i~ 35 (201)
T cd08471 18 PIITDFLDAYPEVSVRLL 35 (201)
T ss_pred HHHHHHHHHCCCcEEEEE
Confidence 457889999999876543
No 59
>COG0284 PyrF Orotidine-5'-phosphate decarboxylase [Nucleotide transport and metabolism]
Probab=20.33 E-value=1.5e+02 Score=22.47 Aligned_cols=28 Identities=25% Similarity=0.465 Sum_probs=19.9
Q ss_pred eeeeCHHHHHHHHHhC-CCcEEEEEeecCCCCCCCeEecCCCC
Q psy9632 3 TPAITISGIHSIAYAF-PNVKIVTSAVDPEINENFYVIPGIGN 44 (83)
Q Consensus 3 SliaS~~Gi~~v~~~f-P~v~I~ta~ID~~Lde~~yIvPGlGD 44 (83)
-+++|++-+..+.+.. |+..| +.||||=
T Consensus 159 gvv~~~~e~~~ir~~~g~~~~i--------------ltPGIg~ 187 (240)
T COG0284 159 GVVCSAEEVAAIREILGPDFLI--------------LTPGIGA 187 (240)
T ss_pred EEEcCHHHHHHHHHhcCCCcEE--------------ECCCcCc
Confidence 3566777777777776 46666 7788887
No 60
>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.
Probab=20.26 E-value=1.3e+02 Score=21.05 Aligned_cols=50 Identities=12% Similarity=0.111 Sum_probs=29.4
Q ss_pred eeeeCHHH-H----HHHHHhCCCcEEEEEeecCCCCC------------C--CeEecCCCCccccccCCC
Q psy9632 3 TPAITISG-I----HSIAYAFPNVKIVTSAVDPEINE------------N--FYVIPGIGNFGDRYFGTE 53 (83)
Q Consensus 3 SliaS~~G-i----~~v~~~fP~v~I~ta~ID~~Lde------------~--~yIvPGlGD~GDR~fgt~ 53 (83)
.+|.+.++ + +++.++||+++|+. .-|+-.++ . ..|+=|||---.-.|-..
T Consensus 50 ~llG~~~~~~~~~~~~l~~~yp~l~i~g-~~~g~~~~~~~~~i~~~I~~~~pdiv~vglG~PkQE~~~~~ 118 (171)
T cd06533 50 FLLGAKPEVLEKAAERLRARYPGLKIVG-YHHGYFGPEEEEEIIERINASGADILFVGLGAPKQELWIAR 118 (171)
T ss_pred EEECCCHHHHHHHHHHHHHHCCCcEEEE-ecCCCCChhhHHHHHHHHHHcCCCEEEEECCCCHHHHHHHH
Confidence 45566555 3 35888899999864 33433321 1 366667776665555443
No 61
>PF00490 ALAD: Delta-aminolevulinic acid dehydratase; InterPro: IPR001731 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. This entry represents porphobilinogen (PBG) synthase (PBGS, or 5-aminoaevulinic acid dehydratase, or ALAD, 4.2.1.24 from EC), which functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses a Knorr-type condensation reaction between two molecules of ALA to generate porphobilinogen, the pyrrolic building block used in later steps []. The structure of the enzyme is based on a TIM barrel topology made up of eight identical subunits, where each subunit binds to a metal ion that is essential for activity, usually zinc (in yeast, mammals and certain bacteria) or magnesium (in plants and other bacteria). A lysine has been implicated in the catalytic mechanism []. The lack of PBGS enzyme causes a rare porphyric disorder known as ALAD porphyria, which appears to involve conformational changes in the enzyme [.; GO: 0004655 porphobilinogen synthase activity, 0046872 metal ion binding, 0033014 tetrapyrrole biosynthetic process; PDB: 2C1H_A 1W1Z_A 1GZG_B 1W5O_B 1W5Q_B 2C18_A 1B4K_A 2C19_B 1W56_B 2C13_B ....
Probab=20.20 E-value=1.2e+02 Score=24.57 Aligned_cols=24 Identities=25% Similarity=0.391 Sum_probs=18.3
Q ss_pred HHHHHHHHHhCCCcEEEE-EeecCC
Q psy9632 8 ISGIHSIAYAFPNVKIVT-SAVDPE 31 (83)
Q Consensus 8 ~~Gi~~v~~~fP~v~I~t-a~ID~~ 31 (83)
++.|+.+.++||++-|+| .++|+=
T Consensus 100 ~~air~iK~~~pdl~vi~Dvclc~Y 124 (324)
T PF00490_consen 100 QRAIRAIKKAFPDLLVITDVCLCEY 124 (324)
T ss_dssp HHHHHHHHHHSTTSEEEEEE-STTT
T ss_pred HHHHHHHHHhCCCcEEEEecccccc
Confidence 578999999999988876 455553
Done!