Query 038122
Match_columns 130
No_of_seqs 106 out of 1030
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 07:49:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038122.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038122hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00212 hemC porphobilinogen 100.0 2.3E-56 4.9E-61 367.9 10.8 130 1-130 61-237 (292)
2 cd00494 HMBS Hydroxymethylbila 100.0 4E-56 8.6E-61 366.4 11.2 130 1-130 61-237 (292)
3 COG0181 HemC Porphobilinogen d 100.0 1.9E-56 4.1E-61 369.5 9.1 130 1-130 64-240 (307)
4 PRK00072 hemC porphobilinogen 100.0 5.6E-56 1.2E-60 365.9 11.3 130 1-130 65-241 (295)
5 PLN02691 porphobilinogen deami 100.0 1.6E-55 3.4E-60 369.8 11.2 130 1-130 108-284 (351)
6 PF01379 Porphobil_deam: Porph 100.0 3.4E-46 7.3E-51 296.5 5.5 105 1-105 62-215 (215)
7 KOG2892 Porphobilinogen deamin 100.0 1.2E-44 2.6E-49 296.6 5.4 130 1-130 68-248 (320)
8 PRK01066 porphobilinogen deami 100.0 2.8E-44 6E-49 287.9 7.0 106 1-111 78-230 (231)
9 PF14503 YhfZ_C: YhfZ C-termin 82.8 3.4 7.4E-05 33.6 5.5 74 41-117 147-220 (232)
10 cd00134 PBPb Bacterial peripla 62.9 13 0.00028 26.1 3.7 28 38-65 133-160 (218)
11 PRK15007 putative ABC transpor 45.6 45 0.00097 25.1 4.5 23 38-60 154-176 (243)
12 PRK15010 ABC transporter lysin 42.3 73 0.0016 24.6 5.3 20 39-58 164-183 (260)
13 cd08417 PBP2_Nitroaromatics_li 30.4 43 0.00093 23.2 2.1 17 2-18 42-58 (200)
14 PRK11063 metQ DL-methionine tr 29.8 1.3E+02 0.0028 24.4 5.1 66 46-116 190-259 (271)
15 cd08467 PBP2_SyrM The C-termin 29.6 48 0.001 23.4 2.3 16 2-17 42-57 (200)
16 PF07302 AroM: AroM protein; 29.6 27 0.00059 28.2 1.1 55 39-95 75-134 (221)
17 PF07849 DUF1641: Protein of u 29.3 1.2E+02 0.0025 18.1 3.6 30 99-128 12-41 (42)
18 PRK09959 hybrid sensory histid 26.5 1.4E+02 0.0031 28.5 5.4 25 38-62 192-216 (1197)
19 TIGR02995 ectoine_ehuB ectoine 26.5 97 0.0021 24.2 3.7 25 38-62 173-197 (275)
20 cd08425 PBP2_CynR The C-termin 25.9 59 0.0013 22.5 2.2 16 2-17 43-58 (197)
21 cd08464 PBP2_DntR_like_2 The C 25.7 59 0.0013 22.5 2.1 17 2-18 42-58 (200)
22 PF03466 LysR_substrate: LysR 24.9 71 0.0015 22.3 2.4 18 2-19 48-65 (209)
23 cd08459 PBP2_DntR_NahR_LinR_li 24.5 64 0.0014 22.4 2.2 17 2-18 42-58 (201)
24 PRK11013 DNA-binding transcrip 24.4 62 0.0013 25.7 2.3 20 2-21 136-155 (309)
25 cd08466 PBP2_LeuO The C-termin 24.0 64 0.0014 22.3 2.1 16 2-17 42-57 (200)
26 cd08456 PBP2_LysR The C-termin 23.8 66 0.0014 22.1 2.1 16 3-18 43-58 (196)
27 cd05466 PBP2_LTTR_substrate Th 23.6 71 0.0015 21.3 2.1 18 2-19 42-59 (197)
28 cd08419 PBP2_CbbR_RubisCO_like 23.5 68 0.0015 21.9 2.1 16 3-18 42-57 (197)
29 KOG2531 Sugar (pentulose and h 23.5 80 0.0017 28.8 2.9 58 68-125 371-429 (545)
30 cd08418 PBP2_TdcA The C-termin 23.4 50 0.0011 22.8 1.4 16 2-17 42-57 (201)
31 TIGR01096 3A0103s03R lysine-ar 23.0 1.4E+02 0.0031 22.3 3.9 25 39-63 161-185 (250)
32 cd03770 SR_TndX_transposase Se 22.9 51 0.0011 23.8 1.4 27 40-68 57-83 (140)
33 PF09940 DUF2172: Domain of un 22.8 66 0.0014 28.3 2.2 42 14-58 66-110 (386)
34 cd08453 PBP2_IlvR The C-termin 22.5 87 0.0019 21.7 2.5 16 2-17 42-57 (200)
35 cd08420 PBP2_CysL_like C-termi 22.4 54 0.0012 22.3 1.4 15 3-17 43-57 (201)
36 PF00497 SBP_bac_3: Bacterial 22.3 41 0.00088 24.2 0.8 60 38-104 139-202 (225)
37 cd08436 PBP2_LTTR_like_3 The C 22.2 75 0.0016 21.6 2.1 18 2-19 42-59 (194)
38 cd08430 PBP2_IlvY The C-termin 21.4 58 0.0012 22.4 1.4 16 2-17 42-57 (199)
39 cd08452 PBP2_AlsR The C-termin 21.0 81 0.0018 22.0 2.1 17 2-18 42-58 (197)
40 cd08469 PBP2_PnbR The C-termin 21.0 89 0.0019 22.3 2.4 18 2-19 42-59 (221)
41 PF15072 DUF4539: Domain of un 20.8 28 0.0006 24.1 -0.4 24 7-32 29-52 (86)
42 cd08438 PBP2_CidR The C-termin 20.7 85 0.0018 21.4 2.1 16 2-17 42-57 (197)
43 cd04050 C2B_Synaptotagmin-like 20.7 71 0.0015 21.4 1.7 13 12-24 4-16 (105)
44 cd08447 PBP2_LTTR_aromatics_li 20.5 87 0.0019 21.5 2.2 16 2-17 42-57 (198)
45 cd08439 PBP2_LrhA_like The C-t 20.2 63 0.0014 22.4 1.4 16 2-17 42-57 (185)
No 1
>TIGR00212 hemC porphobilinogen deaminase. Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin
Probab=100.00 E-value=2.3e-56 Score=367.87 Aligned_cols=130 Identities=46% Similarity=0.722 Sum_probs=128.2
Q ss_pred ChHhhhcCCCcEEeecCCCCCCCCCCCeeeccccCCC-------------------------------------------
Q 038122 1 TEEALINGEIDIAVHSMKDVPTYLLDKTILPCNLQRE------------------------------------------- 37 (130)
Q Consensus 1 ~e~aLl~g~iDiAVHSlKDlP~~~~~gl~i~a~l~R~------------------------------------------- 37 (130)
+|+||++|++|||||||||||+++|+||+++|+++|+
T Consensus 61 le~aLl~g~iDiAVHSlKDlPt~lp~gl~i~av~~RedprD~lv~~~~~~l~~Lp~ga~VGTsS~RR~aql~~~rPdl~i 140 (292)
T TIGR00212 61 LEQALLDGEIDLAVHSLKDVPTVLPEGLEIAAVLKREDPRDVLVSRKYLSLDSLPQGAKVGTSSLRRKAQLKAIRPDLKI 140 (292)
T ss_pred HHHHHhcCCCCEEEeccccCCCCCCCCcEEEEEecCCCCceEEEECCCCChhHCCCCCEeccCCHHHHHHHHHHCCCCEE
Confidence 5899999999999999999999999999999999998
Q ss_pred ----CcHHHHHHhhhcCCcceeehhHhhhhhcCCCCCceeecCCCCCccCcccchhhhhhccCcHHHHHHHhccCCHHHH
Q 038122 38 ----GNVQARLRKLNEGVIQATLSALAGLKCLNMTENVTNILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETR 113 (130)
Q Consensus 38 ----GNv~TRl~KL~~g~~daiiLA~AGL~RLg~~~~i~~~l~~~~~~pA~gQGaiaie~r~~d~~~~~ll~~i~~~~t~ 113 (130)
|||+|||+||++|+|||||||+|||+|||+.++++++|++++|+||||||+||||||++|.++.++++.|||++|+
T Consensus 141 ~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~RLgl~~~i~~~l~~~~~~PA~gQGalaIe~r~~d~~~~~ll~~l~d~~t~ 220 (292)
T TIGR00212 141 EPLRGNIDTRLRKLDEGEYDAIILAEAGLKRLGLEDVITEVLDPEVMLPAPGQGAIAVECRKDDTEIKEILKEINHPPTR 220 (292)
T ss_pred EECcCCHHHHHHHhcCCCCCEeehHhhHHHhCCCccccccccChhhcCCccccceEEEEEecCCHHHHHHHHHcCCHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhHHcCCCC
Q 038122 114 QAVVCERAFLGTLDGSC 130 (130)
Q Consensus 114 ~~~~aER~~l~~l~ggC 130 (130)
.|+.+||+||+.|+|||
T Consensus 221 ~~~~aER~~l~~L~ggC 237 (292)
T TIGR00212 221 VEATAERAFLKELGGGC 237 (292)
T ss_pred HHHHHHHHHHHHhCCCC
Confidence 99999999999999999
No 2
>cd00494 HMBS Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). HMBS consists of three domains, and is believed to bind substrate through a hinge-bending motion of domains I and II. HMBS is found in all organisms except viruses.
Probab=100.00 E-value=4e-56 Score=366.42 Aligned_cols=130 Identities=52% Similarity=0.765 Sum_probs=128.0
Q ss_pred ChHhhhcCCCcEEeecCCCCCCCCCCCeeeccccCCC-------------------------------------------
Q 038122 1 TEEALINGEIDIAVHSMKDVPTYLLDKTILPCNLQRE------------------------------------------- 37 (130)
Q Consensus 1 ~e~aLl~g~iDiAVHSlKDlP~~~~~gl~i~a~l~R~------------------------------------------- 37 (130)
+|+||++|++|||||||||||+++|+||+++|+++|+
T Consensus 61 le~aLl~g~iDiAVHSlKDlP~~lp~gl~i~av~~RedprDvlv~~~~~~l~~Lp~ga~IGTsS~RR~aql~~~rpdl~~ 140 (292)
T cd00494 61 LEEALLNGEIDLAVHSLKDVPTELPEGLVLGAIPKREDPRDALVSRNGSSLEDLPAGSVVGTSSLRRQAQLKRKRPDLKF 140 (292)
T ss_pred HHHHHHcCCCCEEEeccccCCCCCCCCcEEEEEecCCCCceEEEECCCCChhHCCCCCEEecCCHHHHHHHHHHCCCCEE
Confidence 5899999999999999999999999999999999998
Q ss_pred ----CcHHHHHHhhhcCCcceeehhHhhhhhcCCCCCceeecCCCCCccCcccchhhhhhccCcHHHHHHHhccCCHHHH
Q 038122 38 ----GNVQARLRKLNEGVIQATLSALAGLKCLNMTENVTNILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETR 113 (130)
Q Consensus 38 ----GNv~TRl~KL~~g~~daiiLA~AGL~RLg~~~~i~~~l~~~~~~pA~gQGaiaie~r~~d~~~~~ll~~i~~~~t~ 113 (130)
|||+|||+||++|+|||||||+|||+|||+.++++++|++++|+||||||+||||||++|+++.++++.|||++|+
T Consensus 141 ~~iRGNV~TRL~KL~~ge~DaiiLA~AGL~RLgl~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~ll~~i~d~~t~ 220 (292)
T cd00494 141 EPLRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLEDRITQYLSPEVMLPAVGQGALAIECRKGDEELLALLKPLNHEETA 220 (292)
T ss_pred EEcCCCHHHHHHHhcCCCCCEeehHhhHHHHcCCcccCccccCccccCCccccceEEEEEecCCHHHHHHHHHCCCHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhHHcCCCC
Q 038122 114 QAVVCERAFLGTLDGSC 130 (130)
Q Consensus 114 ~~~~aER~~l~~l~ggC 130 (130)
.++.+||+||+.|+|||
T Consensus 221 ~~~~aER~~L~~L~ggC 237 (292)
T cd00494 221 LCVLAERAFLRELEGGC 237 (292)
T ss_pred HHHHHHHHHHHHhCCCC
Confidence 99999999999999999
No 3
>COG0181 HemC Porphobilinogen deaminase [Coenzyme metabolism]
Probab=100.00 E-value=1.9e-56 Score=369.46 Aligned_cols=130 Identities=50% Similarity=0.764 Sum_probs=128.4
Q ss_pred ChHhhhcCCCcEEeecCCCCCCCCCCCeeeccccCCC-------------------------------------------
Q 038122 1 TEEALINGEIDIAVHSMKDVPTYLLDKTILPCNLQRE------------------------------------------- 37 (130)
Q Consensus 1 ~e~aLl~g~iDiAVHSlKDlP~~~~~gl~i~a~l~R~------------------------------------------- 37 (130)
+|++|++|++|+|||||||||+++|+||+++|+++|+
T Consensus 64 le~all~g~~DiAVHSlKDvP~~~p~gL~laai~~R~dprDalVs~~~~~l~~LP~Ga~VGTSSlRR~aql~~~rPdl~i 143 (307)
T COG0181 64 LEQALLEGEIDIAVHSLKDVPTELPEGLVLAAIPEREDPRDALVSRDGYDLEELPEGAVVGTSSLRRQAQLKALRPDLKI 143 (307)
T ss_pred HHHHHHcCCCCEEEeecccCCccCCCCceEEEecCCCChhheEEECCCCchhhCCCCCccccchHHHHHHHHHhCCCCeE
Confidence 5899999999999999999999999999999999998
Q ss_pred ----CcHHHHHHhhhcCCcceeehhHhhhhhcCCCCCceeecCCCCCccCcccchhhhhhccCcHHHHHHHhccCCHHHH
Q 038122 38 ----GNVQARLRKLNEGVIQATLSALAGLKCLNMTENVTNILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETR 113 (130)
Q Consensus 38 ----GNv~TRl~KL~~g~~daiiLA~AGL~RLg~~~~i~~~l~~~~~~pA~gQGaiaie~r~~d~~~~~ll~~i~~~~t~ 113 (130)
|||||||+||++|+|||||||+|||+|||+.++++++|+|+.|+|||||||||||||++|.++.++|+.|||.+|+
T Consensus 144 ~~lRGNVdTRL~KL~~g~yDAIILA~AGL~RLgl~~~~~~~l~p~~~~PA~gQGal~ie~R~~d~~~~~ll~~i~~~~t~ 223 (307)
T COG0181 144 EPLRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLENRITEILDPEEFLPAPGQGALAIECRAGDEKVLELLAELNDEDTR 223 (307)
T ss_pred EeccCcHHHHHHHhhcCCccHHHHHHHHHHhcCCcccceeecChhhcCCCCCCceEEEEEecCcHHHHHHHHhccCchHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhHHcCCCC
Q 038122 114 QAVVCERAFLGTLDGSC 130 (130)
Q Consensus 114 ~~~~aER~~l~~l~ggC 130 (130)
.|+.+||+|++.|+|||
T Consensus 224 ~~v~aERa~l~~L~ggC 240 (307)
T COG0181 224 ICVTAERAFLRELEGGC 240 (307)
T ss_pred HHHHHHHHHHHhhCCCC
Confidence 99999999999999999
No 4
>PRK00072 hemC porphobilinogen deaminase; Reviewed
Probab=100.00 E-value=5.6e-56 Score=365.95 Aligned_cols=130 Identities=52% Similarity=0.803 Sum_probs=128.1
Q ss_pred ChHhhhcCCCcEEeecCCCCCCCCCCCeeeccccCCC-------------------------------------------
Q 038122 1 TEEALINGEIDIAVHSMKDVPTYLLDKTILPCNLQRE------------------------------------------- 37 (130)
Q Consensus 1 ~e~aLl~g~iDiAVHSlKDlP~~~~~gl~i~a~l~R~------------------------------------------- 37 (130)
+|+||++|+||||||||||||+++|+||+++|+++|+
T Consensus 65 le~aLl~g~iDiAVHSlKDlP~~l~~gl~i~avl~R~dprDvlv~~~~~~l~~Lp~ga~IGTsS~RR~aql~~~~Pdl~~ 144 (295)
T PRK00072 65 LEEALLEGEIDIAVHSLKDVPTELPEGLVLAAIPEREDPRDALVSRDYKSLDDLPEGAVVGTSSLRRQAQLLALRPDLEI 144 (295)
T ss_pred HHHHHHcCCCCEEEeccCcCCCCCCCCcEEEEEecCCCCceEEEECCCCChhHCCCCCEEecCcHHHHHHHHHHCcCCEE
Confidence 5899999999999999999999999999999999998
Q ss_pred ----CcHHHHHHhhhcCCcceeehhHhhhhhcCCCCCceeecCCCCCccCcccchhhhhhccCcHHHHHHHhccCCHHHH
Q 038122 38 ----GNVQARLRKLNEGVIQATLSALAGLKCLNMTENVTNILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETR 113 (130)
Q Consensus 38 ----GNv~TRl~KL~~g~~daiiLA~AGL~RLg~~~~i~~~l~~~~~~pA~gQGaiaie~r~~d~~~~~ll~~i~~~~t~ 113 (130)
|||+|||+||++|+|||||||+|||+|||+.++++++|++++|+||||||+||||||++|+++.++|++|||++|+
T Consensus 145 ~~iRGNV~TRL~KL~~g~~DaivLA~AGL~RLgl~~~~~~~l~~~~~~PA~gQGaiave~r~~d~~~~~~l~~i~d~~t~ 224 (295)
T PRK00072 145 KPLRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLEDRITEYLDPEEMLPAPGQGALGIECRADDEEILELLAPLNHEETR 224 (295)
T ss_pred EECccCHHHHHHHhhCCCCCEeehHhhHHHHcCCccccceecChhhcCCcccccceeeeeecCCHHHHHHHHHcCCHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhHHcCCCC
Q 038122 114 QAVVCERAFLGTLDGSC 130 (130)
Q Consensus 114 ~~~~aER~~l~~l~ggC 130 (130)
.++.+||+||+.|+|||
T Consensus 225 ~~~~aER~~L~~L~ggC 241 (295)
T PRK00072 225 LRVTAERAFLRALEGGC 241 (295)
T ss_pred HHHHHHHHHHHHhCCCC
Confidence 99999999999999999
No 5
>PLN02691 porphobilinogen deaminase
Probab=100.00 E-value=1.6e-55 Score=369.83 Aligned_cols=130 Identities=73% Similarity=1.105 Sum_probs=128.3
Q ss_pred ChHhhhcCCCcEEeecCCCCCCCCCCCeeeccccCCC-------------------------------------------
Q 038122 1 TEEALINGEIDIAVHSMKDVPTYLLDKTILPCNLQRE------------------------------------------- 37 (130)
Q Consensus 1 ~e~aLl~g~iDiAVHSlKDlP~~~~~gl~i~a~l~R~------------------------------------------- 37 (130)
+|+||++|+||||||||||||+++|+||+|+|+++|+
T Consensus 108 le~aLl~g~iDiAVHSlKDlP~~l~~gl~i~Avl~RedprDvLv~~~~~~L~~Lp~ga~IGTSS~RR~aql~~~rPdl~v 187 (351)
T PLN02691 108 IDDALLSGRIDIAVHSMKDVPTYLPEGTILPCNLPREDVRDAFISLKAKSLAELPAGSVVGTASLRRQSQILHKYPHLKV 187 (351)
T ss_pred HHHHHHcCCCCEEEeccccCCCCCCCCcEEEEEcCCCCCceEEEECCCCChhHCCCCCEeccCcHHHHHHHHHHCCCCEE
Confidence 5899999999999999999999999999999999998
Q ss_pred ----CcHHHHHHhhhcCCcceeehhHhhhhhcCCCCCceeecCCCCCccCcccchhhhhhccCcHHHHHHHhccCCHHHH
Q 038122 38 ----GNVQARLRKLNEGVIQATLSALAGLKCLNMTENVTNILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETR 113 (130)
Q Consensus 38 ----GNv~TRl~KL~~g~~daiiLA~AGL~RLg~~~~i~~~l~~~~~~pA~gQGaiaie~r~~d~~~~~ll~~i~~~~t~ 113 (130)
|||+|||+||++|+|||||||+|||+|||++++++++|++++|+||||||+||||||++|+++.++|+.|||++|+
T Consensus 188 ~~iRGNVdTRL~KL~~geyDaiILA~AGL~RLgl~~~i~~~l~~~~~~PA~gQGaLaVe~r~~d~~~~~ll~~ind~~T~ 267 (351)
T PLN02691 188 VNFRGNVQTRLRKLQEGVVDATLLALAGLKRLDMTEHATSILSTDEMLPAVAQGAIGIACRTDDDKMLEYLASLNHEETR 267 (351)
T ss_pred EeccCCHHHHHHHhcCCCCCeeehHHHHHHhCCCcccccEecchhhcCCccccceEEEEEecCCHHHHHHHHHCCCHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhHHcCCCC
Q 038122 114 QAVVCERAFLGTLDGSC 130 (130)
Q Consensus 114 ~~~~aER~~l~~l~ggC 130 (130)
.++.+||+||+.|+|||
T Consensus 268 ~~~~aER~~L~~L~GgC 284 (351)
T PLN02691 268 LAVACERAFLAALDGSC 284 (351)
T ss_pred HHHHHHHHHHHHhCCCC
Confidence 99999999999999999
No 6
>PF01379 Porphobil_deam: Porphobilinogen deaminase, dipyromethane cofactor binding domain; InterPro: IPR022417 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) []. Porphobilinogen deaminase (also known as hydroxymethylbilane synthase, 2.5.1.61 from EC) functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the polymerisation of four PBG molecules into the tetrapyrrole structure, preuroporphyrinogen, with the concomitant release of four molecules of ammonia. This enzyme uses a unique dipyrro-methane cofactor made from two molecules of PBG, which is covalently attached to a cysteine side chain. The tetrapyrrole product is synthesized in an ordered, sequential fashion, by initial attachment of the first pyrrole unit (ring A) to the cofactor, followed by subsequent additions of the remaining pyrrole units (rings B, C, D) to the growing pyrrole chain []. The link between the pyrrole ring and the cofactor is broken once all the pyrroles have been added. This enzyme is folded into three distinct domains that enclose a single, large active site that makes use of an aspartic acid as its one essential catalytic residue, acting as a general acid/base during catalysis [, ]. A deficiency of hydroxymethylbilane synthase is implicated in the neuropathic disease, Acute Intermittent Porphyria (AIP) []. This entry represents the N-terminal domains 1 and 2 of porphobilinogen deaminase, an enzyme involved in tetrapyrrole biosynthesis. The structure of this domain consists of a duplication of two similar intertwined domains with three layers of (a/b/a) each. Porphobilinogen deaminase has a three-domain structure. Domains 1 (N-terminal) and 2 are duplications with the same structure, resembling the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 (C-terminal), but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins []. The enzyme has a single catalytic site, and the flexibility between domains is thought to aid elongation of the polypyrrole product in the active-site cleft of the enzyme.; GO: 0033014 tetrapyrrole biosynthetic process; PDB: 1GTK_A 1AH5_A 2YPN_A 1PDA_A 1YPN_A 3EQ1_B 3ECR_A.
Probab=100.00 E-value=3.4e-46 Score=296.52 Aligned_cols=105 Identities=47% Similarity=0.750 Sum_probs=86.4
Q ss_pred ChHhhhcCCCcEEeecCCCCCCCCCCCeeeccccCCC-------------------------------------------
Q 038122 1 TEEALINGEIDIAVHSMKDVPTYLLDKTILPCNLQRE------------------------------------------- 37 (130)
Q Consensus 1 ~e~aLl~g~iDiAVHSlKDlP~~~~~gl~i~a~l~R~------------------------------------------- 37 (130)
+|+||++|+||||||||||||+++|+||.|+|+++|+
T Consensus 62 le~aLl~g~iDiAVHSlKDlP~~l~~gl~iaav~~R~dprD~Lv~~~~~~~~l~~Lp~ga~IGTsS~RR~aql~~~~pdl 141 (215)
T PF01379_consen 62 LEEALLDGEIDIAVHSLKDLPTELPEGLVIAAVLKREDPRDVLVSRGRDGKSLEDLPKGARIGTSSLRRRAQLKRLRPDL 141 (215)
T ss_dssp HHHHHHTTS-SEEEEEGGGS-SS--TTEEEEEE-------EEEEE-GCTTSSCCCS-TT-EEE---HHHHHHHHHH-TTS
T ss_pred HHHHHHcCCccEEEeccccCCCCCCCCceEeccCCCCCCccEEEEecCCCCChHHCccccccCCCCHHHHHHHHHhccCC
Confidence 5899999999999999999999999999999999998
Q ss_pred ------CcHHHHHHhhhcCCcceeehhHhhhhhcCCCCCceeecCCCCCccCcccchhhhhhccCcHHHHHHHh
Q 038122 38 ------GNVQARLRKLNEGVIQATLSALAGLKCLNMTENVTNILPIDDMLLAVAQGAIGIACTSNDKKMAKYLG 105 (130)
Q Consensus 38 ------GNv~TRl~KL~~g~~daiiLA~AGL~RLg~~~~i~~~l~~~~~~pA~gQGaiaie~r~~d~~~~~ll~ 105 (130)
|||+|||+||++|+|||||||+|||+|||++++++++|++++|+||||||+||||||++|.++.++|+
T Consensus 142 ~~~~iRGNv~TRL~KL~~g~~daiiLA~AGL~RLgl~~~~~~~l~~~~~~PA~gQGalave~r~~d~~~~~llK 215 (215)
T PF01379_consen 142 EVVPIRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLEDRISEILDPEEMLPAPGQGALAVECRKDDEEIIELLK 215 (215)
T ss_dssp EEE---S-HHHHHHHHHCTS-SEEEEEHHHHHHCT-GGGESEEE-TTTS-B-TTTT-EEEEEETT-HHHHHHH-
T ss_pred eEEEecCCHHHHHHHhcccCCCEEEhhhChhhhccccceeeeecCchhcCCCCCCeEEEEEEecCcHHHHHHhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999985
No 7
>KOG2892 consensus Porphobilinogen deaminase [Coenzyme transport and metabolism]
Probab=100.00 E-value=1.2e-44 Score=296.62 Aligned_cols=130 Identities=54% Similarity=0.864 Sum_probs=128.0
Q ss_pred ChHhhhcCCCcEEeecCCCCCCCCCCCeeeccccCCC-------------------------------------------
Q 038122 1 TEEALINGEIDIAVHSMKDVPTYLLDKTILPCNLQRE------------------------------------------- 37 (130)
Q Consensus 1 ~e~aLl~g~iDiAVHSlKDlP~~~~~gl~i~a~l~R~------------------------------------------- 37 (130)
||.+|.+|.+||+||||||||+.+|+|++|+|++||+
T Consensus 68 LE~aL~~~~~divVHSLKDlPT~LP~G~~ig~i~kRedp~DalV~~~~s~~kTladLP~GsVVGTSSlRR~Aql~RkyPH 147 (320)
T KOG2892|consen 68 LEDALINGHVDIVVHSLKDLPTYLPEGMIIGCILKREDPRDALVFLTYSAYKTLADLPAGSVVGTSSLRRKAQILRKYPH 147 (320)
T ss_pred HHHHHhcCCccEEEEecccccccCCCCcEeccccCCCCccceEEEecccccccHhhCCCCceechHHHhHHHHHHhhCCc
Confidence 5899999999999999999999999999999999998
Q ss_pred -------CcHHHHHHhhhcCC-cceeehhHhhhhhcCCCCCceeecCCCCCccCcccchhhhhhccCcHHHHHHHhccCC
Q 038122 38 -------GNVQARLRKLNEGV-IQATLSALAGLKCLNMTENVTNILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNH 109 (130)
Q Consensus 38 -------GNv~TRl~KL~~g~-~daiiLA~AGL~RLg~~~~i~~~l~~~~~~pA~gQGaiaie~r~~d~~~~~ll~~i~~ 109 (130)
||++|||+||+.++ |.+||||.|||+|+||.++++++|.|++|+||+|||+++|+||.+|+++..++..++|
T Consensus 148 L~f~~~rgn~~trl~kld~~~~~~~iilA~agl~rmg~~~ri~qil~p~~~~~avgqgalgie~r~~d~~m~~~l~~l~~ 227 (320)
T KOG2892|consen 148 LHVESIRGNLQTRLSKLDGGKPFQAIILALAGLKRMGWTNRIAQILHPDEMLYAVGQGALGIECRADDDKMLTYLASLND 227 (320)
T ss_pred eEEEEecChHHHHHHhhcCCCcchhHHHHHHHHHHhhhHhHHHHhcChHHHHHHhccceeEEEEecChHHHHHHHHHhcC
Confidence 99999999999987 9999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhHHcCCCC
Q 038122 110 EETRQAVVCERAFLGTLDGSC 130 (130)
Q Consensus 110 ~~t~~~~~aER~~l~~l~ggC 130 (130)
.+|+.|+.+||+||+.|+|||
T Consensus 228 ~~t~~~~~~eraflrtl~Ggc 248 (320)
T KOG2892|consen 228 LNTTLRILAERAFLRTLEGGC 248 (320)
T ss_pred hHHHHHHHHHHHHHHhhCCCc
Confidence 999999999999999999999
No 8
>PRK01066 porphobilinogen deaminase; Provisional
Probab=100.00 E-value=2.8e-44 Score=287.91 Aligned_cols=106 Identities=25% Similarity=0.305 Sum_probs=102.1
Q ss_pred ChHhhhcCCCcEEeecCCCCCCCCCCCeeeccccCCC-------------------------------------------
Q 038122 1 TEEALINGEIDIAVHSMKDVPTYLLDKTILPCNLQRE------------------------------------------- 37 (130)
Q Consensus 1 ~e~aLl~g~iDiAVHSlKDlP~~~~~gl~i~a~l~R~------------------------------------------- 37 (130)
+|+||++|++|||||||||||+ |+||+++|+++|+
T Consensus 78 le~aLl~g~iDiAVHSlKDlPt--~~gl~l~av~~RedprDvLv~~~~~~l~~Lp~ga~IGTSS~RR~aql~~~rPdl~v 155 (231)
T PRK01066 78 VDFLVLSGQCDLAIHSAKDLPE--PPKLTVVAITAGLDPRDLLVYAEKYLSQPLPRRPRIGSSSLRREELLKLLFPSGII 155 (231)
T ss_pred HHHHHHcCCCCEEEecCCcCCC--CCCCEEEEEcCCCCCceEEEECCCCchhhCCCCCEEeCChHHHHHHHHHHCCCCEE
Confidence 5899999999999999999999 9999999999997
Q ss_pred ----CcHHHHHHhhhcCCcceeehhHhhhhhcCCCCCceeecCCCCCccCcccchhhhhhccCcHHHHHHHhccCCHH
Q 038122 38 ----GNVQARLRKLNEGVIQATLSALAGLKCLNMTENVTNILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEE 111 (130)
Q Consensus 38 ----GNv~TRl~KL~~g~~daiiLA~AGL~RLg~~~~i~~~l~~~~~~pA~gQGaiaie~r~~d~~~~~ll~~i~~~~ 111 (130)
|||+|||+||++|+|||||||+|||+|||+.++++++|+++ ||||||+||||||++|+++.++++.|||.+
T Consensus 156 ~~iRGNV~TRL~KL~~ge~DaiiLA~AGL~RLgl~~~~~~~l~~~---~A~gQGalaie~R~~d~~~~~ll~~i~~~~ 230 (231)
T PRK01066 156 LDIRGTIEERLKLLEEKKYDAIVVAKAAVLRLGLRLPYTKELPPP---YHPLQGRLAITASKHIRSWKGLFLPLGITE 230 (231)
T ss_pred EeCcCCHHHHHHHhcCCCCCchhhHHHHHHhcCCcccceeECCCC---CCCCCCeEEEEEecCCHHHHHHHHHhcCCC
Confidence 99999999999999999999999999999999999999998 499999999999999999999999999964
No 9
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=82.76 E-value=3.4 Score=33.64 Aligned_cols=74 Identities=18% Similarity=0.131 Sum_probs=40.4
Q ss_pred HHHHHhhhcCCcceeehhHhhhhhcCCCCCceeecCCCCCccCcccchhhhhhccCcHHHHHHHhccCCHHHHHHHH
Q 038122 41 QARLRKLNEGVIQATLSALAGLKCLNMTENVTNILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETRQAVV 117 (130)
Q Consensus 41 ~TRl~KL~~g~~daiiLA~AGL~RLg~~~~i~~~l~~~~~~pA~gQGaiaie~r~~d~~~~~ll~~i~~~~t~~~~~ 117 (130)
+.=++.|.+|+.||.|-=..-++.-.. ......++...+.-..++-+ |.+|++|..+..+|+++=|.+....+.
T Consensus 147 ~q~~~~l~~g~IDA~IWN~d~i~~~~~-~l~~~~l~~~~~~~~~seAV--ivi~~~~~~i~~ll~~~id~~~vl~iQ 220 (232)
T PF14503_consen 147 NQLLELLRSGEIDAAIWNYDEIEDKNF-GLKYVPLKDDPMSKDASEAV--IVIRKDNEPIKALLRKLIDVEKVLEIQ 220 (232)
T ss_dssp HHHHHHHHHTS--EEEEE--HHCCHHC-TEEEEE--SSCHHHHTT-EE--EEEETT-HHHHHHHHHH--HHHHHHHH
T ss_pred HHHHHHHHCCCccEEEECCcccccccC-CeeEEeCCchHHHHhcCeeE--EEEeCCCHHHHHHHHHhcCHHHHHHHH
Confidence 445777888999999986663333321 11123444444444455554 567899999999999887877765554
No 10
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=62.88 E-value=13 Score=26.06 Aligned_cols=28 Identities=21% Similarity=0.260 Sum_probs=22.6
Q ss_pred CcHHHHHHhhhcCCcceeehhHhhhhhc
Q 038122 38 GNVQARLRKLNEGVIQATLSALAGLKCL 65 (130)
Q Consensus 38 GNv~TRl~KL~~g~~daiiLA~AGL~RL 65 (130)
++.+.-++.|.+|.+|+++........+
T Consensus 133 ~~~~~~~~~l~~g~~d~~~~~~~~~~~~ 160 (218)
T cd00134 133 DDNAEALAALENGRADAVIVDEIALAAL 160 (218)
T ss_pred CCHHHHHHHHHcCCccEEEeccHHHHHH
Confidence 5678889999999999999976655543
No 11
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=45.58 E-value=45 Score=25.13 Aligned_cols=23 Identities=26% Similarity=0.271 Sum_probs=19.1
Q ss_pred CcHHHHHHhhhcCCcceeehhHh
Q 038122 38 GNVQARLRKLNEGVIQATLSALA 60 (130)
Q Consensus 38 GNv~TRl~KL~~g~~daiiLA~A 60 (130)
.+.+.-++.|..|++|+++.-..
T Consensus 154 ~~~~~~~~~L~~grvDa~i~~~~ 176 (243)
T PRK15007 154 DSYQNAKLDLQNGRIDAVFGDTA 176 (243)
T ss_pred CCHHHHHHHHHcCCCCEEEeCHH
Confidence 57788888999999999997554
No 12
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=42.30 E-value=73 Score=24.61 Aligned_cols=20 Identities=25% Similarity=0.322 Sum_probs=15.6
Q ss_pred cHHHHHHhhhcCCcceeehh
Q 038122 39 NVQARLRKLNEGVIQATLSA 58 (130)
Q Consensus 39 Nv~TRl~KL~~g~~daiiLA 58 (130)
+.+.-+++|..|++|++|.-
T Consensus 164 ~~~~~~~~l~~griDa~i~d 183 (260)
T PRK15010 164 NQDLVYSDLAAGRLDAALQD 183 (260)
T ss_pred CHHHHHHHHHcCCccEEEeC
Confidence 34455889999999999863
No 13
>cd08417 PBP2_Nitroaromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. 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. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. 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 substrate
Probab=30.39 E-value=43 Score=23.16 Aligned_cols=17 Identities=53% Similarity=0.737 Sum_probs=14.0
Q ss_pred hHhhhcCCCcEEeecCC
Q 038122 2 EEALINGEIDIAVHSMK 18 (130)
Q Consensus 2 e~aLl~g~iDiAVHSlK 18 (130)
.+.|.+|++|++++...
T Consensus 42 ~~~l~~g~~D~~i~~~~ 58 (200)
T cd08417 42 EEALESGEIDLAIGVFP 58 (200)
T ss_pred HHHHHcCCCCEEEeecc
Confidence 45788999999998654
No 14
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=29.84 E-value=1.3e+02 Score=24.44 Aligned_cols=66 Identities=12% Similarity=0.127 Sum_probs=42.2
Q ss_pred hhhcCCcceeehhHhhhhhcCCCC-CceeecCCCCCccCcccchhhhhhc---cCcHHHHHHHhccCCHHHHHHH
Q 038122 46 KLNEGVIQATLSALAGLKCLNMTE-NVTNILPIDDMLLAVAQGAIGIACT---SNDKKMAKYLGSLNHEETRQAV 116 (130)
Q Consensus 46 KL~~g~~daiiLA~AGL~RLg~~~-~i~~~l~~~~~~pA~gQGaiaie~r---~~d~~~~~ll~~i~~~~t~~~~ 116 (130)
-|.+|++||.++..-=..+.|++. .-.-+++..+. +.+..+.+| ++++++.++++.+++++...-+
T Consensus 190 al~~g~vDaa~i~~~~a~~a~~~~~~~~l~~e~~~~-----~~~~~~~v~~~~~~~~~~~~l~~a~~s~~v~~~i 259 (271)
T PRK11063 190 SLDDAQIALAVINTTYASQIGLTPAKDGIFVEDKDS-----PYVNLIVAREDNKDAENVKKFVQAYQSDEVYEAA 259 (271)
T ss_pred hcccccccEEEEChHHHHHcCCCCCCCeeEECCCCC-----CeEEEEEECCcccCCHHHHHHHHHHcCHHHHHHH
Confidence 356788999999777677777653 22223433332 233444444 3667899999999988776544
No 15
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=29.64 E-value=48 Score=23.36 Aligned_cols=16 Identities=44% Similarity=0.632 Sum_probs=13.5
Q ss_pred hHhhhcCCCcEEeecC
Q 038122 2 EEALINGEIDIAVHSM 17 (130)
Q Consensus 2 e~aLl~g~iDiAVHSl 17 (130)
.+.|.+|++|++++..
T Consensus 42 ~~~l~~g~~D~~i~~~ 57 (200)
T cd08467 42 ERGLEQGTIDLAVGRF 57 (200)
T ss_pred HHHhhCCCcCEEEecC
Confidence 5678999999999864
No 16
>PF07302 AroM: AroM protein; InterPro: IPR010843 This family consists of several bacterial and archaeal AroM proteins. In Escherichia coli the aroM gene is cotranscribed with aroL []. The function of this family is unknown.
Probab=29.63 E-value=27 Score=28.23 Aligned_cols=55 Identities=18% Similarity=0.198 Sum_probs=38.1
Q ss_pred cHHHHHHhhhcCCcceeehhHhhhhhcCCCCCceeecCCCCCccCc-----ccchhhhhhcc
Q 038122 39 NVQARLRKLNEGVIQATLSALAGLKCLNMTENVTNILPIDDMLLAV-----AQGAIGIACTS 95 (130)
Q Consensus 39 Nv~TRl~KL~~g~~daiiLA~AGL~RLg~~~~i~~~l~~~~~~pA~-----gQGaiaie~r~ 95 (130)
.++..+++|++..||.|+|...|--. ++..+.. .+.|+.++|.. +.+-++|-+-.
T Consensus 75 ~lq~~i~~le~~G~d~illlCTG~F~-~l~~~~~-lleP~ril~~lV~al~~~~~vGVivP~ 134 (221)
T PF07302_consen 75 RLQACIAQLEAQGYDVILLLCTGEFP-GLTARNP-LLEPDRILPPLVAALVGGHQVGVIVPL 134 (221)
T ss_pred HHHHHHHHHHHCCCCEEEEeccCCCC-CCCCCcc-eeehHHhHHHHHHHhcCCCeEEEEecC
Confidence 45666667998899999999999877 6766655 66677666532 22466665543
No 17
>PF07849 DUF1641: Protein of unknown function (DUF1641); InterPro: IPR012440 Archaeal and bacterial hypothetical proteins are found in this family, with the region in question being approximately 40 residues long.
Probab=29.34 E-value=1.2e+02 Score=18.09 Aligned_cols=30 Identities=20% Similarity=0.240 Sum_probs=24.8
Q ss_pred HHHHHHhccCCHHHHHHHHHHHHHhHHcCC
Q 038122 99 KMAKYLGSLNHEETRQAVVCERAFLGTLDG 128 (130)
Q Consensus 99 ~~~~ll~~i~~~~t~~~~~aER~~l~~l~g 128 (130)
-+..+++.+.|++.+.....=-+|++.+|-
T Consensus 12 gl~gl~~~l~DpdvqrgL~~ll~~lk~lGk 41 (42)
T PF07849_consen 12 GLFGLLRALRDPDVQRGLGFLLAFLKALGK 41 (42)
T ss_pred CHHHHHHHHcCHHHHHHHHHHHHHHHHHcC
Confidence 467899999999999888777788888764
No 18
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=26.51 E-value=1.4e+02 Score=28.46 Aligned_cols=25 Identities=12% Similarity=0.025 Sum_probs=20.0
Q ss_pred CcHHHHHHhhhcCCcceeehhHhhh
Q 038122 38 GNVQARLRKLNEGVIQATLSALAGL 62 (130)
Q Consensus 38 GNv~TRl~KL~~g~~daiiLA~AGL 62 (130)
-|...=++.+.+|+.||+|...+-+
T Consensus 192 ~s~~~al~av~~G~~Da~i~~~~~~ 216 (1197)
T PRK09959 192 TNLYQALASVSAGQNDYFIGSNIIT 216 (1197)
T ss_pred CCHHHHHHHHHcCCCCEEEccHHHH
Confidence 6777888889999999998865433
No 19
>TIGR02995 ectoine_ehuB ectoine/hydroxyectoine ABC transporter solute-binding protein. Members of this family are the extracellular solute-binding proteins of ABC transporters that closely resemble amino acid transporters. The member from Sinorhizobium meliloti is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes.
Probab=26.50 E-value=97 Score=24.23 Aligned_cols=25 Identities=16% Similarity=0.195 Sum_probs=19.2
Q ss_pred CcHHHHHHhhhcCCcceeehhHhhh
Q 038122 38 GNVQARLRKLNEGVIQATLSALAGL 62 (130)
Q Consensus 38 GNv~TRl~KL~~g~~daiiLA~AGL 62 (130)
-+.++=++.|.+|++|++|.-...+
T Consensus 173 ~~~~~~i~~L~~grvDa~i~d~~~~ 197 (275)
T TIGR02995 173 PDGQSGLKMVQDGRADAYSLTVLTI 197 (275)
T ss_pred CCHHHHHHHHHcCCCCEEecChHHH
Confidence 3456778899999999999865543
No 20
>cd08425 PBP2_CynR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold. CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is 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
Probab=25.87 E-value=59 Score=22.48 Aligned_cols=16 Identities=25% Similarity=0.449 Sum_probs=13.1
Q ss_pred hHhhhcCCCcEEeecC
Q 038122 2 EEALINGEIDIAVHSM 17 (130)
Q Consensus 2 e~aLl~g~iDiAVHSl 17 (130)
.+.|.+|++|+|+...
T Consensus 43 ~~~l~~g~~Dl~i~~~ 58 (197)
T cd08425 43 EAALADDRLDLGIAFA 58 (197)
T ss_pred HHHHHcCCccEEEEec
Confidence 3578999999999754
No 21
>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=25.67 E-value=59 Score=22.46 Aligned_cols=17 Identities=35% Similarity=0.530 Sum_probs=13.6
Q ss_pred hHhhhcCCCcEEeecCC
Q 038122 2 EEALINGEIDIAVHSMK 18 (130)
Q Consensus 2 e~aLl~g~iDiAVHSlK 18 (130)
.+.|.+|++|+++...-
T Consensus 42 ~~~l~~g~~D~~i~~~~ 58 (200)
T cd08464 42 GDMLDRGEIDLAIGVFG 58 (200)
T ss_pred HHHHhcCcccEEEecCC
Confidence 36788999999998643
No 22
>PF03466 LysR_substrate: LysR substrate binding domain; InterPro: IPR005119 The structure of this domain is known and is similar to the periplasmic binding proteins []. This domain is found in members of the LysR family of prokaryotic transcriptional regulatory proteins IPR000847 from INTERPRO which share sequence similarities over approximately 280 residues including a putative helix-turn-helix DNA-binding motif at their N terminus.; PDB: 3ONM_B 3FZJ_J 3FXR_B 3N6T_A 3FXQ_A 3FXU_A 3N6U_A 2QSX_B 3HO7_B 1IZ1_B ....
Probab=24.91 E-value=71 Score=22.30 Aligned_cols=18 Identities=39% Similarity=0.444 Sum_probs=15.6
Q ss_pred hHhhhcCCCcEEeecCCC
Q 038122 2 EEALINGEIDIAVHSMKD 19 (130)
Q Consensus 2 e~aLl~g~iDiAVHSlKD 19 (130)
.+.|.+|++|+++.....
T Consensus 48 ~~~l~~g~~Dl~i~~~~~ 65 (209)
T PF03466_consen 48 IEALRSGELDLAITFGPP 65 (209)
T ss_dssp HHHHHTTSSSEEEESSSS
T ss_pred hHHHhcccccEEEEEeec
Confidence 467999999999998877
No 23
>cd08459 PBP2_DntR_NahR_LinR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold. This CD includes LysR-like bacterial transcriptional regulators, 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. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate o
Probab=24.49 E-value=64 Score=22.43 Aligned_cols=17 Identities=53% Similarity=0.743 Sum_probs=13.9
Q ss_pred hHhhhcCCCcEEeecCC
Q 038122 2 EEALINGEIDIAVHSMK 18 (130)
Q Consensus 2 e~aLl~g~iDiAVHSlK 18 (130)
.+.|.+|++|+++....
T Consensus 42 ~~~l~~g~~D~~i~~~~ 58 (201)
T cd08459 42 EEALESGEIDLAIGYLP 58 (201)
T ss_pred HHHhhCCCceEEEEcCC
Confidence 46789999999998653
No 24
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=24.39 E-value=62 Score=25.71 Aligned_cols=20 Identities=25% Similarity=0.297 Sum_probs=15.5
Q ss_pred hHhhhcCCCcEEeecCCCCC
Q 038122 2 EEALINGEIDIAVHSMKDVP 21 (130)
Q Consensus 2 e~aLl~g~iDiAVHSlKDlP 21 (130)
.+.|.+|++|++++.....|
T Consensus 136 ~~~l~~~~~Dl~i~~~~~~~ 155 (309)
T PRK11013 136 EEWLSAQRHDLGLTETLHTP 155 (309)
T ss_pred HHHHHcCCCCEEEEcCCCCC
Confidence 36799999999999764433
No 25
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=24.02 E-value=64 Score=22.34 Aligned_cols=16 Identities=25% Similarity=0.304 Sum_probs=13.1
Q ss_pred hHhhhcCCCcEEeecC
Q 038122 2 EEALINGEIDIAVHSM 17 (130)
Q Consensus 2 e~aLl~g~iDiAVHSl 17 (130)
.+.|.+|++|++++..
T Consensus 42 ~~~l~~g~~Dl~i~~~ 57 (200)
T cd08466 42 FEDLRLQEVDLVIDYV 57 (200)
T ss_pred HHHHHcCCccEEEecc
Confidence 3678899999999763
No 26
>cd08456 PBP2_LysR The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold. LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The 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
Probab=23.75 E-value=66 Score=22.11 Aligned_cols=16 Identities=19% Similarity=0.146 Sum_probs=12.9
Q ss_pred HhhhcCCCcEEeecCC
Q 038122 3 EALINGEIDIAVHSMK 18 (130)
Q Consensus 3 ~aLl~g~iDiAVHSlK 18 (130)
+.|.+|++|+++....
T Consensus 43 ~~l~~g~~Dl~i~~~~ 58 (196)
T cd08456 43 QWLSAQQCDLGLVSTL 58 (196)
T ss_pred HHHHcCCccEEEEecC
Confidence 5689999999997543
No 27
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form 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 bin
Probab=23.56 E-value=71 Score=21.28 Aligned_cols=18 Identities=39% Similarity=0.654 Sum_probs=14.2
Q ss_pred hHhhhcCCCcEEeecCCC
Q 038122 2 EEALINGEIDIAVHSMKD 19 (130)
Q Consensus 2 e~aLl~g~iDiAVHSlKD 19 (130)
.+.|.+|++|+++...-.
T Consensus 42 ~~~l~~g~~D~~i~~~~~ 59 (197)
T cd05466 42 LEALLEGELDLAIVALPV 59 (197)
T ss_pred HHHHHcCCceEEEEcCCC
Confidence 357889999999976543
No 28
>cd08419 PBP2_CbbR_RubisCO_like The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold. CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to t
Probab=23.50 E-value=68 Score=21.93 Aligned_cols=16 Identities=31% Similarity=0.385 Sum_probs=13.1
Q ss_pred HhhhcCCCcEEeecCC
Q 038122 3 EALINGEIDIAVHSMK 18 (130)
Q Consensus 3 ~aLl~g~iDiAVHSlK 18 (130)
+.|.+|++|+++.+..
T Consensus 42 ~~l~~g~~Dl~i~~~~ 57 (197)
T cd08419 42 ERLADNEDDLAIMGRP 57 (197)
T ss_pred HHHhcCCccEEEecCC
Confidence 5788999999997643
No 29
>KOG2531 consensus Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]
Probab=23.48 E-value=80 Score=28.82 Aligned_cols=58 Identities=14% Similarity=0.276 Sum_probs=42.4
Q ss_pred CCCceeecCCCCCccCcccchhhhhhccCcHHHH-HHHhccCCHHHHHHHHHHHHHhHH
Q 038122 68 TENVTNILPIDDMLLAVAQGAIGIACTSNDKKMA-KYLGSLNHEETRQAVVCERAFLGT 125 (130)
Q Consensus 68 ~~~i~~~l~~~~~~pA~gQGaiaie~r~~d~~~~-~ll~~i~~~~t~~~~~aER~~l~~ 125 (130)
...+.-+|+..+++|+.++|..-..+....-... .=+.+.++++....+..|-+||..
T Consensus 371 ~g~~g~~f~~~EIvP~~~~G~~R~~~~~~~~~~~~~~v~kf~~p~~e~rAlvEgQ~L~~ 429 (545)
T KOG2531|consen 371 NGNLGVYFPEREIVPSVPKGTLRFIFENKELSAERIEVAKFSDPEIEARALVEGQFLSK 429 (545)
T ss_pred CCceeEecccccccCCCCccceEEEecCCccchhhcccccCCCchHHHHHHHHHhHhHh
Confidence 3445678999999999999998887754321111 124577888888889999888864
No 30
>cd08418 PBP2_TdcA The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold. TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding
Probab=23.40 E-value=50 Score=22.76 Aligned_cols=16 Identities=25% Similarity=0.509 Sum_probs=13.3
Q ss_pred hHhhhcCCCcEEeecC
Q 038122 2 EEALINGEIDIAVHSM 17 (130)
Q Consensus 2 e~aLl~g~iDiAVHSl 17 (130)
.+.|.+|++|++++..
T Consensus 42 ~~~l~~g~~Dl~i~~~ 57 (201)
T cd08418 42 LPELRDGRLDFAIGTL 57 (201)
T ss_pred HHHHHcCCCcEEEEec
Confidence 4678899999999754
No 31
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=23.00 E-value=1.4e+02 Score=22.34 Aligned_cols=25 Identities=20% Similarity=0.211 Sum_probs=18.6
Q ss_pred cHHHHHHhhhcCCcceeehhHhhhh
Q 038122 39 NVQARLRKLNEGVIQATLSALAGLK 63 (130)
Q Consensus 39 Nv~TRl~KL~~g~~daiiLA~AGL~ 63 (130)
+.+.-++.|.+|++|++|.-...+.
T Consensus 161 s~~~~~~~L~~g~vD~~v~~~~~~~ 185 (250)
T TIGR01096 161 SYDNANMDLKAGRIDAVFTDASVLA 185 (250)
T ss_pred CHHHHHHHHHcCCCCEEEeCHHHHH
Confidence 4566678888999999998555443
No 32
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=22.90 E-value=51 Score=23.76 Aligned_cols=27 Identities=11% Similarity=0.202 Sum_probs=20.8
Q ss_pred HHHHHHhhhcCCcceeehhHhhhhhcCCC
Q 038122 40 VQARLRKLNEGVIQATLSALAGLKCLNMT 68 (130)
Q Consensus 40 v~TRl~KL~~g~~daiiLA~AGL~RLg~~ 68 (130)
.+.=|+.+.+|++|.||+-. +.||+..
T Consensus 57 l~~ll~~~~~g~vd~vvv~~--ldRl~R~ 83 (140)
T cd03770 57 FNRMIEDIEAGKIDIVIVKD--MSRLGRN 83 (140)
T ss_pred HHHHHHHHHcCCCCEEEEec--cchhccC
Confidence 33446677889999988865 9999875
No 33
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=22.76 E-value=66 Score=28.28 Aligned_cols=42 Identities=21% Similarity=0.414 Sum_probs=20.8
Q ss_pred eecCCCCCCCCCCCeeeccccCCC-Cc--HHHHHHhhhcCCcceeehh
Q 038122 14 VHSMKDVPTYLLDKTILPCNLQRE-GN--VQARLRKLNEGVIQATLSA 58 (130)
Q Consensus 14 VHSlKDlP~~~~~gl~i~a~l~R~-GN--v~TRl~KL~~g~~daiiLA 58 (130)
+||+.|.|..+|--+.- -+|. |= -+..+++|.+|+|...|=+
T Consensus 66 l~tlp~~PdaIPY~TsY---Y~~~WGFCl~~~~~~~L~dg~Y~V~IdS 110 (386)
T PF09940_consen 66 LHTLPDQPDAIPYRTSY---YKRRWGFCLSHNQLDALPDGEYEVVIDS 110 (386)
T ss_dssp EE--TTSTT--B--B-S---SS----EE--HHHHHT--SSEEEEEEEE
T ss_pred hccCCCCCCccceeeec---ccCCcccccCHHHHhhCCCCceEEEEee
Confidence 79999999999985432 2222 32 3667788888988777644
No 34
>cd08453 PBP2_IlvR The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold. The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. 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 flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport
Probab=22.46 E-value=87 Score=21.74 Aligned_cols=16 Identities=44% Similarity=0.526 Sum_probs=13.2
Q ss_pred hHhhhcCCCcEEeecC
Q 038122 2 EEALINGEIDIAVHSM 17 (130)
Q Consensus 2 e~aLl~g~iDiAVHSl 17 (130)
.++|.+|++|+++...
T Consensus 42 ~~~l~~g~~D~~i~~~ 57 (200)
T cd08453 42 LEALLAGEIDAGIVIP 57 (200)
T ss_pred HHHHHcCCCCEEEEec
Confidence 4688999999999753
No 35
>cd08420 PBP2_CysL_like C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold. CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology
Probab=22.37 E-value=54 Score=22.35 Aligned_cols=15 Identities=33% Similarity=0.634 Sum_probs=12.7
Q ss_pred HhhhcCCCcEEeecC
Q 038122 3 EALINGEIDIAVHSM 17 (130)
Q Consensus 3 ~aLl~g~iDiAVHSl 17 (130)
+.|.+|++|+++.+.
T Consensus 43 ~~l~~g~~D~~i~~~ 57 (201)
T cd08420 43 ERVLDGEIDLGLVEG 57 (201)
T ss_pred HHHHCCCccEEEecC
Confidence 568899999999864
No 36
>PF00497 SBP_bac_3: Bacterial extracellular solute-binding proteins, family 3; InterPro: IPR001638 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 3N26_A 3QAX_A 3I6V_A 2VHA_B 2IA4_B 2Q89_A 2Q88_A 2YJP_C 1II5_A 1IIW_A ....
Probab=22.26 E-value=41 Score=24.19 Aligned_cols=60 Identities=13% Similarity=0.160 Sum_probs=35.2
Q ss_pred CcHHHHHHhhhcCCcceeehhHhhh----hhcCCCCCceeecCCCCCccCcccchhhhhhccCcHHHHHHH
Q 038122 38 GNVQARLRKLNEGVIQATLSALAGL----KCLNMTENVTNILPIDDMLLAVAQGAIGIACTSNDKKMAKYL 104 (130)
Q Consensus 38 GNv~TRl~KL~~g~~daiiLA~AGL----~RLg~~~~i~~~l~~~~~~pA~gQGaiaie~r~~d~~~~~ll 104 (130)
.+.+.=++.|.+|++|++|....-+ ++.+...... + .+...+.-+++-++++++.+.+.+
T Consensus 139 ~~~~~~~~~l~~g~~d~~i~~~~~~~~~~~~~~~~~~~~--~-----~~~~~~~~~~~~~~~~~~~l~~~~ 202 (225)
T PF00497_consen 139 DSPEEALEALLSGRIDAFIVDESTAEYLLKRHPLENIVV--I-----PPPISPSPVYFAVRKKNPELLEIF 202 (225)
T ss_dssp SSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHTTTCEEEE--E-----EEEEEEEEEEEEEETTTHHHHHHH
T ss_pred ccHHHHHHHHhcCCeeeeeccchhhhhhhhhcccccccc--c-----ccccccceeEEeecccccHHHHHH
Confidence 6778889999999999999866544 3443332211 1 233333334444566666555443
No 37
>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=22.25 E-value=75 Score=21.64 Aligned_cols=18 Identities=22% Similarity=0.427 Sum_probs=14.1
Q ss_pred hHhhhcCCCcEEeecCCC
Q 038122 2 EEALINGEIDIAVHSMKD 19 (130)
Q Consensus 2 e~aLl~g~iDiAVHSlKD 19 (130)
.+.|.+|++|+++.....
T Consensus 42 ~~~l~~~~~Dl~i~~~~~ 59 (194)
T cd08436 42 LAAVREGRLDLAFVGLPE 59 (194)
T ss_pred HHHHHcCCccEEEEecCC
Confidence 367889999999976543
No 38
>cd08430 PBP2_IlvY The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold. In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-i
Probab=21.35 E-value=58 Score=22.41 Aligned_cols=16 Identities=38% Similarity=0.630 Sum_probs=13.0
Q ss_pred hHhhhcCCCcEEeecC
Q 038122 2 EEALINGEIDIAVHSM 17 (130)
Q Consensus 2 e~aLl~g~iDiAVHSl 17 (130)
.+.|.+|++|+++...
T Consensus 42 ~~~l~~g~~Dl~i~~~ 57 (199)
T cd08430 42 IDKVLNGEADIAIAAR 57 (199)
T ss_pred HHHHHCCCCCEEEEec
Confidence 3578899999999763
No 39
>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip
Probab=21.04 E-value=81 Score=22.04 Aligned_cols=17 Identities=35% Similarity=0.481 Sum_probs=13.4
Q ss_pred hHhhhcCCCcEEeecCC
Q 038122 2 EEALINGEIDIAVHSMK 18 (130)
Q Consensus 2 e~aLl~g~iDiAVHSlK 18 (130)
.+.|.+|++|+++....
T Consensus 42 ~~~l~~~~~Dl~i~~~~ 58 (197)
T cd08452 42 VEELLKGRIDIGFLHPP 58 (197)
T ss_pred HHHHHCCCccEEEeeCC
Confidence 35788999999997543
No 40
>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet
Probab=21.03 E-value=89 Score=22.29 Aligned_cols=18 Identities=28% Similarity=0.423 Sum_probs=14.0
Q ss_pred hHhhhcCCCcEEeecCCC
Q 038122 2 EEALINGEIDIAVHSMKD 19 (130)
Q Consensus 2 e~aLl~g~iDiAVHSlKD 19 (130)
.+.|.+|++|+++....+
T Consensus 42 ~~~l~~g~~Di~i~~~~~ 59 (221)
T cd08469 42 AEQLDLGRIDLVIGIFEQ 59 (221)
T ss_pred HHHHHCCCccEEEecCCC
Confidence 457889999999976543
No 41
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=20.77 E-value=28 Score=24.12 Aligned_cols=24 Identities=25% Similarity=0.225 Sum_probs=16.6
Q ss_pred cCCCcEEeecCCCCCCCCCCCeeecc
Q 038122 7 NGEIDIAVHSMKDVPTYLLDKTILPC 32 (130)
Q Consensus 7 ~g~iDiAVHSlKDlP~~~~~gl~i~a 32 (130)
.|+++-+|| |++..+.++.+..++
T Consensus 29 TG~i~~tiH--~~v~~~y~~~l~~Ga 52 (86)
T PF15072_consen 29 TGEIRGTIH--RKVLEEYGDELSPGA 52 (86)
T ss_pred CCcEEEEEe--HHHHhhcCCccccCE
Confidence 477888888 777777666665444
No 42
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has 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 flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=20.75 E-value=85 Score=21.42 Aligned_cols=16 Identities=38% Similarity=0.875 Sum_probs=13.1
Q ss_pred hHhhhcCCCcEEeecC
Q 038122 2 EEALINGEIDIAVHSM 17 (130)
Q Consensus 2 e~aLl~g~iDiAVHSl 17 (130)
.+.|.+|++|+++...
T Consensus 42 ~~~L~~~~~Dl~i~~~ 57 (197)
T cd08438 42 EQAVLNGELDVGITVL 57 (197)
T ss_pred HHHHHcCCCCEEEEec
Confidence 3678999999999754
No 43
>cd04050 C2B_Synaptotagmin-like C2 domain second repeat present in Synaptotagmin-like proteins. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular perm
Probab=20.72 E-value=71 Score=21.44 Aligned_cols=13 Identities=23% Similarity=0.355 Sum_probs=10.9
Q ss_pred EEeecCCCCCCCC
Q 038122 12 IAVHSMKDVPTYL 24 (130)
Q Consensus 12 iAVHSlKDlP~~~ 24 (130)
+.|||+||||..-
T Consensus 4 V~v~~A~~L~~~~ 16 (105)
T cd04050 4 VYLDSAKNLPLAK 16 (105)
T ss_pred EEEeeecCCCCcc
Confidence 6799999999753
No 44
>cd08447 PBP2_LTTR_aromatics_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. 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 Ve
Probab=20.48 E-value=87 Score=21.53 Aligned_cols=16 Identities=38% Similarity=0.455 Sum_probs=13.3
Q ss_pred hHhhhcCCCcEEeecC
Q 038122 2 EEALINGEIDIAVHSM 17 (130)
Q Consensus 2 e~aLl~g~iDiAVHSl 17 (130)
.+.|.+|++|+++...
T Consensus 42 ~~~l~~g~~D~~i~~~ 57 (198)
T cd08447 42 IEALESGRIDLGLLRP 57 (198)
T ss_pred HHHHHcCCceEEEecC
Confidence 3678999999999864
No 45
>cd08439 PBP2_LrhA_like The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold. This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a vari
Probab=20.21 E-value=63 Score=22.37 Aligned_cols=16 Identities=38% Similarity=0.532 Sum_probs=13.1
Q ss_pred hHhhhcCCCcEEeecC
Q 038122 2 EEALINGEIDIAVHSM 17 (130)
Q Consensus 2 e~aLl~g~iDiAVHSl 17 (130)
.+.|.+|++|+++...
T Consensus 42 ~~~l~~~~~Dl~i~~~ 57 (185)
T cd08439 42 MEMLERGEVDLALITH 57 (185)
T ss_pred HHHHHCCCCcEEEEec
Confidence 3678999999999754
Done!