RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2382
(527 letters)
>gnl|CDD|237587 PRK14019, PRK14019, bifunctional 3,4-dihydroxy-2-butanone
4-phosphate synthase/GTP cyclohydrolase II-like protein;
Provisional.
Length = 367
Score = 454 bits (1171), Expect = e-158
Identities = 153/266 (57%), Positives = 208/266 (78%)
Query: 6 ISSTKEIISELKIGNMIILVDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTE 65
++S +EII++++ G M+ILVD E+RENEGD++++++FVTP AINFM+K+ RGLIC+TLTE
Sbjct: 3 LASIEEIIADIRAGRMVILVDEEDRENEGDLVMAAEFVTPEAINFMAKHGRGLICLTLTE 62
Query: 66 KHCIQLKLDMMTKKNNSSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIV 125
+ C QL L +MT +N + +GTNFTVSIEAA GVTTGISA+DRA TI+ A ++ AKP DIV
Sbjct: 63 ERCEQLGLPLMTYRNGTQYGTNFTVSIEAAEGVTTGISAADRARTIQAAVARDAKPEDIV 122
Query: 126 QPGHIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARLPDLIKFS 185
QPGHIFPL A+ GGVL+R GHTEAGCDL LAGLTP+AVICEI+ DDGTMARLPDL +F+
Sbjct: 123 QPGHIFPLMAQPGGVLVRAGHTEAGCDLAALAGLTPAAVICEIMKDDGTMARLPDLEEFA 182
Query: 186 KLHNIKIGTISNLICYRYKYENIIKRKAEYNINTLYGNFKIIVYIDKINNDIHLTLIYGS 245
K H +KIGTI++LI YR + E+I++R AE + T +G F+++ Y DK + HL L+ G+
Sbjct: 183 KEHGLKIGTIADLIHYRSRTESIVERVAERPMQTAHGEFRLVAYRDKPSGSTHLALVKGT 242
Query: 246 INPNKIIPIWLNQQLSIFDFLHAKTS 271
I P++ + +++ LS+ D L
Sbjct: 243 ICPDEETLVRVHEPLSVLDLLEVGQP 268
>gnl|CDD|171535 PRK12485, PRK12485, bifunctional 3,4-dihydroxy-2-butanone
4-phosphate synthase/GTP cyclohydrolase II-like protein;
Provisional.
Length = 369
Score = 319 bits (820), Expect = e-105
Identities = 131/240 (54%), Positives = 180/240 (75%)
Query: 7 SSTKEIISELKIGNMIILVDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEK 66
++ +EII + + G M++LVD E+RENEGD++L+++ AINFM++ ARGLIC+TLT++
Sbjct: 4 NTIEEIIEDYRQGKMVLLVDDEDRENEGDLLLAAERCDAQAINFMAREARGLICLTLTDE 63
Query: 67 HCIQLKLDMMTKKNNSSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQ 126
HC +L L+ M N S F T FTVSIEAA GVTTGISA+DRA T+ A + A+P D+VQ
Sbjct: 64 HCQRLGLEQMVPSNGSVFSTAFTVSIEAATGVTTGISAADRARTVAAAVAPNARPEDLVQ 123
Query: 127 PGHIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARLPDLIKFSK 186
PGHIFPL+A++GGVL R GHTEAGCDL +LAG +P++VI E++NDDGTMAR PDL F+
Sbjct: 124 PGHIFPLRAREGGVLTRAGHTEAGCDLARLAGFSPASVIVEVMNDDGTMARRPDLEVFAA 183
Query: 187 LHNIKIGTISNLICYRYKYENIIKRKAEYNINTLYGNFKIIVYIDKINNDIHLTLIYGSI 246
H IKIGTI++LI YR E+ IKR E + T++G F+++ Y D+I +H+ ++ G I
Sbjct: 184 KHGIKIGTIADLIHYRLSTEHTIKRIGERELPTVHGTFRLVTYEDRIEGGVHMAMVMGDI 243
>gnl|CDD|181774 PRK09311, PRK09311, bifunctional 3,4-dihydroxy-2-butanone
4-phosphate synthase/GTP cyclohydrolase II protein;
Provisional.
Length = 402
Score = 318 bits (817), Expect = e-104
Identities = 113/239 (47%), Positives = 167/239 (69%)
Query: 8 STKEIISELKIGNMIILVDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKH 67
S +E I+++ G +I+VD E+RENEGD+I +++ TP + FM ++ G +C+ LTE+
Sbjct: 6 SIEEAIADIAAGKAVIVVDDEDRENEGDLIFAAEKATPELVAFMVRHTSGYVCVPLTEED 65
Query: 68 CIQLKLDMMTKKNNSSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQP 127
+L L M N S GT FTVS++AANGVTTGISA+DRA TI++ + +KP+D +P
Sbjct: 66 ADRLDLPPMVAHNQDSHGTAFTVSVDAANGVTTGISAADRATTIRLLADPASKPADFTRP 125
Query: 128 GHIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARLPDLIKFSKL 187
GH+FPL+AK GGVL R GHTEA DL +LAGL P+ VICEI+N+DGTMAR+P+L F+
Sbjct: 126 GHVFPLRAKPGGVLRRAGHTEAAVDLARLAGLQPAGVICEIVNEDGTMARVPELRVFADE 185
Query: 188 HNIKIGTISNLICYRYKYENIIKRKAEYNINTLYGNFKIIVYIDKINNDIHLTLIYGSI 246
H++ + TI++LI YR ++E +++R+ E + T +G F+ I Y ++ H+ L+ G I
Sbjct: 186 HDLALITIADLIAYRRRHEKLVEREVEARLPTRFGEFRAIGYTSILDGKEHVALVKGDI 244
>gnl|CDD|216197 pfam00926, DHBP_synthase, 3,4-dihydroxy-2-butanone 4-phosphate
synthase. 3,4-Dihydroxy-2-butanone 4-phosphate is
biosynthesised from ribulose 5-phosphate and serves as
the biosynthetic precursor for the xylene ring of
riboflavin. Sometimes found as a bifunctional enzyme
with pfam00925.
Length = 193
Score = 309 bits (794), Expect = e-104
Identities = 112/193 (58%), Positives = 146/193 (75%), Gaps = 1/193 (0%)
Query: 10 KEIISELKIGNMIILVDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCI 69
+E I LK G +I+VD E+RENEGD++++++ VTP ++NFM ++ARGLIC+ LTE+
Sbjct: 2 EEAIEALKAGKPVIVVDDEDRENEGDLVIAAEKVTPESVNFMIRHARGLICVALTEERAD 61
Query: 70 QLKLDMMTKKNNSSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGH 129
+L L M +N FGT FTVS++A G TTGISA+DRA TI+ + A P D V+PGH
Sbjct: 62 RLGLPPMVDRNTDRFGTAFTVSVDAK-GTTTGISAADRALTIRALADPNAFPEDFVRPGH 120
Query: 130 IFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARLPDLIKFSKLHN 189
+FPL+AK+GGVL R GHTEA DL +LAGLTP+AVICEILNDDGTMARLPDL +F+K H
Sbjct: 121 VFPLRAKEGGVLERRGHTEAAVDLARLAGLTPAAVICEILNDDGTMARLPDLEEFAKEHG 180
Query: 190 IKIGTISNLICYR 202
+ + TI +LI YR
Sbjct: 181 LPLITIEDLIEYR 193
>gnl|CDD|223186 COG0108, RibB, 3,4-dihydroxy-2-butanone 4-phosphate synthase
[Coenzyme metabolism].
Length = 203
Score = 308 bits (791), Expect = e-103
Identities = 108/201 (53%), Positives = 141/201 (70%), Gaps = 1/201 (0%)
Query: 6 ISSTKEIISELKIGNMIILVDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTE 65
+E I L+ G +I+VD E+RENEGD+I +++ VTP I FM ++A GLIC+ LTE
Sbjct: 3 FERVEEAIEALRAGKPVIVVDDEDRENEGDLIFAAEAVTPEQIAFMRRHASGLICVALTE 62
Query: 66 KHCIQLKLDMMTKKNNSSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIV 125
+ +L L M N + GT FTVS++A TTGISA+DRA TI+ + AKPSD
Sbjct: 63 ERAKRLGLPPMVDNNTDAHGTAFTVSVDARE-TTTGISAADRALTIRALADPGAKPSDFR 121
Query: 126 QPGHIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARLPDLIKFS 185
+PGH+FPL+AK GGVL R GHTEA DL +LAGL P+ VICEI+NDDGTMARLP+L +F+
Sbjct: 122 RPGHVFPLRAKDGGVLERRGHTEAAVDLARLAGLKPAGVICEIMNDDGTMARLPELEEFA 181
Query: 186 KLHNIKIGTISNLICYRYKYE 206
K H + + TI +LI YR K+E
Sbjct: 182 KEHGLPVITIEDLIEYRKKHE 202
>gnl|CDD|236465 PRK09319, PRK09319, bifunctional 3,4-dihydroxy-2-butanone
4-phosphate synthase/GTP cyclohydrolase II/unknown
domain fusion protein; Provisional.
Length = 555
Score = 293 bits (753), Expect = 6e-93
Identities = 113/242 (46%), Positives = 165/242 (68%), Gaps = 4/242 (1%)
Query: 11 EIISELKIGNMIILVDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQ 70
+ ++ ++ G +++VD ENRENEGD+I ++ F TP INFM+ ARGLIC+ +T + +
Sbjct: 10 DALAAIRNGECVVVVDDENRENEGDLICAAQFATPEMINFMATEARGLICLAMTGERLDE 69
Query: 71 LKLDMMTKKNNSSFGTNFTVSIEAA--NGVTTGISASDRAHTIKVASSKKAKPSDIVQPG 128
L L +M +N S T FTVSI+A GV+TGISA DRA TI+VA + KP D+ +PG
Sbjct: 70 LDLPLMVDRNTDSNQTAFTVSIDAGPELGVSTGISAEDRARTIQVAINPDTKPEDLRRPG 129
Query: 129 HIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARLPDLIKFSKLH 188
HIFPL+AK+GGVL R GHTEA DL +LAGL P+ VICEI N DG+MARLP+L +++K H
Sbjct: 130 HIFPLRAKEGGVLKRAGHTEAAVDLARLAGLYPAGVICEIQNPDGSMARLPELKEYAKQH 189
Query: 189 NIKIGTISNLICYRYKYENIIKRKAEYNINTLYGNFKIIVYIDKINNDIHLTLIYGSINP 248
+K+ +I++LI YR + E + R+A + + +G F+ Y ++++ H+ L+ G +P
Sbjct: 190 GLKLISIADLISYRLQNERFVYREAVAKLPSQFGQFQAYGYRNELDGSEHVALVKG--DP 247
Query: 249 NK 250
Sbjct: 248 AN 249
>gnl|CDD|235119 PRK03353, ribB, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
Provisional.
Length = 217
Score = 268 bits (687), Expect = 1e-87
Identities = 96/190 (50%), Positives = 136/190 (71%)
Query: 13 ISELKIGNMIILVDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLK 72
+ L+ G ++++D E+RENEGD+I +++ +T + ++ G++C+ LTE+ QL
Sbjct: 20 LDALREGRGVMVLDDEDRENEGDMIFAAETMTVEQMALTIRHGSGIVCLCLTEERRKQLD 79
Query: 73 LDMMTKKNNSSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFP 132
L MM + N S +GT FTV+IEAA GVTTG+SA+DR TI+ A + AKPSD+ +PGH+FP
Sbjct: 80 LPMMVENNTSQYGTAFTVTIEAAEGVTTGVSAADRITTIRAAIADGAKPSDLNRPGHVFP 139
Query: 133 LQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARLPDLIKFSKLHNIKI 192
L+A+ GGVL R GHTEA DL LAGL P+ V+CE+ NDDGTMAR P+ I F+K HN+ +
Sbjct: 140 LRAQPGGVLTRRGHTEATIDLMTLAGLKPAGVLCELTNDDGTMARAPECIAFAKQHNMPV 199
Query: 193 GTISNLICYR 202
TI +L+ YR
Sbjct: 200 LTIEDLVAYR 209
>gnl|CDD|215445 PLN02831, PLN02831, Bifunctional GTP cyclohydrolase II/
3,4-dihydroxy-2-butanone-4-phosphate synthase.
Length = 450
Score = 267 bits (685), Expect = 3e-84
Identities = 108/243 (44%), Positives = 163/243 (67%), Gaps = 3/243 (1%)
Query: 7 SSTKEIISELKIGNMIILVDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEK 66
SS E + +++ G +++VD E+RENEGD+I+++ VTP A+ F+ K+ G++C+++ +
Sbjct: 36 SSIAEALEDIRQGKFVVVVDDEDRENEGDLIMAASLVTPEAMAFLVKHGSGIVCVSMKGE 95
Query: 67 HCIQLKLDMM--TKKNNSSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDI 124
+L+L +M +K+N T FTV+++A +G TTG+SASDRA TI +S +KP D
Sbjct: 96 DLDRLRLPLMVPSKENEEKMATAFTVTVDAKHGTTTGVSASDRAKTILALASPDSKPEDF 155
Query: 125 VQPGHIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILND-DGTMARLPDLIK 183
+PGHIFPL+ ++GGVL R GHTEA DL LAGL P V+CEI+ND DG+MARLP L K
Sbjct: 156 RRPGHIFPLRYREGGVLKRAGHTEAAVDLAVLAGLPPVGVLCEIVNDEDGSMARLPQLRK 215
Query: 184 FSKLHNIKIGTISNLICYRYKYENIIKRKAEYNINTLYGNFKIIVYIDKINNDIHLTLIY 243
F++ H +KI +I++LI YR K E +++R A + T +G F Y K++ H+ +
Sbjct: 216 FAEEHGLKIISIADLIRYRRKREKLVERTAVARLPTKWGLFTAYCYRSKLDGIEHIAFVK 275
Query: 244 GSI 246
G I
Sbjct: 276 GDI 278
>gnl|CDD|181775 PRK09314, PRK09314, bifunctional 3,4-dihydroxy-2-butanone
4-phosphate synthase/GTP cyclohydrolase II protein;
Provisional.
Length = 339
Score = 261 bits (668), Expect = 4e-83
Identities = 116/241 (48%), Positives = 161/241 (66%), Gaps = 2/241 (0%)
Query: 6 ISSTKEIISELKIGNMIILVDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTE 65
I +E I ++K G M+I+VD E+RENEGD++ ++ F TP +NFM+ +ARGLIC++LT+
Sbjct: 3 IKRVEEAIEDIKNGKMLIMVDDEDRENEGDLVYAAIFSTPEKVNFMATHARGLICVSLTK 62
Query: 66 KHCIQLKLDMMTKKNNSSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIV 125
+ +L+L M KN S+ T FTVSI+A TTGISA +R TIK+ + +KPSD V
Sbjct: 63 ELAKKLELPPMVSKNTSNHETAFTVSIDAKEA-TTGISAFERDMTIKLLADDTSKPSDFV 121
Query: 126 QPGHIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARLPDLIKFS 185
+PGHIFPL AK GGVL+R GHTE DL KLAGL P AVICEI+ +DGTMAR DL F+
Sbjct: 122 RPGHIFPLIAKDGGVLVRTGHTEGSVDLCKLAGLKPVAVICEIMKEDGTMARRDDLEDFA 181
Query: 186 KLHNIKIGTISNLICYRYKYENIIKRKAEYNINTLYGNFKIIVYIDKINNDIHLTLIYGS 245
K HN+K+ +S+L+ YR K E++IK + + + ++D + N H+ +G
Sbjct: 182 KKHNLKMIYVSDLVEYRLKNESLIKEEEKEESEFAGFKAEKYTFLDHLQN-EHIAFKFGE 240
Query: 246 I 246
I
Sbjct: 241 I 241
>gnl|CDD|232999 TIGR00506, ribB, 3,4-dihydroxy-2-butanone 4-phosphate synthase.
Several members of the family are bifunctional,
involving both ribA and ribB function. In these cases,
ribA tends to be on the C-terminal end of the protein
and ribB tends to be on the N-terminal [Biosynthesis of
cofactors, prosthetic groups, and carriers, Riboflavin,
FMN, and FAD].
Length = 199
Score = 245 bits (627), Expect = 7e-79
Identities = 98/193 (50%), Positives = 137/193 (70%), Gaps = 1/193 (0%)
Query: 11 EIISELKIGNMIILVDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQ 70
E + LK G ++++ D E+RENEGD+I++++F+TP I FM ++A GLIC+ +T +
Sbjct: 7 EALEALKKGEIVLVYDDEDRENEGDLIVAAEFITPEQIAFMRRHAGGLICVAITPDIADK 66
Query: 71 LKLDMMTKKNNSSFGTNFTVSIEAANG-VTTGISASDRAHTIKVASSKKAKPSDIVQPGH 129
L L M N S+ GT T +I A+ TGISA+DRA TI+ A + KPSD +PGH
Sbjct: 67 LDLPPMVDINTSASGTASTFTITVAHRKTFTGISANDRALTIRAALADVVKPSDFRRPGH 126
Query: 130 IFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARLPDLIKFSKLHN 189
+FPL+A GGVL RGGHTEA DL +LAGL P+ VICE++NDDGTMAR P+L++++K HN
Sbjct: 127 VFPLRAADGGVLTRGGHTEASVDLAELAGLKPAGVICEMMNDDGTMARKPELMEYAKKHN 186
Query: 190 IKIGTISNLICYR 202
+K+ +I +LI YR
Sbjct: 187 LKLISIEDLIEYR 199
>gnl|CDD|167278 PRK01792, ribB, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
Provisional.
Length = 214
Score = 229 bits (586), Expect = 1e-72
Identities = 95/197 (48%), Positives = 135/197 (68%)
Query: 10 KEIISELKIGNMIILVDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCI 69
I+ K GN ++++D E+RENEGD+I ++ +TP + + +Y G++C+ +T++ C
Sbjct: 17 INAINAFKQGNGVLVLDDEDRENEGDLIFPAETITPEQMAKLIRYGSGIVCLCITDELCQ 76
Query: 70 QLKLDMMTKKNNSSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGH 129
QL L M + N S T FTV+IEAA GV+TG+SA+DR TI+ A + AKPSD+ +PGH
Sbjct: 77 QLDLPPMVQHNTSVNKTAFTVTIEAAKGVSTGVSAADRVTTIQAAIADNAKPSDLHRPGH 136
Query: 130 IFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARLPDLIKFSKLHN 189
+FPL+A GGVL R GHTEA DL +LAG + VICEI NDDGTMAR P++++F+K
Sbjct: 137 VFPLRAANGGVLTRRGHTEAAVDLARLAGYKEAGVICEITNDDGTMARTPEIVEFAKKFG 196
Query: 190 IKIGTISNLICYRYKYE 206
+ TI +L+ YR KY
Sbjct: 197 YAVVTIEDLVEYRLKYN 213
>gnl|CDD|179162 PRK00910, ribB, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
Provisional.
Length = 218
Score = 217 bits (554), Expect = 7e-68
Identities = 94/201 (46%), Positives = 139/201 (69%)
Query: 6 ISSTKEIISELKIGNMIILVDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTE 65
I+ + + L+ G ++L+D E+RENEGDII S + +T + M + G++C+ LT+
Sbjct: 14 ITRVENALQALREGRGVLLLDDEDRENEGDIIYSVEHLTNAQMALMIRECSGIVCLCLTD 73
Query: 66 KHCIQLKLDMMTKKNNSSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDIV 125
+L+L M NNS+ T FTVSIEA +GVTTG+SA DR TIK A++ +AKP D+
Sbjct: 74 AQADKLELPPMVVNNNSANQTAFTVSIEAKHGVTTGVSAQDRVTTIKTAANPQAKPEDLA 133
Query: 126 QPGHIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARLPDLIKFS 185
+PGH+FPL+A+ GGVL R GHTE DL ++AGL P+ V+CE+ N DGTMA+ P++I F
Sbjct: 134 RPGHVFPLRARAGGVLARRGHTEGTVDLMQMAGLQPAGVLCELTNPDGTMAKTPEIIAFG 193
Query: 186 KLHNIKIGTISNLICYRYKYE 206
KLHN+ + TI +++ YR +++
Sbjct: 194 KLHNMPVLTIEDMVMYRNQFD 214
>gnl|CDD|134031 PRK00014, ribB, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
Provisional.
Length = 230
Score = 193 bits (492), Expect = 2e-58
Identities = 81/194 (41%), Positives = 119/194 (61%)
Query: 5 FISSTKEIISELKIGNMIILVDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLT 64
F + + + L+IG +IL+D +RENE D+I+++D +T + + + G++C+ L
Sbjct: 17 FATRLERALQHLRIGRPVILMDDFDRENEADLIVAADKLTVPVMAQLIRDGSGIVCLCLP 76
Query: 65 EKHCIQLKLDMMTKKNNSSFGTNFTVSIEAANGVTTGISASDRAHTIKVASSKKAKPSDI 124
+ +L+L M N S + T FTVSIEA GVTTG+SA DR TI+ A + A+ D+
Sbjct: 77 GETLDRLELPPMVDSNRSRYSTAFTVSIEAREGVTTGVSAVDRVTTIRAAIAPGARSGDV 136
Query: 125 VQPGHIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARLPDLIKF 184
V PGH+FPL+A+ GGVL R GHTE DL LAGL P+ V+CE++N DGTM R L ++
Sbjct: 137 VSPGHVFPLRAQPGGVLTRRGHTEGSVDLAALAGLRPAGVLCELMNADGTMMRGASLERY 196
Query: 185 SKLHNIKIGTISNL 198
+ + I L
Sbjct: 197 AAKEGLVALAIDEL 210
>gnl|CDD|234686 PRK00202, nusB, transcription antitermination protein NusB;
Reviewed.
Length = 137
Score = 134 bits (340), Expect = 2e-37
Identities = 50/140 (35%), Positives = 76/140 (54%), Gaps = 9/140 (6%)
Query: 389 PRHRAREFALQGIYQWLFNNMDVNLIETYIKEISNFYKVDKKYFYLILRGVINDINFLRY 448
R +ARE A+Q +YQW + D+ I + K D YF ++RGV+ +
Sbjct: 2 ARRKAREAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQA---- 57
Query: 449 DLSLII-----DRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDG 503
+L +I D ++ L +E +L + YEL +PYKV+INEAIEL K FG+ D
Sbjct: 58 ELDELISPYLKDWTLERLDPVERAILRLALYELLFRDDVPYKVVINEAIELAKKFGDEDS 117
Query: 504 YKYVNKILDKVALNIRNIKF 523
+K+VN +LDK+A +R +
Sbjct: 118 HKFVNGVLDKIAKELRPAEK 137
>gnl|CDD|233652 TIGR01951, nusB, transcription antitermination factor NusB. A
transcription antitermination complex active in many
bacteria was designated N-utilization substance (Nus) in
E. coli because of its interaction with phage lambda
protein N. This model represents NusB. Other components
are NusA and NusG. NusE is, in fact, ribosomal protein
S10 [Transcription, Transcription factors].
Length = 129
Score = 132 bits (335), Expect = 6e-37
Identities = 48/130 (36%), Positives = 74/130 (56%), Gaps = 7/130 (5%)
Query: 390 RHRAREFALQGIYQWLFNNMDVNLIETYIKEISNFYKVDKKYFYLILRGVINDINFLRYD 449
R +ARE ALQ +YQW + D+ I E + D++YF ++RGV+ + +
Sbjct: 1 RRKARELALQALYQWELSGNDLEEIIEEFLEEEELDEEDREYFRELVRGVLENQEEID-- 58
Query: 450 LSLII----DRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDGYK 505
LI D ++ L ++ +L + YEL +PYKV+INEA+EL K FG+ D +K
Sbjct: 59 -ELISPHLEDWTLERLDPVDRAILRLAAYELLYRPDVPYKVVINEAVELAKKFGDDDSHK 117
Query: 506 YVNKILDKVA 515
+VN +LDK+A
Sbjct: 118 FVNGVLDKIA 127
>gnl|CDD|187742 cd09209, Lumazine_synthase-I, lumazine synthase
(6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes
the penultimate step in the biosynthesis of riboflavin
(vitamin B2); type-I. Type-I LS, also known as RibH1,
catalyzes the penultimate step in the biosynthesis of
riboflavin in plants and microorganisms. LS catalyse the
formation of 6,7-dimethyl-8-ribityllumazine by the
condensation of
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with
3,4-dihydroxy- 2-butanone-4-phosphate. Subsequently, the
lumazine intermediate dismutates to yield riboflavin and
5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione, in a
reaction catalyzed by riboflavin synthase synthase (RS);
RS belongs to a different family of the
Lumazine-synthase-like superfamily. Riboflavin is the
precursor of flavin mononucleotide (FMN) and flavin
adenine dinucleotide (FAD) which are essential cofactors
for the catalysis of a wide range of redox reactions.
These cofactors are also involved in many other
processes involving DNA repair, circadian time-keeping,
light sensing, and bioluminescence. Riboflavin is
biosynthesized in plants, fungi and certain
microorganisms; as animals lack the necessary enzymes to
produce this vitamin, they acquire it from dietary
sources. Type II LSs are distinct from type-I LS not
only in protein sequence, but in that they exhibit
different quaternary assemblies; type-I LSs form
pentamers. The pathogen Brucella spp. encode both a
Type-I LS and a Type-II LS called RibH1 and RibH2,
respectively. RibH1/type-I LS appears to be the
functional LS in Brucella spp., whereas RibH2/type-II LS
has much lower catalytic activity as LS. The pathogen
Brucella spp. have both a type-I LS and a type-II LS
called RibH1 and RibH2, respectively. RibH1/type-I LS
appears to be a functional LS in Brucella spp., whereas
RibH2/type-II LS has much lower catalytic activity as
LS.
Length = 133
Score = 131 bits (333), Expect = 1e-36
Identities = 42/101 (41%), Positives = 65/101 (64%), Gaps = 3/101 (2%)
Query: 287 LIKNGAQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETI 346
L ++G +E+NI + VPGA EIPLA K + + K++ +IA+G +IRGET HF+ + NE
Sbjct: 24 LKRHGVKEENIDVVRVPGAFEIPLAAKRLARSGKYDAIIALGCVIRGETPHFDYVCNEVT 83
Query: 347 SNIMQISIKNNIPIINAILTTETIEQANSRILTKVNLIKNK 387
+M++S++ +P+I +LTT+ EQA R K NK
Sbjct: 84 RGLMRLSLETGVPVIFGVLTTDNEEQALERAGGKA---GNK 121
>gnl|CDD|234606 PRK00061, ribH, 6,7-dimethyl-8-ribityllumazine synthase;
Provisional.
Length = 154
Score = 126 bits (319), Expect = 2e-34
Identities = 44/101 (43%), Positives = 65/101 (64%), Gaps = 3/101 (2%)
Query: 287 LIKNGAQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETI 346
L ++G E+NI + VPGA EIPLA K + + K++ +IA+G +IRGET HF+ +ANE
Sbjct: 38 LKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGKYDAVIALGAVIRGETPHFDYVANEVA 97
Query: 347 SNIMQISIKNNIPIINAILTTETIEQANSRILTKVNLIKNK 387
+ +S++ +P+ +LTT+TIEQA R TK NK
Sbjct: 98 KGLADVSLETGVPVGFGVLTTDTIEQAIERAGTKA---GNK 135
>gnl|CDD|201491 pfam00885, DMRL_synthase, 6,7-dimethyl-8-ribityllumazine synthase.
This family includes the beta chain of 6,7-dimethyl-8-
ribityllumazine synthase EC:2.5.1.9, an enzyme involved
in riboflavin biosynthesis. The family also includes a
subfamily of distant archaebacterial proteins that may
also have the same function.
Length = 144
Score = 121 bits (307), Expect = 9e-33
Identities = 40/113 (35%), Positives = 67/113 (59%), Gaps = 8/113 (7%)
Query: 286 KLIKNGAQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANET 345
L ++G E++I + VPGA E+PLA K + + +++ ++A+G +IRG TYHF+ +A E
Sbjct: 28 ALKRHGVSEEDIDVVRVPGAFELPLAAKKLAKSGRYDAVVALGAVIRGGTYHFDYVAQEV 87
Query: 346 ISNIMQISIKNNIPIINAILTTETIEQANSRILTKVNLIKNKTPRHRAREFAL 398
+MQ+S++ +P+ +LTT+T EQA R K ++ E AL
Sbjct: 88 SRGLMQVSLETGVPVGFGVLTTDTFEQALERAGGKA--------GNKGAEAAL 132
>gnl|CDD|223132 COG0054, RibH, Riboflavin synthase beta-chain [Coenzyme
metabolism].
Length = 152
Score = 119 bits (300), Expect = 9e-32
Identities = 42/94 (44%), Positives = 63/94 (67%)
Query: 287 LIKNGAQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETI 346
L ++GA NI + VPGA EIPLA K + + K++ ++A+G +IRGETYHF+ +ANE
Sbjct: 38 LKRHGADVDNIDVVRVPGAFEIPLAAKKLARTGKYDAVVALGAVIRGETYHFDYVANEVA 97
Query: 347 SNIMQISIKNNIPIINAILTTETIEQANSRILTK 380
+M +S++ +P+ +LTT+ IEQA R TK
Sbjct: 98 RGLMDVSLETGVPVTFGVLTTDNIEQAIERAGTK 131
>gnl|CDD|236464 PRK09318, PRK09318, bifunctional 3,4-dihydroxy-2-butanone
4-phosphate synthase/GTP cyclohydrolase II protein;
Provisional.
Length = 387
Score = 122 bits (308), Expect = 1e-30
Identities = 74/237 (31%), Positives = 121/237 (51%), Gaps = 14/237 (5%)
Query: 19 GNMIILVDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQLKLDMMTK 78
G +IL+D NRENE D + + +T +NF Y +GL+C+T E+ LK
Sbjct: 11 GKPVILID-RNRENEADFVYPAQIITEEVVNFFLSYGKGLLCLTADEEDL--LKRGFFKL 67
Query: 79 KNNSSFGTNFTVSIEAANGVTTGISASDRAHTI-KVASSKKAKPSDIVQPGHIFPLQAKK 137
+N TNF + ++ G TGISAS+RA T K+A + PGH+ L
Sbjct: 68 PSNGG-ETNFFIPVDY--GTGTGISASERALTCRKLAEGLYV--HEFRYPGHVTLLGGI- 121
Query: 138 GGVLIRGGHTEAGCDLTKLAGLTPSAVICEILNDDGTMARLPDLIKFSKLHNIKIGTISN 197
G R GHTEA +L++L G AVI EIL++ G L ++K ++ ++ + I +
Sbjct: 122 -GFNRRRGHTEASLELSELLGFKRYAVIVEILDEKGDSHDLDYVLKLAEKFSLPVLEIDD 180
Query: 198 LICYRYKYENIIKRKAEYNINTLYGNFKIIVYIDKINNDIHLTLI---YGSINPNKI 251
+ + + +IK KAE + T YG F+I+ + + ++ H+ ++ G + +I
Sbjct: 181 VWKEFVRRKQLIKVKAEAKLPTDYGEFEIVSFENHLDGKEHVAIVKEPLGEVPLVRI 237
>gnl|CDD|223852 COG0781, NusB, Transcription termination factor [Transcription].
Length = 151
Score = 109 bits (274), Expect = 4e-28
Identities = 47/146 (32%), Positives = 77/146 (52%), Gaps = 15/146 (10%)
Query: 385 KNKTPRHRAREFALQGIYQWLFNN------MDVNLIETYIKEISNFYKVDKKYFYLILRG 438
K R +ARE A+Q +YQW + + ++ E +++ + D +YF +++G
Sbjct: 5 PPKLTRRQARELAVQALYQWELSGSVSAEDILEDIEEEFVENELDIELADSEYFRSLVKG 64
Query: 439 VINDINFLRYDLSLII-----DRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIE 493
V+ + +L +I S+ L +E +L + YEL +PYKV+INEAIE
Sbjct: 65 VLENQE----ELDELISPHLKKWSLERLDLVERAILRLALYELLFRDDVPYKVVINEAIE 120
Query: 494 LVKSFGNIDGYKYVNKILDKVALNIR 519
L K F D +K+VN +LDK+A +R
Sbjct: 121 LAKKFSGEDSHKFVNGVLDKIAKKLR 146
>gnl|CDD|216253 pfam01029, NusB, NusB family. The NusB protein is involved in the
regulation of rRNA biosynthesis by transcriptional
antitermination.
Length = 126
Score = 97.7 bits (244), Expect = 2e-24
Identities = 36/128 (28%), Positives = 62/128 (48%), Gaps = 6/128 (4%)
Query: 391 HRAREFALQGIYQWLFNN--MDVNLIETYIKEISNFYKVDKKYFYLILRGVINDINFLRY 448
ARE ALQ +Y ++ L + ++ + D+ + ++ GV+ ++ L
Sbjct: 1 RNARELALQALYAVEERGASLNELLDKLLEADLD---ERDRAFATELVYGVLRNLEELDA 57
Query: 449 DLS-LIIDRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDGYKYV 507
+ L+ + + L ++ +L +G YEL IP V INEA+EL K FG +V
Sbjct: 58 LIEKLLENWPLERLDPVDRAILRLGLYELLYLDDIPPHVAINEAVELAKKFGGEKSAGFV 117
Query: 508 NKILDKVA 515
N +L K+A
Sbjct: 118 NGVLRKIA 125
>gnl|CDD|211550 TIGR00114, lumazine-synth, 6,7-dimethyl-8-ribityllumazine synthase.
This enzyme catalyzes the cyclo-ligation of
3,4-dihydroxy-2-butanone-4-P and
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione to
form 6,7-dimethyl-8-ribityllumazine, the immediate
precursor of riboflavin. Sometimes referred to as
riboflavin synthase, beta subunit, this should not be
confused with the alpha subunit which carries out the
subsequent reaction. Archaeal members of this family are
considered putative, although included in the seed and
scoring above the trusted cutoff [Biosynthesis of
cofactors, prosthetic groups, and carriers, Riboflavin,
FMN, and FAD].
Length = 138
Score = 96.7 bits (241), Expect = 7e-24
Identities = 43/90 (47%), Positives = 59/90 (65%)
Query: 291 GAQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIM 350
GA+ NI I VPGA E+PLA+K + + K++ +IA+G +IRG T HFE +A+E I
Sbjct: 30 GAEVDNIDVIWVPGAFELPLAVKKLAESGKYDAVIALGTVIRGGTPHFEYVADEAAKGIA 89
Query: 351 QISIKNNIPIINAILTTETIEQANSRILTK 380
+++ P+I ILTTETIEQA R TK
Sbjct: 90 DLALDYGKPVIFGILTTETIEQAIERAGTK 119
>gnl|CDD|238342 cd00619, Terminator_NusB, Transcription termination factor NusB (N
protein-Utilization Substance B). NusB plays a key role
in the regulation of ribosomal RNA biosynthesis in
eubacteria by modulating the efficiency of
transcriptional antitermination. NusB along with other
Nus factors (NusA, NusE/S10 and NusG) forms the core
complex with the boxA element of the nut site of the
rRNA operons. These interactions help RNA polymerase to
counteract polarity during transcription of rRNA operons
and allow stable antitermination. The transcription
antitermination system can be appropriated by some
bacteriophages such as lambda, which use the system to
switch between the lysogenic and lytic modes of phage
propagation.
Length = 130
Score = 92.7 bits (231), Expect = 2e-22
Identities = 42/134 (31%), Positives = 75/134 (55%), Gaps = 9/134 (6%)
Query: 390 RHRAREFALQGIYQWLFNNMDVNLIETYIKEISNFYKVDKKYFYLILRGVINDINFLRYD 449
R RARE A+Q +Y W + + + ++ + K + ++RGV+ +I +
Sbjct: 1 RRRARELAVQALYAWELAPEILAEVVSLLELLQYKSKKVLPFALKLVRGVLENIE----E 56
Query: 450 LSLIIDR-----SINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDGY 504
+ +I++ S++ L+ +E +L + YEL +P+ V+INEAIEL K FG D +
Sbjct: 57 IDELIEKHLRNWSLDRLAIVERAILRLAVYELLFLPDVPHPVVINEAIELAKRFGGDDSH 116
Query: 505 KYVNKILDKVALNI 518
K+VN +LDK+A ++
Sbjct: 117 KFVNGVLDKIAKDL 130
>gnl|CDD|178026 PLN02404, PLN02404, 6,7-dimethyl-8-ribityllumazine synthase.
Length = 141
Score = 86.3 bits (214), Expect = 4e-20
Identities = 28/88 (31%), Positives = 55/88 (62%)
Query: 289 KNGAQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISN 348
+ +E+NI + VPG+ EIP+ + + + K++ ++ IG +IRG+T H++ +AN S
Sbjct: 35 RYSVKEENIDVVWVPGSFEIPVVAQRLAKSGKYDAILCIGAVIRGDTTHYDAVANSAASG 94
Query: 349 IMQISIKNNIPIINAILTTETIEQANSR 376
++ + + +P I +LT + +EQA +R
Sbjct: 95 VLSAGLNSGVPCIFGVLTCDDMEQALNR 122
>gnl|CDD|187740 cd08371, Lumazine_synthase-like, lumazine synthase and riboflavin
synthase; involved in the riboflavin (vitamin B2)
biosynthetic pathway. This superfamily contains
lumazine synthase (6,7-dimethyl-8-ribityllumazine
synthase, LS) and riboflavin synthase (RS). Both enzymes
play important roles in the riboflavin biosynthetic
pathway. Riboflavin is the precursor of flavin
mononucleotide (FMN) and flavin adenine dinucleotide
(FAD) which are essential cofactors for the catalysis of
a wide range of redox reactions. These cofactors are
also involved in many other processes involving DNA
repair, circadian time-keeping, light sensing, and
bioluminescence. Riboflavin is biosynthesized in plants,
fungi and certain microorganisms; as animals lack the
necessary enzymes to produce this vitamin, they acquire
it from dietary sources. In the final steps of the
riboflavin biosynthetic pathway, LS catalyzes the
condensation of the
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with
3,4-dihydroxy- 2-butanone-4-phosphate to release water,
inorganic phosphate and 6,7-dimethyl-8-ribityllumazine
(DMRL), and RS catalyzes a dismutation of DMRL which
yields riboflavin and
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In
the latter reaction, a four-carbon moiety is transferred
between two DMRL molecules serving as donor and
acceptor, respectively. Both the LS and RS catalyzed
reactions are thermodynamically irreversible and can
proceed in the absence of a catalyst. In bacteria and
eukaryotes, there are two types of LS: type-I LS forms
homo-pentamers or icosahedrally arranged dodecamers of
pentamers, type-II LS forms decamers (dimers of
pentamers). In archaea LSs and RSs appear to have
diverged early in the evolution of archaea from a common
ancestor.
Length = 129
Score = 82.1 bits (203), Expect = 1e-18
Identities = 34/89 (38%), Positives = 59/89 (66%), Gaps = 1/89 (1%)
Query: 294 EKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQIS 353
I+ ++VPGA EIPLA K +++ + ++ ++AIGV+I+GETYHFE++A+E +M +
Sbjct: 30 NIKIIVVTVPGAYEIPLAAKKLLEKEDYDAVVAIGVVIKGETYHFEIVAHEVSRGLMNLQ 89
Query: 354 IKNNIPIINAILTTETI-EQANSRILTKV 381
++ + P+I +LT + EQA+ R
Sbjct: 90 LETDKPVIFGVLTPDNAEEQADERAKRGN 118
>gnl|CDD|235601 PRK05773, PRK05773, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
Validated.
Length = 219
Score = 80.9 bits (200), Expect = 2e-17
Identities = 61/203 (30%), Positives = 87/203 (42%), Gaps = 33/203 (16%)
Query: 11 EIISELKIGNMIILVDSENRENEGDIILSSDFVTPNAINFMSKYARGLICMTLTEKHCIQ 70
E L+ G +++ D + RE E D++ + VT +I + K A GLIC +
Sbjct: 5 EARKALESGIPVLIYDFDGREEEVDMVFYAGAVTWKSIYTLRKNAGGLICYATSNSEGKT 64
Query: 71 LKLDMMT-------------KKNNSSFGTN--FTVSIEAANGVTTGISASDRAHTI---- 111
L L+ + KK S+G F++ + TGIS DRA TI
Sbjct: 65 LGLNFLAEILKRHELYRKLVKK--PSYGDEPAFSLWVNHVK-TKTGISDYDRALTIRELH 121
Query: 112 KVASSKKAKPSDIVQ--------PGHIFPLQAKKGGVLIRGGHTEAGCDLTKLAGLTPSA 163
KV K P + + PGH+ L + G+ R GHTE L + AGL PSA
Sbjct: 122 KVVELAKTNPEEAREEFYENFYSPGHVPILIGR--GIRERRGHTELSIALAQAAGLEPSA 179
Query: 164 VICEILNDDGTMARLPDLIKFSK 186
VI E+L D+ K +K
Sbjct: 180 VIAEML-DEKLSLSKEKAKKIAK 201
>gnl|CDD|238253 cd00447, NusB_Sun, RNA binding domain of NusB (N
protein-Utilization Substance B) and Sun (also known as
RrmB or Fmu) proteins. This family includes two
orthologous groups exemplified by the transcription
termination factor NusB and the N-terminal domain of the
rRNA-specific 5-methylcytidine transferase
(m5C-methyltransferase) Sun. The NusB protein plays a
key role in the regulation of ribosomal RNA biosynthesis
in eubacteria by modulating the efficiency of
transcriptional antitermination. NusB along with other
Nus factors (NusA, NusE/S10 and NusG) forms the core
complex with the boxA element of the nut site of the
rRNA operons. These interactions help RNA polymerase to
counteract polarity during transcription of rRNA operons
and allow stable antitermination. The transcription
antitermination system can be appropriated by some
bacteriophages such as lambda, which use the system to
switch between the lysogenic and lytic modes of phage
propagation. The m5C-methyltransferase Sun shares the
N-terminal non-catalytic RNA-binding domain with NusB.
Length = 129
Score = 70.8 bits (174), Expect = 8e-15
Identities = 37/130 (28%), Positives = 70/130 (53%), Gaps = 4/130 (3%)
Query: 392 RAREFALQGIYQWLFNNMD-VNLIETYIKEISNFYKVDKKYFYLILRGVINDINFLRYDL 450
ARE A Q +YQ N + + + ++++ K D+ + ++ GV+ ++ L +
Sbjct: 1 SAREIAFQALYQVEIRNGISLEAVLSALEKLQLA-KKDRPFALELVYGVLRNLPELDDII 59
Query: 451 SLIIDR-SINELSSIEYVVLLIGTYEL-KSHYKIPYKVIINEAIELVKSFGNIDGYKYVN 508
S ++ + ++ L ++ +L + YEL + Y +P V INEA+EL K FG+ D K+VN
Sbjct: 60 SPLLKKWLLDRLDKVDRAILRLLLYELYQLLYDVPPPVAINEAVELAKRFGDDDSAKFVN 119
Query: 509 KILDKVALNI 518
+L ++A
Sbjct: 120 GVLRRIAKES 129
>gnl|CDD|187744 cd09211, Lumazine_synthase_archaeal, lumazine synthase
(6,7-dimethyl-8-ribityllumazine synthase, LS); catalyzes
the penultimate step in the biosynthesis of riboflavin
(vitamin B2). Archaeal LS is an important enzyme in the
riboflavin biosynthetic pathway. Riboflavin is the
precursor of flavin mononucleotide (FMN) and flavin
adenine dinucleotide (FAD) which are essential cofactors
for the catalysis of a wide range of redox reactions.
These cofactors are also involved in many other
processes involving DNA repair, circadian time-keeping,
light sensing, and bioluminescence. In the final steps
of the riboflavin biosynthetic pathway LS catalyzes the
condensation of the
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with
3,4-dihydroxy- 2-butanone-4-phosphate to release water,
inorganic phosphate and 6,7-dimethyl-8-ribityllumazine
(DMRL), and riboflavin synthase (RS) catalyzes a
dismutation of DMRL which yields riboflavin and
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In
the latter reaction, a four-carbon moiety is transferred
between two DMRL molecules serving as donor and
acceptor, respectively. Both the LS and RS catalyzed
reactions are thermodynamically irreversible and can
proceed in the absence of a catalyst. LS from
Methanococcus jannaschii forms capsids with icosahedral
532 symmetry consisting of 60 subunits. Archaeal LSs
share sequence similarity with archaeal RSs, both appear
to have diverged early in the evolution of archaea from
a common ancestor.
Length = 131
Score = 58.9 bits (143), Expect = 1e-10
Identities = 21/61 (34%), Positives = 40/61 (65%)
Query: 300 ISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQISIKNNIP 359
+ VPG ++PLA+K +++ + ++ +G +I+GET H ELIAN+ I+ +S++ P
Sbjct: 35 LRVPGVFDMPLAVKKLLEKDDIDAVVTLGAVIKGETKHDELIANQAARKILDLSLEYGKP 94
Query: 360 I 360
+
Sbjct: 95 V 95
>gnl|CDD|187741 cd09208, Lumazine_synthase-II, lumazine synthase
(6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes
the penultimate step in the biosynthesis of riboflavin
(vitamin B2); type-II. Type-II LS also known as RibH2,
catalyzes the penultimate step in the biosynthesis of
riboflavin in plants and microorganisms. LS catalyses
the formation of 6,7-dimethyl-8-ribityllumazine by the
condensation of 5-amino-6-ribitylamino-
2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy-
2-butanone-4-phosphate. Subsequently, the lumazine
intermediate dismutates yielding riboflavin and
5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione, in a
reaction catalyzed by riboflavin synthase (RS); RS
belongs to a different family of the
Lumazine-synthase-like superfamily. Riboflavin is the
precursor of flavin mononucleotide (FMN) and flavin
adenine dinucleotide (FAD) which are essential cofactors
for the catalysis of a wide range of redox reactions.
These cofactors are also involved in many other
processes involving DNA repair, circadian time-keeping,
light sensing, and bioluminescence. Riboflavin is
biosynthesized in plants, fungi and certain
microorganisms; as animals lack the necessary enzymes to
produce this vitamin, they acquire it from dietary
sources. Type II LSs are distinct from type-I LS not
only in protein sequence, but in that they exhibit
different quaternary assemblies; type-II LSs form
decamers (dimers of pentamers). The pathogen Brucella
spp. have both a type-I LS and a type-II LS called RibH1
and RibH2, respectively. RibH1/type-I LS appears to be a
functional LS in Brucella spp., whereas RibH2/type-II LS
has much lower catalytic activity as LS and may be
regulated by a riboswitch that senses FMN, suggesting
that the type-II LSs may have evolved into very poor
catalysts or, that they may harbor a new, as-yet-unknown
function.
Length = 137
Score = 55.9 bits (135), Expect = 2e-09
Identities = 19/76 (25%), Positives = 39/76 (51%)
Query: 291 GAQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIM 350
G + VPGA EIPL K + + ++ ++ +++ G Y E +A I +M
Sbjct: 30 GGASDEVDIFDVPGAFEIPLHAKRLARTGRYAAIVGAALVVDGGIYRHEFVAQAVIDGLM 89
Query: 351 QISIKNNIPIINAILT 366
++ ++ +P+ + +LT
Sbjct: 90 RVQLETEVPVFSVVLT 105
>gnl|CDD|216196 pfam00925, GTP_cyclohydro2, GTP cyclohydrolase II. GTP
cyclohydrolase II catalyzes the first committed step in
the biosynthesis of riboflavin.
Length = 169
Score = 54.2 bits (131), Expect = 1e-08
Identities = 16/77 (20%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 209 IKRKAEYNINTLYGNFKIIVYIDKINNDIHLTLIYGSINPNKIIPIWLNQQLSIFDFLHA 268
++R AE + T +G F+++ Y D ++ HL L+ G I+P++ + + ++ + D +
Sbjct: 1 VERVAEAPLPTRFGEFRLVAYRDLVDGKEHLALVKGDISPDEPVLVRVHSECLTGDVFGS 60
Query: 269 KTSSCTQNNISSIMKIM 285
C + + ++ +
Sbjct: 61 LRCDCGE-QLEKALRRI 76
>gnl|CDD|237096 PRK12419, PRK12419, riboflavin synthase subunit beta; Provisional.
Length = 158
Score = 49.3 bits (118), Expect = 5e-07
Identities = 18/65 (27%), Positives = 37/65 (56%)
Query: 302 VPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANETISNIMQISIKNNIPII 361
VPGA EIPL + + + ++ ++A +++ G Y E +A I +M++ + +P+
Sbjct: 51 VPGAFEIPLHAQTLAKTGRYAAIVAAALVVDGGIYRHEFVAQAVIDGLMRVQLDTEVPVF 110
Query: 362 NAILT 366
+ +LT
Sbjct: 111 SVVLT 115
>gnl|CDD|182007 PRK09634, nusB, transcription antitermination protein NusB;
Provisional.
Length = 207
Score = 42.6 bits (101), Expect = 2e-04
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 11/61 (18%)
Query: 454 IDRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDGYKYVNKILDK 513
IDR I L+ +E + L P V INEA+EL K + + G +++N +L +
Sbjct: 149 IDRDILRLAVVEILFL-----------NTPAAVAINEAVELAKRYSDEQGRRFINGVLRR 197
Query: 514 V 514
+
Sbjct: 198 L 198
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 41.3 bits (98), Expect = 9e-04
Identities = 34/133 (25%), Positives = 57/133 (42%), Gaps = 16/133 (12%)
Query: 393 AREFALQGIYQWLFNNMDVNL-IETYIKEISNFYKVDKKYFYLILRGVINDINFLRYDLS 451
ARE AL+ + + N N+ + +K+ S DK ++ G I L Y
Sbjct: 5 ARELALEVLIKVENNGAYSNIALNKVLKK-SELSDKDKALLTELVYGTIQRKLTLDY--- 60
Query: 452 LIIDRSINELSSIE---YVVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDGYKYVN 508
+ I + ++ +L + Y+L K+P +NEA+E+ K G+ K+VN
Sbjct: 61 -YLAPFIKKRKKLDPWVRNLLRMSLYQLLYLDKVPDHAAVNEAVEIAKKRGHKGIAKFVN 119
Query: 509 KILDKVALNIRNI 521
+L RNI
Sbjct: 120 GVL-------RNI 125
>gnl|CDD|223878 COG0807, RibA, GTP cyclohydrolase II [Coenzyme metabolism].
Length = 193
Score = 40.0 bits (94), Expect = 0.001
Identities = 16/40 (40%), Positives = 24/40 (60%)
Query: 207 NIIKRKAEYNINTLYGNFKIIVYIDKINNDIHLTLIYGSI 246
+++R AE + T G F+I+ Y DKI+ HL L+ G I
Sbjct: 1 PLVERVAEAKLPTELGEFRIVGYRDKIDGKEHLALVKGDI 40
>gnl|CDD|238348 cd00641, GTP_cyclohydro2, GTP cyclohydrolase II (RibA). GTP
cyclohydrolase II catalyzes the conversion of GTP to
2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'
phosphate, formate, pyrophosphate (APy), and GMP in the
biosynthetic pathway of riboflavin. Riboflavin is the
precursor molecule for the synthesis of the coenzymes
flavin mononucleotide (FMN) and flavin adenine
dinucleotide (FAD) which are essential to cell
metabolism. The enzyme is present in plants and numerous
pathogenic bacteria, especially gram negative organisms,
who are dependent on endogenous synthesis of the vitamin
because they lack an appropriate uptake system. For
animals and humans, which lack this biosynthetic
pathway, riboflavin is the essential vitamin B2. GTP
cyclohydrolase II requires magnesium ions for activity
and has a bound catalytic zinc. The functionally active
form is thought to be a homodimer. A paralogous protein
is encoded in the genome of Streptomyces coelicolor,
which converts GTP to
2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone
5'-phosphate (FAPy), an activity that has otherwise been
reported for unrelated GTP cyclohydrolases III.
Length = 193
Score = 35.6 bits (83), Expect = 0.034
Identities = 10/46 (21%), Positives = 25/46 (54%)
Query: 209 IKRKAEYNINTLYGNFKIIVYIDKINNDIHLTLIYGSINPNKIIPI 254
+++ AE + T +G+F+I+ + D + H+ L+ G + + +
Sbjct: 2 VEKVAEAPLPTRFGDFRIVAFEDTDDGKEHVALVKGDPADGEPVLV 47
>gnl|CDD|238343 cd00620, Methyltransferase_Sun, N-terminal RNA binding domain of
the methyltransferase Sun. The rRNA-specific
5-methylcytidine transferase Sun, also known as RrmB or
Fmu shares the RNA-binding non-catalytic domain with the
transcription termination factor NusB. The precise
biological role of this domain in Sun is unknown,
although it is likely to be involved in
sequence-specific RNA binding. The C-terminal
methyltransferase domain of Sun has been shown to
catalyze formation of m5C at position 967 of 16S rRNA in
Escherichia coli.
Length = 126
Score = 34.2 bits (79), Expect = 0.037
Identities = 13/78 (16%), Positives = 34/78 (43%), Gaps = 1/78 (1%)
Query: 438 GVINDINFLRYDLSLIIDRSINELSSIEYVVLLIGTYELKSHYKIPYKVIINEAIELVKS 497
G + + L + ++ ++ + +L +G Y+L + +P ++E +E+ K
Sbjct: 47 GTLRWLALLDWIINPLLKKPDVGKDPDVRNLLRLGLYQLL-YLDVPPHAAVDETVEIAKI 105
Query: 498 FGNIDGYKYVNKILDKVA 515
++ VN +L +
Sbjct: 106 RKDLGRAGLVNAVLRRFE 123
>gnl|CDD|179586 PRK03512, PRK03512, thiamine-phosphate pyrophosphorylase;
Provisional.
Length = 211
Score = 30.8 bits (70), Expect = 1.1
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 5/46 (10%)
Query: 91 SIEAANGVTTGISASDRAHTIKVASSKKAKPSDIVQPGHIFPLQAK 136
+I AA G+ G+S D ++ + A+PS I GH+FP Q K
Sbjct: 97 AIRAA-GLRLGVSTHDDM---EIDVALAARPSYIAL-GHVFPTQTK 137
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 31.4 bits (71), Expect = 1.2
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 467 VVLLIGTYELKSHYKIPYKVIINEAIELVKSFGNIDGYKYVNKILDKVA 515
V L +G Y+L +P ++E ++LVK N + K VN +L ++
Sbjct: 75 VALRMGAYQLLFMNSVPDYAAVSETVKLVK---NENFKKLVNAVLRRLR 120
>gnl|CDD|233025 TIGR00563, rsmB, ribosomal RNA small subunit methyltransferase
RsmB. This protein is also known as sun protein. The
reading frame was originally interpreted as two reading
frames, fmu and fmv. The recombinant protein from E.
coli was shown to methylate only C967 of small subunit
(16S) ribosomal RNA and to produce only m5C at that
position. The seed alignment is built from bacterial
sequences only. Eukaryotic homologs include Nop2, a
protein required for processing pre-rRNA, that is likely
also a rRNA methyltransferase, although the fine
specificity may differ. Cutoff scores are set to avoid
treating archaeal and eukaroytic homologs automatically
as functionally equivalent, although they may have very
similar roles [Protein synthesis, tRNA and rRNA base
modification].
Length = 426
Score = 30.2 bits (68), Expect = 2.8
Identities = 16/84 (19%), Positives = 36/84 (42%), Gaps = 1/84 (1%)
Query: 428 DKKYFYLILRGVINDINFLRYDLSLIIDRSINELSSIEYVVLLIGTYELKSHYKIPYKVI 487
D+ + GV+ ++ L + + ++DR + + ++L+G + +IP
Sbjct: 32 DRALLQELCFGVLRTLSQLDWLIKKLMDRPMKGKPRTVHYLILVG-LYQLLYTRIPAHAA 90
Query: 488 INEAIELVKSFGNIDGYKYVNKIL 511
+ E +E K+ VN +L
Sbjct: 91 VAETVEGAKAIKRKGLKGLVNGVL 114
>gnl|CDD|234745 PRK00393, ribA, GTP cyclohydrolase II; Reviewed.
Length = 197
Score = 29.4 bits (67), Expect = 3.5
Identities = 11/42 (26%), Positives = 24/42 (57%)
Query: 209 IKRKAEYNINTLYGNFKIIVYIDKINNDIHLTLIYGSINPNK 250
+KR AE + T +G+F ++ + + H+ L++G I+ +
Sbjct: 3 LKRVAEAKLPTPWGDFLMVGFEELATGKEHVALVFGDISGTE 44
>gnl|CDD|187743 cd09210, Riboflavin_synthase_archaeal, archaeal riboflavin synthase
(RS); involved in the biosynthesis pathway of riboflavin
(vitamin B2). Archaeal RSs are homopentamers catalyzing
the formation of riboflavin from
6,7-dimethyl-8-ribityllumazine in riboflavin
biosynthesis. Divalent metal ions, preferably manganese
or magnesium, are needed for maximum activity.
Riboflavin serves as the precursor of flavin
mononucleotide (FMN) and flavin adenine dinucleotide
(FAD), essential cofactors for several oxidoreductases
that are indispensable in most living cells. In the
final steps of the riboflavin biosynthetic pathway,
lumazine synthase (6,7-dimethyl-8-ribityllumazine
synthase, LS) catalyzes the condensation of the
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with
3,4-dihydroxy- 2-butanone-4-phosphate to release water,
inorganic phosphate and 6,7-dimethyl-8-ribityllumazine
(DMRL), followed by RS which catalyzes a dismutation of
DMRL yielding riboflavin and
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In
the latter reaction, a four-carbon moiety is transferred
between two DMRL molecules serving as donor and
acceptor, respectively. Both the LS and RS catalyzed
reactions are thermodynamically irreversible and can
proceed in the absence of a catalyst. Archaeal RSs share
sequence similarity with LSs, both appear to have
diverged early in the evolution of archaea from a common
ancestor.
Length = 143
Score = 28.5 bits (64), Expect = 4.4
Identities = 17/77 (22%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 285 MKLIKNGAQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANE 344
+ +K I+ +VPG ++P+A K +I+ + ++++A+G + G T ++ +E
Sbjct: 18 IDELKKLLPGIKIVRYTVPGIKDLPVAAKKLIEEEGCDIVMALGWV--GPTEKDKVSYHE 75
Query: 345 TISNIMQISIKNNIPII 361
++ + + N II
Sbjct: 76 ASLGLILVQLMTNKHII 92
>gnl|CDD|218909 pfam06138, Chordopox_E11, Chordopoxvirus E11 protein. This family
consists of several Chordopoxvirus E11 proteins. The E11
gene of vaccinia virus encodes a 15-kDa polypeptide.
Mutations in the E11 gene makes the virus
temperature-sensitive due to either the fact that virus
infectivity requires a threshold level of active E11
protein or that E11 function is conditionally essential.
Length = 130
Score = 28.1 bits (63), Expect = 4.9
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 13/69 (18%)
Query: 413 LIETYIKEISNFYKVDKKYFYLILR-----------GVIN--DINFLRYDLSLIIDRSIN 459
I+ +I + + VDK FYL+++ G ++ + F +D L+ S N
Sbjct: 36 AIDYFISVLKKYIHVDKSTFYLVIKDKDIFYFKCDKGSVSQVENEFYTFDEELLFVDSYN 95
Query: 460 ELSSIEYVV 468
E++ IE+++
Sbjct: 96 EITGIEFII 104
>gnl|CDD|224645 COG1731, COG1731, Archaeal riboflavin synthase [Coenzyme
metabolism].
Length = 154
Score = 28.6 bits (64), Expect = 5.5
Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 2/76 (2%)
Query: 286 KLIKNGAQEKNILHISVPGALEIPLALKNIIQIKKFNVLIAIGVIIRGETYHFELIANET 345
+K I +VPG ++P+A K +I+ + +++IA+G + G T +
Sbjct: 22 DELKKLLPGIKIKRYTVPGIKDLPVAAKRLIEEEGCDIVIALGWV--GPTEKDKYSYLAA 79
Query: 346 ISNIMQISIKNNIPII 361
++ + N II
Sbjct: 80 SIGLIMAQLMTNKHII 95
>gnl|CDD|219279 pfam07044, DUF1329, Protein of unknown function (DUF1329). This
family consists of several hypothetical bacterial
proteins of around 475 residues in length. The majority
of family members are from Pseudomonas species but the
family also contains sequences from Shewanella
oneidensis and Thauera aromatica.
Length = 368
Score = 29.1 bits (66), Expect = 6.5
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 114 ASSKKAKPSDIVQPGHIFP 132
S K D+V+PGHI P
Sbjct: 235 LDSPGLKYDDLVKPGHINP 253
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.138 0.388
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,680,799
Number of extensions: 2706073
Number of successful extensions: 2626
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2596
Number of HSP's successfully gapped: 113
Length of query: 527
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 426
Effective length of database: 6,457,848
Effective search space: 2751043248
Effective search space used: 2751043248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.4 bits)