RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780359|ref|YP_003064772.1| GTP cyclohydrolase II protein
(riboflavin biosynthesis) [Candidatus Liberibacter asiaticus str.
psy62]
(210 letters)
>1g57_A DHBP synthase, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
riboflavine biosynthesis, skeletal rearrangement,
antimicrobial target; 1.40A {Escherichia coli} SCOP:
d.115.1.2 PDB: 1g58_A 1iez_A 3h07_A
Length = 217
Score = 242 bits (619), Expect = 4e-65
Identities = 81/198 (40%), Positives = 127/198 (64%)
Query: 12 IEDVIQSFQKGEMVIVTDADDRENEADLVLAAIHCTSEKMAFIIRHTCGIVCTPMPFHTA 71
+E+ + + ++G V+V D +DRENE D++ A T E+MA IRH GIVC +
Sbjct: 16 VENALAALREGRGVMVLDDEDRENEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRR 75
Query: 72 HKLKLNPMVLENESVHKTAFTVSVDSKHGITTGISADDRAYTIKNLANPHSIADNFVRPG 131
+L L MV N S + T FTV++++ G+TTG+SA DR T++ + + RPG
Sbjct: 76 KQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRITTVRAAIADGAKPSDLNRPG 135
Query: 132 HIFPLISRDGGVLVRPGHTEASVDLCKITGLPPIAVICELVNDDGTIKKGKQVIEFSKKY 191
H+FPL ++ GGVL R GHTEA++DL + G P V+CEL NDDGT+ + + IEF+ K+
Sbjct: 136 HVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIEFANKH 195
Query: 192 DLKIISVQDLIAWRKKKE 209
++ +++++DL+A+R+ E
Sbjct: 196 NMALVTIEDLVAYRQAHE 213
>1k4i_A 3,4-dihydroxy-2-butanone 4-phosphate synthase; riboflavin
biosynthesis, antimicrobial target, structure-based
design, isomerase; 0.98A {Magnaporthe grisea} SCOP:
d.115.1.2 PDB: 1k49_A 1k4l_A 1k4o_A 1k4p_A
Length = 233
Score = 239 bits (611), Expect = 4e-64
Identities = 92/210 (43%), Positives = 134/210 (63%), Gaps = 12/210 (5%)
Query: 12 IEDVIQSFQKGEMVIVTDADDRENEADLVLAAIHCTSEKMAFIIRHTCGIVCTPMPFHTA 71
I DVIQ+F+ GE V+V D RENEADL++AA T+E+MAF++RH+ G++C P+
Sbjct: 15 IPDVIQAFKNGEFVVVLDDPSRENEADLIIAAESVTTEQMAFMVRHSSGLICAPLTPERT 74
Query: 72 HKLKLNPMVLENESVHKTAFTVSVDSKH-GITTGISADDRAYTIKNLANPHSIADNFVRP 130
L L MV N TA+TVSVD++H TTGISA DRA + LA P + +F RP
Sbjct: 75 TALDLPQMVTHNADPRGTAYTVSVDAEHPSTTTGISAHDRALACRMLAAPDAQPSHFRRP 134
Query: 131 GHIFPLISRDGGVLVRPGHTEASVDLCKITGLPPIAVICELVNDDGTIK----------- 179
GH+FPL + GGV R GHTEA V+LC++ G P+AVI E+V+D ++
Sbjct: 135 GHVFPLRAVAGGVRARRGHTEAGVELCRLAGKRPVAVISEIVDDGQEVEGRAVRAAPGML 194
Query: 180 KGKQVIEFSKKYDLKIISVQDLIAWRKKKE 209
+G + + F++++ LK+ +++D+IA +K E
Sbjct: 195 RGDECVAFARRWGLKVCTIEDMIAHVEKTE 224
>1snn_A DHBP synthase, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
riboflavin biosynthesis, isomerase; HET: 5RP; 1.55A
{Methanocaldococcus jannaschii} SCOP: d.115.1.2 PDB:
1pvy_A* 1pvw_A
Length = 227
Score = 214 bits (546), Expect = 1e-56
Identities = 64/223 (28%), Positives = 116/223 (52%), Gaps = 25/223 (11%)
Query: 12 IEDVIQSFQKGEMVIVTDADDRENEADLVLAAIHCTSEKMAFIIRHTCGIVCTPMPFHTA 71
+E I++ +KGE+++V D+D+RE E D+V+A+ T E + + + G++CT +
Sbjct: 4 VEKAIEALKKGEIILVYDSDEREGETDMVVASQFITPEHIRIMRKDAGGLICTALHPDIC 63
Query: 72 HKLKLNPMVLENESV------------------HKTAFTVSVDSKHGITTGISADDRAYT 113
+KL + MV E K++F+++++ + TGI+ +DRA+T
Sbjct: 64 NKLGIPFMVDILEFASQKFKVLRELYPNDIPYDEKSSFSITINHRKT-FTGITDNDRAFT 122
Query: 114 IKNLAN------PHSIADNFVRPGHIFPLISRDGGVLVRPGHTEASVDLCKITGLPPIAV 167
IK LA + F PG + L + +G V R GHTE +V L ++ L PI
Sbjct: 123 IKKLAELVKEGRFNDFGKEFRSPGSVTLLRAAEGLVKNRQGHTEMTVALAELANLVPITT 182
Query: 168 ICELVNDDGTIKKGKQVIEFSKKYDLKIISVQDLIAWRKKKEI 210
ICE++ DDG + +++K++L +S +++I + K +
Sbjct: 183 ICEMMGDDGNAMSKNETKRYAEKHNLIYLSGEEIINYYLDKYL 225
>1tks_A 3,4-dihydroxy-2-butanone 4-phosphate synthase; riboflavin
biosynthesis, synthetic gene, isomerase; 1.60A {Candida
albicans SC5314} SCOP: d.115.1.2 PDB: 1tku_A* 2ris_A
2riu_A*
Length = 204
Score = 196 bits (499), Expect = 3e-51
Identities = 90/197 (45%), Positives = 131/197 (66%), Gaps = 1/197 (0%)
Query: 12 IEDVIQSFQKGEMVIVTDADDRENEADLVLAAIHCTSEKMAFIIRHTCGIVCTPMPFHTA 71
IE+ +++++ GE +IV D +DRENE DL++AA T EKMAF++R++ G VC P+ A
Sbjct: 8 IEEALEAYKNGEFLIVMDDEDRENEGDLIMAAELITQEKMAFLVRYSSGYVCVPLSEERA 67
Query: 72 HKLKLNPMVLENESVHKTAFTVSVDSKHGITTGISADDRAYTIKNLANPHSIADNFVRPG 131
++L+L PM+ H TA+T++ D G TTGISA DRA T ++LANP+S +F++PG
Sbjct: 68 NQLELPPMLANRSDRHGTAYTITCDFAEGTTTGISAHDRALTTRSLANPNSKPQDFIKPG 127
Query: 132 HIFPLISRDGGVLVRPGHTEASVDLCKITGLPPIAVICELVND-DGTIKKGKQVIEFSKK 190
HI PL + G + R GHTEA+V L + GL P VICELV D DG + + I+F KK
Sbjct: 128 HILPLRAVPGLLKKRRGHTEAAVQLSTLAGLQPAGVICELVRDEDGLMMRLDDCIQFGKK 187
Query: 191 YDLKIISVQDLIAWRKK 207
+ +KII++ L+ + K
Sbjct: 188 HGIKIININQLVEYISK 204
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 40.7 bits (95), Expect = 2e-04
Identities = 33/174 (18%), Positives = 57/174 (32%), Gaps = 60/174 (34%)
Query: 33 RENEADLVL--AAIHCTSEKMAFIIRHTCGIVCTPM--PFHTAHKLKLNPMVLENESVHK 88
R+ +A L + I + K+ F R P+ PFH+ + + ++ +
Sbjct: 394 RKAKAPSGLDQSRIPFSERKLKFSNRFL------PVASPFHSHLLVPASDLINK------ 441
Query: 89 TAFTVSVD-SKHGITTGISADDRA------YTIKNLANPHSIADNFVRPGHIFPLISRDG 141
D K+ ++ +A D + +L ++ + I I R
Sbjct: 442 -------DLVKNNVS--FNAKDIQIPVYDTFDGSDLR---VLSGSISE--RIVDCIIRL- 486
Query: 142 GVLVRPGHTEASVDLCKIT--------GLPPIAVICELV--NDDGTIKKGKQVI 185
P E + K T G + V L N DGT G +VI
Sbjct: 487 -----PVKWETTTQ-FKATHILDFGPGGASGLGV---LTHRNKDGT---GVRVI 528
Score = 37.2 bits (86), Expect = 0.003
Identities = 30/225 (13%), Positives = 58/225 (25%), Gaps = 70/225 (31%)
Query: 18 SFQKGEMVIVTD--ADDRENEADLVLAAIHCTSEKMAFIIRHTCGIVCTPMPFHTAHKLK 75
F K + T+ A D E L + + ++ V L
Sbjct: 36 QFNK-ILPEPTEGFAADDEPTTPAELVG-----KFLGYVSSL----VEPSKVGQFDQVLN 85
Query: 76 L-----NPMVLENESVHKTAFTVSVDSKHGITTGISADD---RAY------TIKNLANPH 121
L LE +H A + + T + + Y +
Sbjct: 86 LCLTEFENCYLEGNDIH--ALAAKLLQE--NDTTLVKTKELIKNYITARIMAKRPFDKKS 141
Query: 122 ------SIADNFVRPGHIFPLISRDGGVLVRPGHTEASVD-LCKI----TGL--PPIAVI 168
++ + + IF GG G+T+ + L + L I
Sbjct: 142 NSALFRAVGEGNAQLVAIF------GG----QGNTDDYFEELRDLYQTYHVLVGDLIKFS 191
Query: 169 CE----LVNDDGTIKKGKQVIEFSKKYDLKIISVQDLIAWRKKKE 209
E L+ +K F++ ++ + W +
Sbjct: 192 AETLSELIRTTLDAEK-----VFTQGLNI--------LEWLENPS 223
Score = 31.8 bits (72), Expect = 0.10
Identities = 15/59 (25%), Positives = 19/59 (32%), Gaps = 28/59 (47%)
Query: 117 LANPHSIADNFVRPGHI------FPLISRDGGV--LVRPGH---TEASVDLCKITGLPP 164
L NP + D ++ PLI GV L H T K+ G P
Sbjct: 219 LENPSNTPDK----DYLLSIPISCPLI----GVIQLA---HYVVT------AKLLGFTP 260
Score = 26.1 bits (57), Expect = 6.1
Identities = 12/59 (20%), Positives = 20/59 (33%), Gaps = 15/59 (25%)
Query: 9 ERYIEDVI---QSFQKGEMVI-V---TDADD-RENEADLVLAAIHCTSEKMAFIIRHTC 59
+ +D++ SF ++ I V D D R + + C IIR
Sbjct: 437 DLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDC-------IIRLPV 488
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 29.9 bits (67), Expect = 0.49
Identities = 14/70 (20%), Positives = 22/70 (31%), Gaps = 27/70 (38%)
Query: 1 MKQKKSLD---ERYIEDV-IQSF----QKGEMVIVTDADDRENEADLVLAAIHCTSEKMA 52
M ++S+D R ++ I + IV E D+V C
Sbjct: 1 MMTRESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFS----EGDVV-----CAL---- 47
Query: 53 FIIRHTCGIV 62
CG+V
Sbjct: 48 ------CGLV 51
>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase,
A1AO, ATP synthesis, hydrogen ION transport, ION
transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A*
3b2q_A* 2rkw_A* 3eiu_A*
Length = 469
Score = 27.4 bits (60), Expect = 2.4
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 156 LCKITGLPPIAV--ICELVNDDGTIKKGKQVIEFS 188
L + P+ I + DGT+++G QV++ S
Sbjct: 24 LIFVEKTEPVGYNEIVNIKMGDGTVRRG-QVLDSS 57
>2c1o_A IGK-C protein; FAB fragment, enantioselective, finrozole, immune
system, antibody, ENA11His antibody, immunoglobulin
domain; 2.75A {Mus musculus}
Length = 254
Score = 27.5 bits (60), Expect = 2.6
Identities = 12/22 (54%), Positives = 13/22 (59%), Gaps = 4/22 (18%)
Query: 141 GGVLVRPGHTEASVDL-CKITG 161
G LVRPG SV L CK +G
Sbjct: 7 GAELVRPG---TSVKLSCKASG 25
>2d3i_A Ovotransferrin; aluminum, metal-binding, transport, metal
transport; 2.15A {Gallus gallus} SCOP: c.94.1.2 c.94.1.2
PDB: 1ovt_A 1aiv_A* 1n04_A 1ryx_A 1dot_A* 1aov_A*
1iq7_A*
Length = 686
Score = 27.3 bits (60), Expect = 2.9
Identities = 23/127 (18%), Positives = 34/127 (26%), Gaps = 1/127 (0%)
Query: 65 PMPFHTAHKLKLNPMVLENESVHKTAFTVSVDSKHGITTGISADDRAYTIKNLANPHSIA 124
+TA L P++ E ++ D NL S
Sbjct: 396 GGLVYTAGVCGLVPVMAERYDDESQCSKTDERPASYFAVAVARKDSNVNWNNLKGKKSCH 455
Query: 125 DNFVRPGHIFPLISRDGGVLVRPGHTEASVDLCKITGLPPIAVICELVNDDGTIKKGKQV 184
R + E + C G PP + +C+L G I K V
Sbjct: 456 TAVGRTAGWVIPMGLIHNRTGTCNFDEYFSEGCAP-GSPPNSRLCQLCQGSGGIPPEKCV 514
Query: 185 IEFSKKY 191
+KY
Sbjct: 515 ASSHEKY 521
>2grv_A LPQW; substrate-binding protein scaffold, biosynthetic protein;
2.40A {Mycobacterium smegmatis str}
Length = 621
Score = 26.8 bits (58), Expect = 3.9
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 5/63 (7%)
Query: 70 TAHKLKLNPMVLEN-ESVHKTAFTVSVDSKHGIT----TGISADDRAYTIKNLANPHSIA 124
T + +L+ +LE+ E + FTV+ + I+ADD Y + + + +
Sbjct: 95 TGSRWELDTTLLESAEVTQENPFTVTYKIRPEAQWTDNAPIAADDYWYLWRQMVSQPGVV 154
Query: 125 DNF 127
D
Sbjct: 155 DPA 157
>2j5v_A Glutamate 5-kinase; proline biosynthesis, gamma glutamyl kinase,
amino-acid biosynthesis, transferase, feedback
regulation, PUA domain; HET: RGP; 2.5A {Escherichia
coli} PDB: 2j5t_A*
Length = 367
Score = 26.2 bits (57), Expect = 5.9
Identities = 11/57 (19%), Positives = 27/57 (47%), Gaps = 4/57 (7%)
Query: 1 MKQKKSLDERYIEDVIQSFQKGEMVIVTDADDRENEADLVLAAIHCTSEKMAFIIRH 57
+++ SL + I+ V +F +GE++ + + + R+ + S+ + I H
Sbjct: 289 LERGSSLLPKGIKSVTGNFSRGEVIRICNLEGRD----IAHGVSRYNSDALRRIAGH 341
>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription,
transcription regulation; HET: BOG; 1.90A {Anabaena}
PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*
Length = 243
Score = 25.9 bits (56), Expect = 7.8
Identities = 2/22 (9%), Positives = 11/22 (50%)
Query: 5 KSLDERYIEDVIQSFQKGEMVI 26
+ + V+++F++ + +
Sbjct: 34 RQMATGAFPPVVETFERNKTIF 55
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.320 0.136 0.398
Gapped
Lambda K H
0.267 0.0509 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,813,366
Number of extensions: 81826
Number of successful extensions: 452
Number of sequences better than 10.0: 1
Number of HSP's gapped: 445
Number of HSP's successfully gapped: 17
Length of query: 210
Length of database: 5,693,230
Length adjustment: 88
Effective length of query: 122
Effective length of database: 3,559,758
Effective search space: 434290476
Effective search space used: 434290476
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: 54 (25.1 bits)