BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy4641
(229 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1I8D|A Chain A, Crystal Structure Of Riboflavin Synthase
pdb|1I8D|B Chain B, Crystal Structure Of Riboflavin Synthase
pdb|1I8D|C Chain C, Crystal Structure Of Riboflavin Synthase
Length = 213
Score = 216 bits (551), Expect = 7e-57, Method: Compositional matrix adjust.
Identities = 103/207 (49%), Positives = 146/207 (70%), Gaps = 2/207 (0%)
Query: 1 MFTGIVQGIGKVSAVFSYNDFKSMTIWFPSDLLDGISISCSVAINGVCLSVTKIEGNYIS 60
MFTGIVQG K+ ++ +F++ + P +LDG+ SVA NG CL+VT+I GN++S
Sbjct: 1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVS 60
Query: 61 FDVINETLKITNLKAVAVDQFVNLERSAKMNTEVGGHFLSGHIIDVANVRAIQALEKNYR 120
FD++ ETL+ITNL + V +VN+ER+AK + E+GGH +SGHI+ A V I E N +
Sbjct: 61 FDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGHLMSGHIMTTAEVAKILTSENNRQ 120
Query: 121 MEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEKTTMSKKAVGDAL 180
+ ++ + LMKY+ YKG++ IDGISLT+G+V F VHLIPET+E+TT+ KK +G +
Sbjct: 121 IWFKVQDSQLMKYILYKGFIGIDGISLTVGEVTPTRFCVHLIPETLERTTLGKKKLGARV 180
Query: 181 NIEVDSQTQVIVNTVERVL--KENYGN 205
NIE+D QTQ +V+TVERVL +EN N
Sbjct: 181 NIEIDPQTQAVVDTVERVLAARENAMN 207
>pdb|1KZL|A Chain A, Riboflavin Synthase From S.Pombe Bound To
Carboxyethyllumazine
Length = 208
Score = 120 bits (300), Expect = 9e-28, Method: Compositional matrix adjust.
Identities = 71/187 (37%), Positives = 106/187 (56%), Gaps = 4/187 (2%)
Query: 1 MFTGIVQGIGKVSAVFSY--NDFKSMTIWFPSDLLDGISISCSVAINGVCLSVTKIEGNY 58
MFTG+V+ IG V V N F +M I P +LD S+A+NG CL+VT + +
Sbjct: 1 MFTGLVEAIGVVKDVQGTIDNGF-AMKIEAPQ-ILDDCHTGDSIAVNGTCLTVTDFDRYH 58
Query: 59 ISFDVINETLKITNLKAVAVDQFVNLERSAKMNTEVGGHFLSGHIIDVANVRAIQALEKN 118
+ + E+L++TNL VNLER+ +T +GGHF+ GH+ VA + + +
Sbjct: 59 FTVGIAPESLRLTNLGQCKAGDPVNLERAVLSSTRMGGHFVQGHVDTVAEIVEKKQDGEA 118
Query: 119 YRMEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEKTTMSKKAVGD 178
+ + ++KY+ YKGY+A+DG SLTI V + F + +I T K M+KK VGD
Sbjct: 119 IDFTFRPRDPFVLKYIVYKGYIALDGTSLTITHVDDSTFSIMMISYTQSKVIMAKKNVGD 178
Query: 179 ALNIEVD 185
+N+EVD
Sbjct: 179 LVNVEVD 185
>pdb|1HZE|A Chain A, Solution Structure Of The N-Terminal Domain Of
Riboflavin Synthase From E. Coli
pdb|1HZE|B Chain B, Solution Structure Of The N-Terminal Domain Of
Riboflavin Synthase From E. Coli
pdb|1I18|A Chain A, Solution Structure Of The N-Terminal Domain Of
Riboflavin Synthase From E. Coli
pdb|1I18|B Chain B, Solution Structure Of The N-Terminal Domain Of
Riboflavin Synthase From E. Coli
pdb|1PKV|A Chain A, The N-Terminal Domain Of Riboflavin Synthase In Complex
With Riboflavin
pdb|1PKV|B Chain B, The N-Terminal Domain Of Riboflavin Synthase In Complex
With Riboflavin
Length = 97
Score = 103 bits (258), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 47/97 (48%), Positives = 69/97 (71%)
Query: 1 MFTGIVQGIGKVSAVFSYNDFKSMTIWFPSDLLDGISISCSVAINGVCLSVTKIEGNYIS 60
MFTGIVQG K+ ++ +F++ + P +LDG+ SVA NG CL+VT+I GN++S
Sbjct: 1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVS 60
Query: 61 FDVINETLKITNLKAVAVDQFVNLERSAKMNTEVGGH 97
FD++ ETL+ITNL + V +VN+ER+AK + E+GGH
Sbjct: 61 FDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGH 97
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 33/68 (48%)
Query: 116 EKNYRMEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEKTTMSKKA 175
+ N+R + ++ + VA +G LT+ ++ ++ L+ ET+ T +
Sbjct: 18 KPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLK 77
Query: 176 VGDALNIE 183
VGD +N+E
Sbjct: 78 VGDWVNVE 85
>pdb|3A35|A Chain A, Crystal Structure Of Lump Complexed With Riboflavin
pdb|3A35|B Chain B, Crystal Structure Of Lump Complexed With Riboflavin
pdb|3A3B|B Chain B, Crystal Structure Of Lump Complexed With Flavin
Mononucleotide
pdb|3A3B|A Chain A, Crystal Structure Of Lump Complexed With Flavin
Mononucleotide
pdb|3A3G|A Chain A, Crystal Structure Of Lump Complexed With
6,7-Dimethyl-8-(1'- D-Ribityl) Lumazine
pdb|3A3G|B Chain B, Crystal Structure Of Lump Complexed With
6,7-Dimethyl-8-(1'- D-Ribityl) Lumazine
Length = 190
Score = 80.9 bits (198), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 52/184 (28%), Positives = 99/184 (53%), Gaps = 4/184 (2%)
Query: 1 MFTGIVQGIGKVSAVFSYNDFKSMTIWFPSDLLDGISISCSVAINGVCLSVTKIEGNYIS 60
MF GIVQG G + + +D + I FP D+L+ + + +NG L+V +I G+ +
Sbjct: 1 MFKGIVQGAGIIKKISKNDDTQRHGITFPKDILESVEKGTVMLVNGCSLTVVRISGDVVY 60
Query: 61 FDVINETLKITNLKAVAVDQFVNLERSAKMNTEVGGHFLSGHIIDVANVRAIQALEKNYR 120
FD I++ + T + + V VNLE + + +G L+G+I VA V I E +
Sbjct: 61 FD-IDQAINTTTFRELEVGNKVNLEVRPEFGSLLGKGALTGNIKGVATVDNITEEEDRLK 119
Query: 121 MEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEKTT-MSKKAVGDA 179
+ I++ K L++ + + ++ I+G+S +I ++ +D +++ P+ + TT + G
Sbjct: 120 VYIKIP-KDLIENILSEDHIGINGVSHSIEEISDDIIFINY-PKNLSITTNLGTLEKGSD 177
Query: 180 LNIE 183
+N+E
Sbjct: 178 VNVE 181
>pdb|3DDY|A Chain A, Structure Of Lumazine Protein, An Optical Transponder Of
Luminescent Bacteria
Length = 186
Score = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 51/184 (27%), Positives = 88/184 (47%), Gaps = 2/184 (1%)
Query: 1 MFTGIVQGIGKVSAVFSYNDFKSMTIWFPSDLLDGISISCSVAINGVCLSVTKIEGNYIS 60
MF GIVQG G + ++ D + I FP + + + + +NG +V +I G+ +
Sbjct: 1 MFRGIVQGRGVIRSISKSEDSQRHGIAFPEGMFQLVDVDTVMLVNGCSNTVVRILGDMVY 60
Query: 61 FDVINETLKITNLKAVAVDQFVNLERSAKMNTEVGGHFLSGHIIDVANVRAIQALEKNYR 120
FD I++ L T + VNLE K VG L+G+I A V AI+ + +
Sbjct: 61 FD-IDQALGTTTFDGLKEGDQVNLEIHPKFGEVVGRGGLTGNIKGTALVAAIEENDAGFS 119
Query: 121 MEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEKTTMSKKAVGDAL 180
+ I + K L + + K + IDGISL I + + ++ + + T ++ A +
Sbjct: 120 VLIDIP-KGLAENLTVKDDIGIDGISLPITDMSDSIITLNYSRDLLASTNIASLAKDVKV 178
Query: 181 NIEV 184
N+E+
Sbjct: 179 NVEI 182
>pdb|1E5D|A Chain A, Rubredoxin Oxygen:oxidoreductase (Roo) From Anaerobe
Desulfovibrio Gigas
pdb|1E5D|B Chain B, Rubredoxin Oxygen:oxidoreductase (Roo) From Anaerobe
Desulfovibrio Gigas
Length = 402
Score = 30.8 bits (68), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 24/106 (22%), Positives = 48/106 (45%), Gaps = 11/106 (10%)
Query: 112 IQALEKNYRMEIQMTNKSLMKYVFYKGY---VAIDGISLTIGKVFEDYFYVHLI--PETM 166
I+A + + K++ + YK + V G +L++GK ++ ++ P++M
Sbjct: 92 IEACQPEKIFTSSLGQKAMESHFHYKDWPVQVVKHGETLSLGKRTVTFYETRMLHWPDSM 151
Query: 167 ------EKTTMSKKAVGDALNIEVDSQTQVIVNTVERVLKENYGNL 206
EK +S G + Q+ V+T+ER ++E Y N+
Sbjct: 152 VSWFADEKVLISNDIFGQNIAASERFSDQIPVHTLERAMREYYANI 197
>pdb|2HA9|A Chain A, Crystal Structure Of Protein Sp0239 From Streptococcus
Pneumoniae
pdb|2HA9|B Chain B, Crystal Structure Of Protein Sp0239 From Streptococcus
Pneumoniae
Length = 446
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 50 SVTKIEGNYISFDVINETLKITNLKAVAVDQFVNLERSAKMNTEVG 95
++ K+ G SFDV+ ET+K T K + Q V S ++ E G
Sbjct: 223 ALEKVRGQ--SFDVVAETVKKTAFKITRIGQLVGQXASERLGVEFG 266
>pdb|3HBC|A Chain A, Crystal Structure Of Choloylglycine Hydrolase From
Bacteroides Thetaiotaomicron Vpi
Length = 320
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 6/85 (7%)
Query: 113 QALEKNYRMEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEKTTMS 172
Q + R E+Q+ K V G + G + + + FY+H IP+T + +
Sbjct: 173 QVXTNSPRYELQLAVNDYWKEV--GGLQXLPGTNRSSDRFVRASFYIHAIPQTAD----A 226
Query: 173 KKAVGDALNIEVDSQTQVIVNTVER 197
K AV L++ + +NT E+
Sbjct: 227 KIAVPSVLSVXRNVSVPFGINTPEK 251
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.134 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,197,228
Number of Sequences: 62578
Number of extensions: 230609
Number of successful extensions: 549
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 531
Number of HSP's gapped (non-prelim): 10
length of query: 229
length of database: 14,973,337
effective HSP length: 95
effective length of query: 134
effective length of database: 9,028,427
effective search space: 1209809218
effective search space used: 1209809218
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)