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= 043480
(493 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2UY1|A Chain A, Crystal Structure Of Cstf-77
Length = 493
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 40/176 (22%), Positives = 70/176 (39%), Gaps = 25/176 (14%)
Query: 314 GQTRRAYKLFEGMRRRGIELDVVTFTILIKAFLREGSSAMAEKLLNQMRGMNLSPDRILY 373
GQ +A K+ E RGIE+ F L + + + + G S +++
Sbjct: 227 GQKEKAKKVVE----RGIEMSDGMFLSLYYGLVMDEEAVYGDLKRKYSMGEAESAEKVFS 282
Query: 374 TTI-------IDCLCKSREIGTAYGVFLDMVEQGITPDVISYNALINGLCKSSRVSEAMH 426
+ ++ + K R + +F+++ +G+ P V Y A I SR + +
Sbjct: 283 KELDLLRINHLNYVLKKRGLELFRKLFIELGNEGVGPHVFIYCAFIEYYATGSRAT-PYN 341
Query: 427 LYEEMQIRGAHPDEVTFK-------LLIGGLVQE----KKLELACRLWDQMMEKGF 471
++ ++ HPD K L IG K+LE R+WD M+E F
Sbjct: 342 IFSSGLLK--HPDSTLLKEEFFLFLLRIGDEENARALFKRLEKTSRMWDSMIEYEF 395
>pdb|2UY1|B Chain B, Crystal Structure Of Cstf-77
Length = 493
Score = 34.3 bits (77), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 40/176 (22%), Positives = 70/176 (39%), Gaps = 25/176 (14%)
Query: 314 GQTRRAYKLFEGMRRRGIELDVVTFTILIKAFLREGSSAMAEKLLNQMRGMNLSPDRILY 373
GQ +A K+ E RGIE+ F L + + + + G S +++
Sbjct: 227 GQKEKAKKVVE----RGIEMSDGMFLSLYYGLVMDEEAVYGDLKRKYSMGEAESAEKVFS 282
Query: 374 TTI-------IDCLCKSREIGTAYGVFLDMVEQGITPDVISYNALINGLCKSSRVSEAMH 426
+ ++ + K R + +F+++ +G+ P V Y A I SR + +
Sbjct: 283 KELDLLRINHLNYVLKKRGLELFRKLFIELGNEGVGPHVFIYCAFIEYYATGSRAT-PYN 341
Query: 427 LYEEMQIRGAHPDEVTFK-------LLIGGLVQE----KKLELACRLWDQMMEKGF 471
++ ++ HPD K L IG K+LE R+WD M+E F
Sbjct: 342 IFSSGLLK--HPDSTLLKEEFFLFLLRIGDEENARALFKRLEKTSRMWDSMIEYEF 395
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 32.7 bits (73), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 252 LVMEMESCGIEPDVYSYNQLLKGLCNSNQLDKAY 285
+V +M++ GI+P + SY L G C DKAY
Sbjct: 127 MVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAY 160
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 24/106 (22%), Positives = 48/106 (45%), Gaps = 3/106 (2%)
Query: 288 MVKKMEAKGLRDKV-SYNTVIEAFCKGGQTRRAYKLFEGMRRRGIELDVVTFTILIKAFL 346
MVK+M+A G++ ++ SY + FC+ G +AY++ M + + L+K +
Sbjct: 127 MVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSM 186
Query: 347 REGSSAMAEKLLNQMRGMNLSPDRILYTTIIDCLCKSREIGTAYGV 392
++ K L ++R + + + I + E+ T GV
Sbjct: 187 DTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWF--KSEVATKTGV 230
>pdb|1LRW|A Chain A, Crystal Structure Of Methanol Dehydrogenase From P.
Denitrificans
pdb|1LRW|C Chain C, Crystal Structure Of Methanol Dehydrogenase From P.
Denitrificans
Length = 600
Score = 32.3 bits (72), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 31/135 (22%), Positives = 62/135 (45%), Gaps = 27/135 (20%)
Query: 87 SGLCEVKNFTLIN--ILLDNMDKLALEVFHKMVSKGREPDVVTYTIVIDGLCKAKEFDKA 144
SGL ++K + I+ + + M++ ++ + G +T+ +DG KA++ D
Sbjct: 450 SGLGQIKAYDAISGEMKWEKMERFSVWGGTMATAGG-----LTFYATLDGFIKARDSDTG 504
Query: 145 VQAWEHMIENGI-------KPDNKACAALVVGLCGDGKVDLAYEL--------TVGAMKG 189
W+ + +G+ K D + A++ G+ G V L ++L +VGA K
Sbjct: 505 DLLWKFKLPSGVIGHPMTYKHDGRQYVAIMYGVGGWPGVGLVFDLADPTAGLGSVGAFKR 564
Query: 190 KVEF-----GVLIYN 199
EF GV++++
Sbjct: 565 LQEFTQMGGGVMVFS 579
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 175 KVDLAYELTV---GAMKGKVEFGVLIYNALISGFCRTGRIRRAMAIKSFMKWNGCEPDLV 231
++ LA+ L V G + + + +YNA++ G+ R G + + + +K G PDL+
Sbjct: 142 QLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLL 201
Query: 232 TYNAILN 238
+Y A L
Sbjct: 202 SYAAALQ 208
>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana, Semet Substituted Form With Sr
Length = 501
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 253 VMEMESCGIEPDVYSYNQLLKGLCNSNQLDKAY 285
V + ++ GI+P + SY L G C DKAY
Sbjct: 128 VKQXKAFGIQPRLRSYGPALFGFCRKGDADKAY 160
>pdb|3CRV|A Chain A, "xpd_helicase"
pdb|3CRW|1 Chain 1, "xpd_apo"
Length = 551
Score = 28.5 bits (62), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 33/139 (23%), Positives = 56/139 (40%), Gaps = 28/139 (20%)
Query: 272 LKGLCNSNQLDKAYMFMVKKMEAKGLRDKV-SYNTVIEAFCKGGQTRRAYKLFEGMR-RR 329
LKG + D + + +VKK++ GL+DK Y +++ + K Y F R R
Sbjct: 107 LKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSLYKADVIALTYPYFFIDRYRE 166
Query: 330 GIELDV--------------------------VTFTILIKAFLREGSSAMAEKLLNQMRG 363
I++D+ +T + IK E S + KLLNQ+R
Sbjct: 167 FIDIDLREYMIVIDEAHNLDKVNELEERSLSEITIQMAIKQSKSEESRRILSKLLNQLRE 226
Query: 364 MNLSPDRILYTTIIDCLCK 382
+ L ++ + + L K
Sbjct: 227 VVLPDEKYIKVENVPKLSK 245
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
0.324 0.139 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,866,105
Number of Sequences: 62578
Number of extensions: 561093
Number of successful extensions: 1670
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1649
Number of HSP's gapped (non-prelim): 23
length of query: 493
length of database: 14,973,337
effective HSP length: 103
effective length of query: 390
effective length of database: 8,527,803
effective search space: 3325843170
effective search space used: 3325843170
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)