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= 011341
(488 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1VJ7|A Chain A, Crystal Structure Of The Bifunctional Catalytic Fragment
Of Relseq, The RelaSPOT HOMOLOG FROM STREPTOCOCCUS
EQUISIMILIS.
pdb|1VJ7|B Chain B, Crystal Structure Of The Bifunctional Catalytic Fragment
Of Relseq, The RelaSPOT HOMOLOG FROM STREPTOCOCCUS
EQUISIMILIS
Length = 393
Score = 247 bits (631), Expect = 9e-66, Method: Compositional matrix adjust.
Identities = 133/315 (42%), Positives = 199/315 (63%), Gaps = 13/315 (4%)
Query: 1 MRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLSYDYIFRTFGAGVADLV 60
+R SG+PY++H ++ A +LA + ++ VA G LHD ++D ++ D I FG V D+V
Sbjct: 43 VRKSGEPYIVHPIQVAGILADLHLDAVTVACGFLHDVVEDTDITLDNIEFDFGKDVRDIV 102
Query: 61 EGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMA-DARAVLIKLADRLHNMMTLDALP 119
+GV+KL ++ + E A M +AM+ D R +L+KLADRLHNM TL L
Sbjct: 103 DGVTKLGKVEYKSHEEQLAENH------RKMLMAMSKDIRVILVKLADRLHNMRTLKHLR 156
Query: 120 LCKRQRFAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPDQHTELSSKLVECFDE--A 177
K++R ++ET+EI+ PLA+RLGIS K +LE+L F++LN + ++S + E E A
Sbjct: 157 KDKQERISRETMEIYAPLAHRLGISRIKWELEDLAFRYLNETEFYKISHMMNEKRREREA 216
Query: 178 MVTSAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKMLKKKLTMDEIHDIYGLRLIVENE 237
+V + K++ ++ + F + GR K +YSI+ KM KK D+I D+ +R ++E +
Sbjct: 217 LVDDIVTKIKSYTTEQGL-FGDVYGRPKHIYSIYRKMRDKKKRFDQIFDLIAIRCVMETQ 275
Query: 238 EDCYQALRVVHQLWAEVPGKMKDYITRPKFNGYQSLHTVVTG-EGLVPLEVQIRTKEMHL 296
D Y + +H+LW +PG+ KDYI PK NGYQS+HT V G +G P+E+QIRTKEMH
Sbjct: 276 SDVYAMVGYIHELWRPMPGRFKDYIAAPKANGYQSIHTTVYGPKG--PIEIQIRTKEMHQ 333
Query: 297 QAEFGFAAHWRYKEG 311
AE+G AAHW YK+G
Sbjct: 334 VAEYGVAAHWAYKKG 348
>pdb|3L9D|A Chain A, The Crystal Structure Of Smu.1046c From Streptococcus
Mutans Ua159
pdb|3L9D|B Chain B, The Crystal Structure Of Smu.1046c From Streptococcus
Mutans Ua159
Length = 255
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 38/121 (31%), Positives = 64/121 (52%), Gaps = 13/121 (10%)
Query: 200 LCGRHKSLYSIHCKML-----KKKLTMDEIHDIYGLRLIVENEEDCYQALRVVHQLWAEV 254
+ GR K + SI KM+ K+ LT D + DI GLR++V+ +D L ++ Q
Sbjct: 74 VTGRVKPIESIKEKMVLRGIKKENLTQD-MQDIAGLRIMVQFVDDVNDVLELLRQRKDMK 132
Query: 255 PGKMKDYITRPKFNGYQSLHTVV-------TGEGLVPLEVQIRTKEMHLQAEFGFAAHWR 307
+ +DYI K +GY+S H +V +G+ ++ E+QIRT M+ A + +++
Sbjct: 133 VIQERDYINNLKPSGYRSYHVIVEYPVDTISGQRIIMAEIQIRTLAMNFWATIEHSLNYK 192
Query: 308 Y 308
Y
Sbjct: 193 Y 193
>pdb|3NR1|A Chain A, A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Plays A
Role In Starvation Responses
pdb|3NR1|B Chain B, A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Plays A
Role In Starvation Responses
Length = 178
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 48/159 (30%), Positives = 75/159 (47%), Gaps = 19/159 (11%)
Query: 4 SGDPYLLHCVETAMLLA--AIGANSTVVAAGLLHDTLDDAFLSYDYIFRTFGAGVADLVE 61
G PY+ H + A +L A + V+ A LLHDT++D + D + FGA V LVE
Sbjct: 27 EGTPYINHPIGVARILTHEAGITDIVVLQAALLHDTVEDTDTTLDEVELHFGAQVRRLVE 86
Query: 62 GVSKLSQLSKLARENNTASKTVEADRLHTMFLAMADARAVLIKLADRLHNMMTLDALPLC 121
V+ L KL R+ RL + A L+KLAD+L+N+ L+ C
Sbjct: 87 EVTDDKTLPKLERK-----------RLQVEQAPHSSPGAKLVKLADKLYNLRDLNR---C 132
Query: 122 KRQRFAKETLEIFVPLANRL--GISTWKVQLENLCFKHL 158
+ +++ ++ + A ++ G+ QLE KHL
Sbjct: 133 TPEGWSEHRVQEYFEWAAQVVKGLQGTNRQLEE-ALKHL 170
>pdb|3NQW|A Chain A, A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Plays A
Role In Starvation Responses
pdb|3NQW|B Chain B, A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Plays A
Role In Starvation Responses
Length = 179
Score = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 36/111 (32%), Positives = 54/111 (48%), Gaps = 13/111 (11%)
Query: 7 PYLLHCVETAMLLA--AIGANSTVVAAGLLHDTLDDAFLSYDYIFRTFGAGVADLVEGVS 64
PY+ H + + +L+ A + V+ A LLHD ++D S++ + + FG V LV V+
Sbjct: 32 PYVNHVINVSTILSVEACITDEGVLMAALLHDVVEDTDASFEDVEKLFGPDVCGLVREVT 91
Query: 65 KLSQLSKLARENNTASKTVEADRLHTMFLAMADARAVLIKLADRLHNMMTL 115
L K R+ RL A + RA LIKLAD+L N+ L
Sbjct: 92 DDKSLEKQERK-----------RLQIENAAKSSCRAKLIKLADKLDNLRDL 131
>pdb|2BE3|A Chain A, Structure Of A Gtp Pyrophosphokinase Family Protein From
Streptococcus Pneumoniae
pdb|2BE3|B Chain B, Structure Of A Gtp Pyrophosphokinase Family Protein From
Streptococcus Pneumoniae
Length = 226
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 36/124 (29%), Positives = 63/124 (50%), Gaps = 12/124 (9%)
Query: 200 LCGRHKSLYSIHCKMLKKKLTM----DEIHDIYGLRLIVENEEDCYQALRVVHQLWAEVP 255
+ GR K + SI K ++ +T ++ DI GLR+ V+ +D + + ++H+
Sbjct: 45 VTGRVKPIESIKEKXARRGITYATLEHDLQDIAGLRVXVQFVDDVKEVVDILHKRQDXRI 104
Query: 256 GKMKDYITRPKFNGYQSLHTVV-------TGEGLVPLEVQIRTKEMHLQAEFGFAAHWRY 308
+ +DYIT K +GY+S H VV G + E+QIRT + A + +++Y
Sbjct: 105 IQERDYITHRKASGYRSYHVVVEYTVDTINGAKTILAEIQIRTLAXNFWATIEHSLNYKY 164
Query: 309 KEGD 312
+GD
Sbjct: 165 -QGD 167
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%)
Query: 390 QEFPTSSTVMDLLERAGRGSSRWSPYGFPLKEELRPRLN 428
+ P + T D+L RA G+ + + + P E+++P+LN
Sbjct: 50 EAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLN 88
>pdb|1P9J|A Chain A, Solution Structure And Dynamics Of The EgfTGF-Alpha
Chimera T1e
Length = 54
Score = 28.9 bits (63), Expect = 5.9, Method: Composition-based stats.
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 358 SHADDCPFSYKPQCSHDG 375
SH +DCP S+ C HDG
Sbjct: 3 SHFNDCPLSHDGYCLHDG 20
>pdb|2R77|A Chain A, Crystal Structure Of Phosphatidylethanolamine-Binding
Protein, Pfl0955c, From Plasmodium Falciparum
Length = 205
Score = 28.5 bits (62), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 257 KMKDYITRPKFNGYQSLHTV 276
K + YITR KFN Y+S+H +
Sbjct: 169 KGEKYITRVKFNNYESVHNI 188
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
0.321 0.134 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,287,365
Number of Sequences: 62578
Number of extensions: 578117
Number of successful extensions: 1278
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1263
Number of HSP's gapped (non-prelim): 9
length of query: 488
length of database: 14,973,337
effective HSP length: 103
effective length of query: 385
effective length of database: 8,527,803
effective search space: 3283204155
effective search space used: 3283204155
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)