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= 004703
(735 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 = 257 bits (656), Expect = 2e-68, Method: Compositional matrix adjust.
Identities = 141/331 (42%), Positives = 207/331 (62%), Gaps = 13/331 (3%)
Query: 232 FVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLS 291
FV KA A AH Q+R SG+PY++H ++ A +LA + ++ VA G LHD ++D ++
Sbjct: 27 FVKKALDYATAAHFYQVRKSGEPYIVHPIQVAGILADLHLDAVTVACGFLHDVVEDTDIT 86
Query: 292 YDYIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMA-DARAVLI 350
D I FG V D+V+GV+KL ++ + E A M +AM+ D R +L+
Sbjct: 87 LDNIEFDFGKDVRDIVDGVTKLGKVEYKSHEEQLAENH------RKMLMAMSKDIRVILV 140
Query: 351 KLADRLHNMMTLDALPLCKRQRFAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPDQH 410
KLADRLHNM TL L K++R ++ET+EI+ PLA+RLGIS K +LE+L F++LN +
Sbjct: 141 KLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGISRIKWELEDLAFRYLNETEF 200
Query: 411 TELSSKLVECFDE--AMVTSAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKMLKKKLTM 468
++S + E E A+V + K++ ++ + F + GR K +YSI+ KM KK
Sbjct: 201 YKISHMMNEKRREREALVDDIVTKIKSYTTEQGL-FGDVYGRPKHIYSIYRKMRDKKKRF 259
Query: 469 DEIHDIYGLRLIVENEEDCYQALRVVHQLWAEVPGKMKDYITRPKFNGYQSLHTVVTG-E 527
D+I D+ +R ++E + D Y + +H+LW +PG+ KDYI PK NGYQS+HT V G +
Sbjct: 260 DQIFDLIAIRCVMETQSDVYAMVGYIHELWRPMPGRFKDYIAAPKANGYQSIHTTVYGPK 319
Query: 528 GLVPLEVQIRTKEMHLQAEFGFAAHWRYKEG 558
G P+E+QIRTKEMH AE+G AAHW YK+G
Sbjct: 320 G--PIEIQIRTKEMHQVAEYGVAAHWAYKKG 348
>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 = 57.8 bits (138), Expect = 2e-08, Method: Composition-based stats.
Identities = 54/172 (31%), Positives = 81/172 (47%), Gaps = 21/172 (12%)
Query: 240 AERAHRGQMRA--SGDPYLLHCVETAMLLA--AIGANSTVVAAGLLHDTLDDAFLSYDYI 295
A R HR Q R G PY+ H + A +L A + V+ A LLHDT++D + D +
Sbjct: 14 AARKHRQQRRKDPEGTPYINHPIGVARILTHEAGITDIVVLQAALLHDTVEDTDTTLDEV 73
Query: 296 FRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMADARAVLIKLADR 355
FGA V LVE V+ L KL R+ RL + A L+KLAD+
Sbjct: 74 ELHFGAQVRRLVEEVTDDKTLPKLERK-----------RLQVEQAPHSSPGAKLVKLADK 122
Query: 356 LHNMMTLDALPLCKRQRFAKETLEIFVPLANRL--GISTWKVQLENLCFKHL 405
L+N+ L+ C + +++ ++ + A ++ G+ QLE KHL
Sbjct: 123 LYNLRDLNR---CTPEGWSEHRVQEYFEWAAQVVKGLQGTNRQLEE-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 = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 40/123 (32%), Positives = 58/123 (47%), Gaps = 15/123 (12%)
Query: 244 HRGQMRASGD--PYLLHCVETAMLLA--AIGANSTVVAAGLLHDTLDDAFLSYDYIFRTF 299
HR Q R PY+ H + + +L+ A + V+ A LLHD ++D S++ + + F
Sbjct: 20 HRQQRRKDPQETPYVNHVINVSTILSVEACITDEGVLMAALLHDVVEDTDASFEDVEKLF 79
Query: 300 GAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMADARAVLIKLADRLHNM 359
G V LV V+ L K R+ RL A + RA LIKLAD+L N+
Sbjct: 80 GPDVCGLVREVTDDKSLEKQERK-----------RLQIENAAKSSCRAKLIKLADKLDNL 128
Query: 360 MTL 362
L
Sbjct: 129 RDL 131
>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 = 3e-07, Method: Compositional matrix adjust.
Identities = 38/121 (31%), Positives = 64/121 (52%), Gaps = 13/121 (10%)
Query: 447 LCGRHKSLYSIHCKML-----KKKLTMDEIHDIYGLRLIVENEEDCYQALRVVHQLWAEV 501
+ GR K + SI KM+ K+ LT D + DI GLR++V+ +D L ++ Q
Sbjct: 74 VTGRVKPIESIKEKMVLRGIKKENLTQD-MQDIAGLRIMVQFVDDVNDVLELLRQRKDMK 132
Query: 502 PGKMKDYITRPKFNGYQSLHTVV-------TGEGLVPLEVQIRTKEMHLQAEFGFAAHWR 554
+ +DYI K +GY+S H +V +G+ ++ E+QIRT M+ A + +++
Sbjct: 133 VIQERDYINNLKPSGYRSYHVIVEYPVDTISGQRIIMAEIQIRTLAMNFWATIEHSLNYK 192
Query: 555 Y 555
Y
Sbjct: 193 Y 193
>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 = 3e-06, Method: Composition-based stats.
Identities = 37/133 (27%), Positives = 67/133 (50%), Gaps = 12/133 (9%)
Query: 438 KDKNISFLVLCGRHKSLYSIHCKMLKKKLTM----DEIHDIYGLRLIVENEEDCYQALRV 493
++K+ + GR K + SI K ++ +T ++ DI GLR+ V+ +D + + +
Sbjct: 36 QNKHSPIEFVTGRVKPIESIKEKXARRGITYATLEHDLQDIAGLRVXVQFVDDVKEVVDI 95
Query: 494 VHQLWAEVPGKMKDYITRPKFNGYQSLHTVV-------TGEGLVPLEVQIRTKEMHLQAE 546
+H+ + +DYIT K +GY+S H VV G + E+QIRT + A
Sbjct: 96 LHKRQDXRIIQERDYITHRKASGYRSYHVVVEYTVDTINGAKTILAEIQIRTLAXNFWAT 155
Query: 547 FGFAAHWRYKEGD 559
+ +++Y +GD
Sbjct: 156 IEHSLNYKY-QGD 167
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 636 VQE--FPTSSTVMDLLERAGRGSSRWSPYGFPLKEELRPRLN 675
+QE P + T D+L RA G+ + + + P E+++P+LN
Sbjct: 47 IQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLN 88
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
0.320 0.134 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,630,310
Number of Sequences: 62578
Number of extensions: 762983
Number of successful extensions: 1571
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1558
Number of HSP's gapped (non-prelim): 6
length of query: 735
length of database: 14,973,337
effective HSP length: 106
effective length of query: 629
effective length of database: 8,340,069
effective search space: 5245903401
effective search space used: 5245903401
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: 55 (25.8 bits)