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= 010869
(498 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2F1L|A Chain A, Crystal Structure Of A Putative 16s Ribosomal Rna
Processing Protein Rimm (Pa3744) From Pseudomonas
Aeruginosa At 2.46 A Resolution
Length = 187
Score = 62.0 bits (149), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 47/149 (31%), Positives = 78/149 (52%), Gaps = 15/149 (10%)
Query: 76 DFVDVGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWL--RQQVLGRET-IREVKLIDG 132
D V +G + SV+G++GE+ V FT P L R+ L R+ IR+ +L+ G
Sbjct: 19 DLVVIGKIVSVYGIRGEVKV--------YSFTDPLDNLLDYRRWTLRRDGEIRQAELVRG 70
Query: 133 REHPGQKSWILTFEGIDTVEQARPLVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKET 192
R H K +G+D E+AR G + + P LE+GE+Y L G++V+ +
Sbjct: 71 RLH--GKVLAAKLKGLDDREEARTFTGYEICIPRSELPSLEEGEYYWHQLEGLKVI-DQG 127
Query: 193 GELVGTVVNVFNSGANDLLHVM-CYSSVN 220
+L+G + ++ +GAND+ V C S++
Sbjct: 128 RQLLGVIDHLLETGANDVXVVKPCAGSLD 156
>pdb|3H9N|A Chain A, Crystal Structure Of The Ribosome Maturation Factor Rimm
(Hi0203) From H.Influenzae. Northeast Structural
Genomics Consortium Target Ir66
Length = 177
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 52/191 (27%), Positives = 87/191 (45%), Gaps = 23/191 (12%)
Query: 80 VGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWLRQQVLGRETIREVKLIDGREHPGQK 139
VG + S +G++G + + ST+ E F W + + + ++L + R H +
Sbjct: 5 VGKLGSTYGIRGWLRIYSSTEQAESIFDYQ--PWFLKI---KGEWQSIELENWRYHNHEI 59
Query: 140 SWILTFEGIDTVEQARPLVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKETGELVGTV 199
I+ +G+D E A+ L + PELE+G++Y DL+G VV E G GTV
Sbjct: 60 --IVKLKGVDDREAAQILANVEIGVDLSVFPELEEGDYYWHDLIGCTVVNLE-GYTXGTV 116
Query: 200 VNVFNSGANDLLHVMCYSSVNVIXXXXXXXXXXXXXXXRLVWIPFV-EEIVPIVDMNGRE 258
+G+ND+L V + RL IPF+ E++V VD+ +
Sbjct: 117 TEXXETGSNDVLVVKANTK------------DAFGKQERL--IPFLYEQVVKRVDLTTKT 162
Query: 259 MQITPPKGLLE 269
+++ G LE
Sbjct: 163 IEVDWDAGFLE 173
>pdb|2DYI|A Chain A, Crystal Structure Of 16s Ribosomal Rna Processing Protein
Rimm From Thermus Thermophilus Hb8
pdb|3A1P|A Chain A, Structure Of Ribosome Maturation Protein Rimm And
Ribosomal Protein S19
pdb|3A1P|C Chain C, Structure Of Ribosome Maturation Protein Rimm And
Ribosomal Protein S19
Length = 162
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 142 ILTFEGIDTVEQARPLVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKETGELVGTVVN 201
++ G+ A LVG + A D P LE+G +Y L+G+ V ++ G VG VV+
Sbjct: 54 VVHLAGVTDRTLAEALVGLRVYAEVADLPPLEEGRYYYFALIGLPVYVE--GRQVGEVVD 111
Query: 202 VFNSGANDLL 211
+ ++GA D+L
Sbjct: 112 ILDAGAQDVL 121
>pdb|3T2L|A Chain A, Crystal Structure Of A Putative Cell Adhesion Protein
(Bf1858) From Bacteroides Fragilis Nctc 9343 At 2.33 A
Resolution
Length = 308
Score = 33.1 bits (74), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 15/78 (19%)
Query: 371 LKISGEGSLGPCARAKKVVTNSSLQKKGN-HLVSEGKKAMVLVVHNSEEGN-------EC 422
LKIS E PC +K + NS+L KKG ++ +G +H+SE GN +
Sbjct: 156 LKISRENYFXPCEISKITLKNSNLIKKGTINIAVDGS------IHSSETGNYDLTTVTDA 209
Query: 423 DPHSV-VSESTANKSLAL 439
PH++ V ES + L +
Sbjct: 210 SPHTLSVGESYVCRVLXI 227
>pdb|1UD2|A Chain A, Crystal Structure Of Calcium-Free Alpha-Amylase From
Bacillus Sp. Strain Ksm-K38 (Amyk38)
pdb|1UD4|A Chain A, Crystal Structure Of Calcium Free Alpha Amylase From
Bacillus Sp. Strain Ksm-K38 (Amyk38, In Calcium
Containing Solution)
pdb|1UD5|A Chain A, Crystal Structure Of Amyk38 With Rubidium Ion
pdb|1UD6|A Chain A, Crystal Structure Of Amyk38 With Potassium Ion
pdb|1UD8|A Chain A, Crystal Structure Of Amyk38 With Lithium Ion
Length = 480
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 11/68 (16%)
Query: 114 LRQQVLGRETIREVKLIDGRE-HPGQ--KSWILTFEGIDTVEQARPLVGSTLLAREGDRP 170
LR ++ + V +D + PG+ +SW+ + +PL +T+L REG P
Sbjct: 308 LRGSLVEAHPMHAVTFVDNHDTQPGESLESWV--------ADWFKPLAYATILTREGGYP 359
Query: 171 ELEDGEFY 178
+ G++Y
Sbjct: 360 NVFYGDYY 367
>pdb|1UD3|A Chain A, Crystal Structure Of Amyk38 N289h Mutant
Length = 480
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 11/68 (16%)
Query: 114 LRQQVLGRETIREVKLIDGRE-HPGQ--KSWILTFEGIDTVEQARPLVGSTLLAREGDRP 170
LR ++ + V +D + PG+ +SW+ + +PL +T+L REG P
Sbjct: 308 LRGSLVEAHPMHAVTFVDNHDTQPGESLESWV--------ADWFKPLAYATILTREGGYP 359
Query: 171 ELEDGEFY 178
+ G++Y
Sbjct: 360 NVFYGDYY 367
>pdb|2VR2|A Chain A, Human Dihydropyrimidinase
Length = 541
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 44/88 (50%), Gaps = 6/88 (6%)
Query: 346 IEIPSKRWNATELMNATKAELMISSLKISGEGSLGPCARAKKVVTNSSLQKKGNHLVSEG 405
I + K N+ ++ A K M++ L++ S R K++ + + + L++EG
Sbjct: 170 ILVQDKGVNSFKMFMAYKDLYMVTDLELYEAFS-----RCKEIGAIAQVHAENGDLIAEG 224
Query: 406 KKAMVLVVHNSEEGNE-CDPHSVVSEST 432
K M+ + EG+E C P +V +E+T
Sbjct: 225 AKKMLALGITGPEGHELCRPEAVEAEAT 252
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
0.317 0.133 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,830,630
Number of Sequences: 62578
Number of extensions: 489359
Number of successful extensions: 1424
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1416
Number of HSP's gapped (non-prelim): 9
length of query: 498
length of database: 14,973,337
effective HSP length: 103
effective length of query: 395
effective length of database: 8,527,803
effective search space: 3368482185
effective search space used: 3368482185
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)