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= 011972
(474 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CW9|A Chain A, Crystal Structure Of Human Tim44 C-Terminal Domain
Length = 194
Score = 85.5 bits (210), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 47/169 (27%), Positives = 86/169 (50%), Gaps = 5/169 (2%)
Query: 298 IVHKIQDMNETIFQETDAAASIKEIRRRDPSFSLPDFVSEVQEAIRP-VLSAYMKGDVET 356
+ K+ D+ +F +T+ + + EI R DP+F F+ + + I P VL A + G+++
Sbjct: 21 LTDKVTDLLGGLFSKTEXSEVLTEILRVDPAFDKDRFLKQCENDIIPNVLEAXISGELDI 80
Query: 357 LKKYCSPEVIERCKAEHTAYQSHGIFFDNRILHVSEVEVRETKMMGSSPIIIVAFQTQQI 416
LK +C + ++ G+ F +RIL + V++ K + P++I+ FQ Q +
Sbjct: 81 LKDWCYEATYSQLAHPIQQAKALGLQFHSRILDIDNVDLAXGKXVEQGPVLIITFQAQLV 140
Query: 417 YCVRDKHGTITEGGKDTIQTVYYAWAMQQVDAEELGEDVLYPIWKLREM 465
VR+ G + EG D + Y WA+ + D +EL Y W+L ++
Sbjct: 141 XVVRNPKGEVVEGDPDKVLRXLYVWALCR-DQDELNP---YAAWRLLDI 185
>pdb|3QK9|A Chain A, Yeast Tim44 C-Terminal Domain Complexed With Cymal-3
pdb|3QK9|B Chain B, Yeast Tim44 C-Terminal Domain Complexed With Cymal-3
Length = 222
Score = 80.9 bits (198), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 55/186 (29%), Positives = 93/186 (50%), Gaps = 9/186 (4%)
Query: 291 WETSDNPIV---HKIQDMNETIFQETDAAASIKEIRRRDPSFSLPDFVSEVQEAIRP-VL 346
W+ S+NP++ KI + F ET+++ + + DP+FS F ++E I P +L
Sbjct: 34 WDESENPLIVVMRKITNKVGGFFAETESSRVYSQFKLMDPTFSNESFTRHLREYIVPEIL 93
Query: 347 SAYMKGDVETLKKYCSPEVIERCKAEHTAYQSHGIFFDNRILHVSEVEVRETKMMGSS-- 404
AY+KGDV+ LKK+ S A+ ++ ++ D RIL + VE+ K++
Sbjct: 94 EAYVKGDVKVLKKWFSEAPFNVYAAQQKIFKEQDVYADGRILDIRGVEIVSAKLLAPQDI 153
Query: 405 PIIIVAFQTQQIYCVRDKH-GTITEGGKDTIQTVYYAWAMQQVDAEELGEDVLYPIWKLR 463
P+++V + Q+I R K G I G + I YA + D E++ +D WK+
Sbjct: 154 PVLVVGCRAQEINLYRKKKTGEIAAGDEANILMSSYAMVFTR-DPEQIDDDETEG-WKIL 211
Query: 464 EMQQLG 469
E + G
Sbjct: 212 EFVRGG 217
>pdb|2FXT|A Chain A, Crystal Structure Of Yeast Tim44
Length = 192
Score = 79.7 bits (195), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 51/171 (29%), Positives = 87/171 (50%), Gaps = 8/171 (4%)
Query: 291 WETSDNPIV---HKIQDMNETIFQETDAAASIKEIRRRDPSFSLPDFVSEVQEAIRP-VL 346
W+ S+NP++ KI + F ET+++ + + DP+FS F ++E I P +L
Sbjct: 10 WDESENPLIVVMRKITNKVGGFFAETESSRVYSQFKLMDPTFSNESFTRHLREYIVPEIL 69
Query: 347 SAYMKGDVETLKKYCSPEVIERCKAEHTAYQSHGIFFDNRILHVSEVEVRETKMMGSS-- 404
AY+KGDV+ LKK+ S A+ ++ ++ D RIL + VE+ K++
Sbjct: 70 EAYVKGDVKVLKKWFSEAPFNVYAAQQKIFKEQDVYADGRILDIRGVEIVSAKLLAPQDI 129
Query: 405 PIIIVAFQTQQIYCVRDKH-GTITEGGKDTIQTVYYAWAMQQVDAEELGED 454
P+++V + Q+I R K G I G + I YA + D E++ +D
Sbjct: 130 PVLVVGCRAQEINLYRKKKTGEIAAGDEANILMSSYAMVFTR-DPEQIDDD 179
>pdb|2IHM|A Chain A, Polymerase Mu In Ternary Complex With Gapped 11mer Dna
Duplex And Bound Incoming Nucleotide
pdb|2IHM|B Chain B, Polymerase Mu In Ternary Complex With Gapped 11mer Dna
Duplex And Bound Incoming Nucleotide
Length = 360
Score = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 36/160 (22%), Positives = 69/160 (43%), Gaps = 30/160 (18%)
Query: 108 EAESTVKKVSASMKEKISAATEEVKGTFRTGSTDTSAKHDDDVRDGFKASSGEEKQK--- 164
+AE+ + + A++++ + AT + G FR G HD D F + EE Q+
Sbjct: 158 DAEALQQLIEAAVRQTLPGATVTLTGGFRRGKLQ---GHDVD----FLITHPEEGQEVGL 210
Query: 165 -----QTVSSDTAETFYGKLKSSISSPKFTLAFQKLKEAKVVDLAKKGYDIVKDELSGSP 219
+ S ++ +S ++ L + + +D+ ++ + I+ G P
Sbjct: 211 LPKVMSCLQSQGLVLYHQYHRSHLADSAHNLR----QRSSTMDVFERSFCIL-----GLP 261
Query: 220 SKRKHL---EYTPSPSWTGEKSTRTDLVVTPSKKSMWSKL 256
++ P P+W K+ R DLVVTPS + ++ L
Sbjct: 262 QPQQAALAGALPPCPTW---KAVRVDLVVTPSSQFPFALL 298
>pdb|2CFO|A Chain A, Non-discriminating Glutamyl-trna Synthetase From
Thermosynechococcus Elongatus In Complex With Glu
pdb|2CFO|B Chain B, Non-discriminating Glutamyl-trna Synthetase From
Thermosynechococcus Elongatus In Complex With Glu
Length = 492
Score = 32.3 bits (72), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 360 YCSPEVIERCKAEHTAYQSHGIFFDNRILHVSEVEVRETKMMGSSPII 407
YC+PE +E +AE A + +DNR H++ E + G +P+I
Sbjct: 98 YCTPEELEALRAEQKA-KGQAPRYDNRHRHLTPEEQAAFEAAGRTPVI 144
>pdb|2ON7|A Chain A, Structure Of Nagst-1
pdb|2ON7|B Chain B, Structure Of Nagst-1
pdb|2ON7|C Chain C, Structure Of Nagst-1
pdb|2ON7|D Chain D, Structure Of Nagst-1
Length = 206
Score = 32.0 bits (71), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 195 LKEAKVVDLAKKGYDIVKDELSGSPSKRKHLEYTPSPSWTGEKSTRTDLVVTPSKKSMWS 254
++E V L K+ +D+ G +K L+ +PS G+ T DL+V+ +M +
Sbjct: 112 MREGDVEQLKKEVLLPARDKFFGFITK--FLKKSPSGFLVGDSLTWVDLLVSEHNATMLT 169
Query: 255 KLKEKMQGYP 264
+ E ++GYP
Sbjct: 170 FVPEFLEGYP 179
>pdb|2OEJ|A Chain A, Crystal Structure Of A Rubisco-like Protein From
Geobacillus Kaustophilus (tetramutant Form), Liganded
With Phosphate Ions
pdb|2OEJ|B Chain B, Crystal Structure Of A Rubisco-like Protein From
Geobacillus Kaustophilus (tetramutant Form), Liganded
With Phosphate Ions
Length = 413
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 28/140 (20%), Positives = 55/140 (39%), Gaps = 8/140 (5%)
Query: 327 PSFSLPDFVSEVQEAIRPVLSAYMKGDVETLKKYCSPEV-------IERCKAEHTAYQSH 379
P F + V RP+L + KG + Y +PE+ ++ K + + S
Sbjct: 123 PRFGIDGIRDRVGVHNRPLLMSIFKGMIGRDLAYLTPELKKQALGGVDLVKDDEILFDSE 182
Query: 380 GIFFDNRILHVSEVEVRETKMMGSSPIIIVAFQTQQIYCVRDKHGTITEGGKDTIQTVYY 439
+ F+ RI + ++E + T + + ++DK E G D + +
Sbjct: 183 LLPFEKRITE-GKAALQEVYEQTGKRTLYAVNLTGKTFALKDKAKRAAELGADVLLFNVF 241
Query: 440 AWAMQQVDAEELGEDVLYPI 459
A+ + + A E++ PI
Sbjct: 242 AYGLDVLQALREDEEIAVPI 261
>pdb|2IKQ|A Chain A, Crystal Structure Of Mouse Sts-1 Pgm Domain In Complex
With Phosphate
pdb|2IKQ|B Chain B, Crystal Structure Of Mouse Sts-1 Pgm Domain In Complex
With Phosphate
pdb|2IKQ|M Chain M, Crystal Structure Of Mouse Sts-1 Pgm Domain In Complex
With Phosphate
Length = 270
Score = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 4/82 (4%)
Query: 383 FDNRILHVSEVEVRETKMMGSSPIIIVAFQTQQIYCVRDKHGTITEGGKDTIQTVYYAWA 442
+ NR V++ + E K G++ I+IVA + C G + KD +Q V
Sbjct: 170 YINRSFQVTKEIISECKSKGNN-ILIVAHASSLEACTCQLQGLSPQNSKDFVQMVRKIPY 228
Query: 443 MQQVDAEELGEDVLYPIWKLRE 464
+ EELGE IW+L +
Sbjct: 229 LGFCSCEELGET---GIWQLTD 247
>pdb|2H0Q|A Chain A, Crystal Structure Of The Pgm Domain Of The Suppressor Of
T-Cell Receptor (Sts-1)
pdb|2H0Q|B Chain B, Crystal Structure Of The Pgm Domain Of The Suppressor Of
T-Cell Receptor (Sts-1)
pdb|2H0Q|C Chain C, Crystal Structure Of The Pgm Domain Of The Suppressor Of
T-Cell Receptor (Sts-1)
Length = 261
Score = 29.6 bits (65), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 4/82 (4%)
Query: 383 FDNRILHVSEVEVRETKMMGSSPIIIVAFQTQQIYCVRDKHGTITEGGKDTIQTVYYAWA 442
+ NR V++ + E K G++ I+IVA + C G + KD +Q V
Sbjct: 166 YINRSFQVTKEIISECKSKGNN-ILIVAHASSLEACTCQLQGLSPQNSKDFVQMVRKIPY 224
Query: 443 MQQVDAEELGEDVLYPIWKLRE 464
+ EELGE IW+L +
Sbjct: 225 LGFCSCEELGET---GIWQLTD 243
>pdb|2QE7|G Chain G, Crystal Structure Of The F1-Atpase From The
Thermoalkaliphilic Bacterium Bacillus Sp. Ta2.A1
Length = 286
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 22/28 (78%), Gaps = 1/28 (3%)
Query: 259 KMQGYPVFKRITGISE-PVVTKGQEIAE 285
K +GYPV + +TGIS+ P +T+ Q+IA+
Sbjct: 127 KKRGYPVVEEVTGISDTPSLTEIQDIAQ 154
>pdb|3MBK|A Chain A, The 1.35 A Structure Of The Phosphatase Domain Of The
Suppressor Of T Cell Receptor Signalling Protein In
Complex With Sulphate
pdb|3MBK|B Chain B, The 1.35 A Structure Of The Phosphatase Domain Of The
Suppressor Of T Cell Receptor Signalling Protein In
Complex With Sulphate
Length = 264
Score = 29.6 bits (65), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 4/82 (4%)
Query: 383 FDNRILHVSEVEVRETKMMGSSPIIIVAFQTQQIYCVRDKHGTITEGGKDTIQTVYYAWA 442
+ NR V++ + E K G++ I+IVA + C G + KD +Q V
Sbjct: 166 YINRSFQVTKEIISECKSKGNN-ILIVAHASSLEACTCQLQGLSPQNSKDFVQMVRKIPY 224
Query: 443 MQQVDAEELGEDVLYPIWKLRE 464
+ EELGE IW+L +
Sbjct: 225 LGFCSCEELGET---GIWQLTD 243
>pdb|1F1M|A Chain A, Crystal Structure Of Outer Surface Protein C (Ospc)
pdb|1F1M|B Chain B, Crystal Structure Of Outer Surface Protein C (Ospc)
pdb|1F1M|C Chain C, Crystal Structure Of Outer Surface Protein C (Ospc)
pdb|1F1M|D Chain D, Crystal Structure Of Outer Surface Protein C (Ospc)
Length = 164
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 347 SAYMKGDVETLKKYCSPEVIERCKAEHTAYQSHGIFFDN 385
S +K ++E KK CS E + K EHT G+ DN
Sbjct: 80 SGELKAEIEKAKK-CSEEFTAKLKGEHTDLGKEGVTDDN 117
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
0.312 0.128 0.354
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,349,133
Number of Sequences: 62578
Number of extensions: 546723
Number of successful extensions: 1709
Number of sequences better than 100.0: 34
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 1690
Number of HSP's gapped (non-prelim): 40
length of query: 474
length of database: 14,973,337
effective HSP length: 102
effective length of query: 372
effective length of database: 8,590,381
effective search space: 3195621732
effective search space used: 3195621732
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)