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= 038542
(475 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 35.0 bits (79), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 39/145 (26%), Positives = 62/145 (42%), Gaps = 32/145 (22%)
Query: 148 GLCNALIDMFAKCGDVDKALKLFRSM--NGRTIVSW-----------------TSVIAGL 188
L +DM +K GDV +AL+L+ NG + + +S GL
Sbjct: 27 ALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGL 86
Query: 189 AMHGRGLEAVALFEEMLEAGVPPDDVAFV-GLLSACSHCGLVDKGREYFDSMKN--DFGI 245
+ RG + +F++M+ V P++ F G A + D FD +K FGI
Sbjct: 87 S---RGFD---IFKQMIVDKVVPNEATFTNGARLAVAK----DDPEMAFDMVKQMKAFGI 136
Query: 246 IPKIEHYGCMVDMLCRSGRVKEAHE 270
P++ YG + CR G +A+E
Sbjct: 137 QPRLRSYGPALFGFCRKGDADKAYE 161
>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 = 32.0 bits (71), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 60/145 (41%), Gaps = 32/145 (22%)
Query: 148 GLCNALIDMFAKCGDVDKALKLFRSM--NGRTIVSW-----------------TSVIAGL 188
L +D +K GDV +AL+L+ NG + + +S GL
Sbjct: 27 ALLKQKLDXCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGL 86
Query: 189 AMHGRGLEAVALFEEMLEAGVPPDDVAFV-GLLSACSHCGLVDKGREYFDSMKND--FGI 245
+ RG + +F++ + V P++ F G A + D FD +K FGI
Sbjct: 87 S---RGFD---IFKQXIVDKVVPNEATFTNGARLAVAK----DDPEXAFDXVKQXKAFGI 136
Query: 246 IPKIEHYGCMVDMLCRSGRVKEAHE 270
P++ YG + CR G +A+E
Sbjct: 137 QPRLRSYGPALFGFCRKGDADKAYE 161
>pdb|1F2J|A Chain A, Crystal Structure Analysis Of Aldolase From T. Brucei
Length = 370
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 38 KFQFGDDIHVQNTLVHMYGSCEGGIELGRKVFDEMSERDSVSWSAMIGGYARLGLSTDAI 97
K F +Q++ + +G E G+E GR+ F ++ +S+ A +G Y R D+
Sbjct: 306 KLTFSYARALQSSAIKRWGGKESGVEAGRRAFMHRAKMNSL---AQLGKYNRADDDKDSQ 362
Query: 98 DLF 100
L+
Sbjct: 363 SLY 365
>pdb|2PPV|A Chain A, Crystal Structure Of A Protein Belonging To The Upf0052
(Se_0549) From Staphylococcus Epidermidis Atcc 12228 At
2.00 A Resolution
Length = 332
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 57/140 (40%), Gaps = 36/140 (25%)
Query: 283 IWRTLISACCARG--ELKLAESITKRLIGN---EPMHESNYVLLSHI------------- 324
++ ++IS C +G E L S K + N +P NY + HI
Sbjct: 188 LYTSVISNLCVKGISEALLRTSAPKLYVSNVXTQPGETDNYDVKEHIDALTRQVGEPFID 247
Query: 325 --------YAK--LLRWEKKTKI-----REVMDKRGMKKIPGSTLIELDNEIYEFVCGDK 369
Y+K L R+E+K +E + G++ + S L+E+ NE Y
Sbjct: 248 FVICSSESYSKDVLQRYEEKNSKPVAVHKEQLKDSGIRVLTASNLVEISNEHY---VRHN 304
Query: 370 SHHQSKEIYEMLDEMGRKMK 389
+ SK IYE+ E+ ++
Sbjct: 305 TKVLSKXIYELALELTSTIR 324
>pdb|2G29|A Chain A, Crystal Structure Of The Periplasmic Nitrate-binding
Protein Nrta From Synechocystis Pcc 6803
Length = 417
Score = 28.9 bits (63), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 24/123 (19%), Positives = 56/123 (45%), Gaps = 17/123 (13%)
Query: 332 EKKTKIREVMDKRGMKKIPGSTLIELDNEIYEFVCGDKSHHQSKEIYE--MLDEMGRKMK 389
E K ++ +++ KR K+P +I+ IY F G ++ + +EI + +D K
Sbjct: 274 ENKEEMCQILSKREWFKVPFEDIIDRSKGIYNFGNGQET-FEDQEIMQKYWVDNASYPYK 332
Query: 390 -----------KAGYVPTTSEVLLDINEEDKEDALNKHSEKLAIAFALLKTPPGTPIRIV 438
+ GY+P +++ +++ ++ED + ++ L + + P +P R +
Sbjct: 333 SHDQWFLTENIRWGYLPASTDTKAIVDKVNREDLWREAAQALEVPADQI---PSSPSRGI 389
Query: 439 KNL 441
+
Sbjct: 390 ETF 392
>pdb|3IXC|A Chain A, Crystal Structure Of Hexapeptide Transferase Family
Protein From Anaplasma Phagocytophilum
Length = 191
Score = 28.5 bits (62), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 9/58 (15%)
Query: 5 GVSPNKFTYPFVLKACAGIGDLNLGKSV---HGAVL-----KFQFGDDIHVQ-NTLVH 53
GVSP+ + F+ IGD+ +GK+ +G VL K + G+ ++Q NT+VH
Sbjct: 31 GVSPSVDSTAFIAGNARIIGDVCIGKNASIWYGTVLRGDVDKIEVGEGTNIQDNTVVH 88
>pdb|3U5C|B Chain B, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|B Chain B, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 255
Score = 28.5 bits (62), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 27/113 (23%), Positives = 51/113 (45%), Gaps = 20/113 (17%)
Query: 284 WRTLISACCARGELKLAESITKRLIG-------NEPMHESNYVLLSHIYAKLLRWEKKTK 336
W+TLI A +K ++ R+ + +Y SHI A
Sbjct: 117 WQTLIEANVT---VKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRA---------- 163
Query: 337 IREVMDKRGMKKIPGSTLIELDNEIYEFVCGDKSHHQSKEIYEMLDEMGRKMK 389
IR+V+ + K++ GSTL +L +++ V + + +K+I+ + + RK+K
Sbjct: 164 IRKVISEILTKEVQGSTLAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVK 216
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
0.322 0.138 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,475,327
Number of Sequences: 62578
Number of extensions: 599761
Number of successful extensions: 1413
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1407
Number of HSP's gapped (non-prelim): 8
length of query: 475
length of database: 14,973,337
effective HSP length: 102
effective length of query: 373
effective length of database: 8,590,381
effective search space: 3204212113
effective search space used: 3204212113
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)