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= 044576
(141 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1TIG|A Chain A, Translation Initiation Factor 3 C-Terminal Domain
Length = 94
Score = 60.1 bits (144), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 51/85 (60%), Gaps = 1/85 (1%)
Query: 31 MDLKELKMGYNIDQHDYSVRLKAARKFLKDGDKVKVIVNLKGRENEFRNIAIELIRRFQN 90
+++KE+++ I++HD++ +L+ ARKFL+ GDKVK + KGR + I ++ R
Sbjct: 5 INVKEVRLSPTIEEHDFNTKLRNARKFLEKGDKVKATIRFKGRAITHKEIGQRVLDRLSE 64
Query: 91 DVGELASEENKNFRD-RNIFIILVP 114
++A E D RN+F++L P
Sbjct: 65 ACADIAVVETAPKMDGRNMFLVLAP 89
>pdb|2IFE|A Chain A, Translation Initiation Factor If3 From Escherichia Coli
Ribosome Binding Domain (Residues 84-180)
Length = 100
Score = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 50/84 (59%), Gaps = 2/84 (2%)
Query: 35 ELKMGYNIDQHDYSVRLKAARKFLKDGDKVKVIVNLKGRENEFRNIAIELIRRFQNDVGE 94
E+K D+ DY V+L++ +FL++GDK K+ + +GRE + I +E++ R ++D+ E
Sbjct: 15 EIKFRPGTDEGDYQVKLRSLIRFLEEGDKAKITLRFRGREMAHQQIGMEVLNRVKDDLQE 74
Query: 95 LASEEN--KNFRDRNIFIILVPNK 116
LA E+ R + ++L P K
Sbjct: 75 LAVVESFPTKIEGRQMIMVLAPKK 98
>pdb|1I96|V Chain V, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With The Translation
Initiation Factor If3 (C-Terminal Domain)
Length = 89
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 48/87 (55%), Gaps = 1/87 (1%)
Query: 32 DLKELKMGYNIDQHDYSVRLKAARKFLKDGDKVKVIVNLKGRENEFRNIAIELIRRFQND 91
++K +K ID+HDY +L ++FL++G KVKV + +GRE + ++ R D
Sbjct: 1 EVKSIKFRVKIDEHDYQTKLGHIKRFLQEGHKVKVTIMFRGREVAHPELGERILNRVTED 60
Query: 92 VGELASEENK-NFRDRNIFIILVPNKA 117
+ +LA E K R++ ++L P K
Sbjct: 61 LKDLAVVEMKPEMLGRDMNMLLAPVKV 87
>pdb|2GTL|M Chain M, Lumbricus Erythrocruorin At 3.5a Resolution
Length = 217
Score = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 29 NRMDLKELKMGYNIDQHDYSVRLKAARKFLKDGDKVKVIVNLKGRENEFRNIA 81
NR+ L+ + Y +D+HD++V R F G + ++ LKG+ + I
Sbjct: 135 NRVWLRA-TLSYELDEHDHTVSTTQLRGFYNFGKRELLLAPLKGQSEGYGVIC 186
>pdb|4E2U|A Chain A, Crystal Structures Of Radamin Intein From Pyrococcus
Horikoshii
Length = 168
Score = 27.7 bits (60), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 11/66 (16%)
Query: 58 LKDGDKVKVIVNLKGRENEFRNIAIELIRRFQNDVGELASEENKNFRDRNIFIILVPNKA 117
+K GD V+V ++ E EF ++ I + N V +L E NF + PN
Sbjct: 114 VKPGD---VVVGVRNGELEFHEVSSVRIIDYNNWVYDLVIPETHNF--------IAPNGL 162
Query: 118 LLQKAQ 123
+L AQ
Sbjct: 163 VLHNAQ 168
>pdb|3P4Y|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
- P2 Form
Length = 415
Score = 26.9 bits (58), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 83 ELIRRFQNDVGELASEENKNFRD 105
E ++RF+ +VGE SE KNF D
Sbjct: 271 EYLKRFKFNVGETWSEFEKNFED 293
>pdb|3OIY|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
pdb|3OIY|B Chain B, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
Length = 414
Score = 26.9 bits (58), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 83 ELIRRFQNDVGELASEENKNFRD 105
E ++RF+ +VGE SE KNF D
Sbjct: 270 EYLKRFKFNVGETWSEFEKNFED 292
>pdb|3P4X|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
pdb|3P4X|B Chain B, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
Length = 413
Score = 26.9 bits (58), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 83 ELIRRFQNDVGELASEENKNFRD 105
E ++RF+ +VGE SE KNF D
Sbjct: 269 EYLKRFKFNVGETWSEFEKNFED 291
>pdb|4DDT|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 2
pdb|4DDU|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 1
pdb|4DDV|A Chain A, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDV|B Chain B, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDW|A Chain A, Thermotoga Maritima Reverse Gyrase, C-centered
Orthorhombic Form
pdb|4DDX|A Chain A, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
pdb|4DDX|B Chain B, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
Length = 1104
Score = 26.2 bits (56), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 83 ELIRRFQNDVGELASEENKNFRD 105
E ++RF+ +VGE SE KNF D
Sbjct: 327 EYLKRFKFNVGETWSEFEKNFED 349
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 0.138 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,520,844
Number of Sequences: 62578
Number of extensions: 125766
Number of successful extensions: 323
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 315
Number of HSP's gapped (non-prelim): 20
length of query: 141
length of database: 14,973,337
effective HSP length: 89
effective length of query: 52
effective length of database: 9,403,895
effective search space: 489002540
effective search space used: 489002540
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: 46 (22.3 bits)