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= 041164
(357 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3A2K|A Chain A, Crystal Structure Of Tils Complexed With Trna
pdb|3A2K|B Chain B, Crystal Structure Of Tils Complexed With Trna
Length = 464
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 41/184 (22%), Positives = 80/184 (43%), Gaps = 30/184 (16%)
Query: 46 EEIHQVIVGNQLFKAGERIAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEGISG 105
+++ I +QL G + +G SGG DS L V L+ R + L + +D G
Sbjct: 3 DKVRAFIHRHQLLSEGAAVIVGVSGGPDSLALLHVF--LSLRDEWKLQVIAAHVDHMFRG 60
Query: 106 YR-DDSLQTVKRNEIQYGL-----PLKIVSYKDLYGWTMDEIVKVIGLKNNCTFCGVFRR 159
++ ++ VKR ++ + + + +++ G E ++ C + F
Sbjct: 61 RESEEEMEFVKRFCVERRILCETAQIDVPAFQRSAGLGAQEAARI------CRY--RFFA 112
Query: 160 QALDRGASLLKVDKIATGHNADDIAETVLLNILRGDIARLSRCTLITTGEDGPIPRCKPF 219
+ +++ + +A GH+ DD ET+L+ ++RG ++ G G IP +PF
Sbjct: 113 ELMEKH----QAGYVAVGHHGDDQVETILMRLVRGSTSK---------GYAG-IPVKRPF 158
Query: 220 KYTY 223
Y
Sbjct: 159 HGGY 162
>pdb|1NI5|A Chain A, Structure Of The Mesj Pp-Atpase From Escherichia Coli
Length = 433
Score = 35.4 bits (80), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 39/145 (26%), Positives = 62/145 (42%), Gaps = 22/145 (15%)
Query: 55 NQLFKAGERIAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEGISGYRDDSLQTV 114
N+ +I + SGG DSTVL L + R N G+ L + + G+S D +
Sbjct: 7 NRQLLTSRQILVAFSGGLDSTVLLHQLVQW-RTENPGVALRAIHVHHGLSANADAWVTHC 65
Query: 115 KRNEIQYGLPLKIVSYKDLYGWTMDEIVKV----IGLKNNCTFCGVFRRQALDRGASLLK 170
+ Q+ +PL + E V++ +G++ R QA R +LL
Sbjct: 66 ENVCQQWQVPLVV------------ERVQLAQEGLGIEAQARQA---RYQAFAR--TLLP 108
Query: 171 VDKIATGHNADDIAETVLLNILRGD 195
+ + T + DD ET LL + RG
Sbjct: 109 GEVLVTAQHLDDQCETFLLALKRGS 133
>pdb|2YWB|A Chain A, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus
pdb|2YWB|B Chain B, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus
pdb|2YWB|C Chain C, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus
pdb|2YWB|D Chain D, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus
Length = 503
Score = 35.0 bits (79), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 46/176 (26%), Positives = 74/176 (42%), Gaps = 42/176 (23%)
Query: 24 AALKRPKTLEQICRECFYEVFEEEIHQVIVGNQLFKAG-ERIAIGASGGKDSTVLAFVLS 82
A +KR T E + E EV E +AG +R+ + SGG DS+ LA +L+
Sbjct: 184 AGVKRDWTPEHVLEELLREVRE-------------RAGKDRVLLAVSGGVDSSTLALLLA 230
Query: 83 ELNRRHNYGLDLFLLSIDEGISGYRDDSLQTVKRNEIQ-----YGLPLKIVSYKDLYGWT 137
G+D + +D G+ L+ +R E++ G+ L +V K+ +
Sbjct: 231 ------KAGVDHLAVFVDHGL-------LRLGEREEVEGALRALGVNLLVVDAKERFLKA 277
Query: 138 M------DEIVKVIGLKNNCTFCGVFRRQA----LDRGASLLKVDKIATGHNADDI 183
+ +E K+IG + F V R + L +G V + A GH A I
Sbjct: 278 LKGVEDPEEKRKIIGREFVAAFSQVARERGPFRFLAQGTLYPDVIESAGGHGAAKI 333
>pdb|2YWC|A Chain A, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus In Complex With Xmp
pdb|2YWC|B Chain B, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus In Complex With Xmp
pdb|2YWC|C Chain C, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus In Complex With Xmp
pdb|2YWC|D Chain D, Crystal Structure Of Gmp Synthetase From Thermus
Thermophilus In Complex With Xmp
Length = 503
Score = 35.0 bits (79), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 46/176 (26%), Positives = 74/176 (42%), Gaps = 42/176 (23%)
Query: 24 AALKRPKTLEQICRECFYEVFEEEIHQVIVGNQLFKAG-ERIAIGASGGKDSTVLAFVLS 82
A +KR T E + E EV E +AG +R+ + SGG DS+ LA +L+
Sbjct: 184 AGVKRDWTPEHVLEELLREVRE-------------RAGKDRVLLAVSGGVDSSTLALLLA 230
Query: 83 ELNRRHNYGLDLFLLSIDEGISGYRDDSLQTVKRNEIQ-----YGLPLKIVSYKDLYGWT 137
G+D + +D G+ L+ +R E++ G+ L +V K+ +
Sbjct: 231 ------KAGVDHLAVFVDHGL-------LRLGEREEVEGALRALGVNLLVVDAKERFLKA 277
Query: 138 M------DEIVKVIGLKNNCTFCGVFRRQA----LDRGASLLKVDKIATGHNADDI 183
+ +E K+IG + F V R + L +G V + A GH A I
Sbjct: 278 LKGVEDPEEKRKIIGREFVAAFSQVARERGPFRFLAQGTLYPDVIESAGGHGAAKI 333
>pdb|3HXR|A Chain A, Nucleoporin Nup120 From S.Cerevisiae (Aa 1-757)
Length = 761
Score = 28.9 bits (63), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 34/133 (25%), Positives = 55/133 (41%), Gaps = 8/133 (6%)
Query: 153 FCGVFRR---QALDRGASLLKVDKIATGHNADDIAETVLLNILRGDIARLSRCTLITT-G 208
FC + R Q +R +L +KI HN D+ L ILR + + IT G
Sbjct: 412 FCNLKSRYGTQIFERAQQILSENKIIXAHNEDEEYLANLETILRDVKTAFNEASSITLYG 471
Query: 209 EDGPIPRC-KPFKYTYEK--EIMFTYAYFKRLDYFSTECIYSPNAYRGFAREFIKDLERL 265
++ + C +P+ ++ K + + Y + +E GFA D+ R
Sbjct: 472 DEIILVNCFQPYNHSLYKLNTTVENWFYNXHSETDGSELFKYLRTLNGFASTLSNDVLRS 531
Query: 266 RPRAILDIIKSGE 278
+ LDII +GE
Sbjct: 532 ISKKFLDII-TGE 543
>pdb|3F7F|A Chain A, Structure Of Nup120
pdb|3F7F|B Chain B, Structure Of Nup120
pdb|3F7F|C Chain C, Structure Of Nup120
pdb|3F7F|D Chain D, Structure Of Nup120
Length = 729
Score = 28.9 bits (63), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 34/133 (25%), Positives = 55/133 (41%), Gaps = 8/133 (6%)
Query: 153 FCGVFRR---QALDRGASLLKVDKIATGHNADDIAETVLLNILRGDIARLSRCTLITT-G 208
FC + R Q +R +L +KI HN D+ L ILR + + IT G
Sbjct: 408 FCNLKSRYGTQIFERAQQILSENKIIMAHNEDEEYLANLETILRDVKTAFNEASSITLYG 467
Query: 209 EDGPIPRC-KPFKYTYEKEIMFTYAYFKRLDYFS--TECIYSPNAYRGFAREFIKDLERL 265
++ + C +P+ ++ K +F + + +E GFA D+ R
Sbjct: 468 DEIILVNCFQPYNHSLYKLNTTVENWFYNMHSETDGSELFKYLRTLNGFASTLSNDVLRS 527
Query: 266 RPRAILDIIKSGE 278
+ LDII +GE
Sbjct: 528 ISKKFLDII-TGE 539
>pdb|3H7N|A Chain A, Structure Of Nup120
pdb|3H7N|B Chain B, Structure Of Nup120
pdb|3H7N|C Chain C, Structure Of Nup120
pdb|3H7N|D Chain D, Structure Of Nup120
Length = 729
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 34/133 (25%), Positives = 55/133 (41%), Gaps = 8/133 (6%)
Query: 153 FCGVFRR---QALDRGASLLKVDKIATGHNADDIAETVLLNILRGDIARLSRCTLITT-G 208
FC + R Q +R +L +KI HN D+ L ILR + + IT G
Sbjct: 408 FCNLKSRYGTQIFERAQQILSENKIIMAHNEDEEYLANLETILRDVKTAFNEASSITLYG 467
Query: 209 EDGPIPRC-KPFKYTYEKEIMFTYAYFKRLDYFS--TECIYSPNAYRGFAREFIKDLERL 265
++ + C +P+ ++ K +F + + +E GFA D+ R
Sbjct: 468 DEIILVNCFQPYNHSLYKLNTTVENWFYNMHSETDGSELFKYLRTLNGFASTLSNDVLRS 527
Query: 266 RPRAILDIIKSGE 278
+ LDII +GE
Sbjct: 528 ISKKFLDII-TGE 539
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 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,415,506
Number of Sequences: 62578
Number of extensions: 433815
Number of successful extensions: 918
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 915
Number of HSP's gapped (non-prelim): 8
length of query: 357
length of database: 14,973,337
effective HSP length: 100
effective length of query: 257
effective length of database: 8,715,537
effective search space: 2239893009
effective search space used: 2239893009
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: 52 (24.6 bits)