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= psy1676
(343 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4B4T|S Chain S, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 523
Score = 236 bits (602), Expect = 1e-62, Method: Compositional matrix adjust.
Identities = 122/311 (39%), Positives = 202/311 (64%), Gaps = 12/311 (3%)
Query: 8 NRRTSDLIAAKCYFYHSRVHEL---------TNNLDKV-RSFLNARLRIATLRNDFEGQA 57
N R+ +LI AK +FY HE ++N + + RS + L+IA+L++D E +A
Sbjct: 172 NLRSLNLINAKLWFYIYLSHETLARSSEEINSDNQNIILRSTMMKFLKIASLKHDNETKA 231
Query: 58 VLINCLLRNYLHYNLYDQADKLVKKSAFPE-NASNNEWARFHFYLGRIKAVRLEYSTAHK 116
+LIN +LR++L+ D A + K +P + S++ AR+ FYL +I A++L+YSTA++
Sbjct: 232 MLINLILRDFLNNGEVDSASDFISKLEYPHTDVSSSLEARYFFYLSKINAIQLDYSTANE 291
Query: 117 NLVQALRKAPQTA-AVGFRQTTQKLAVVVELLLGDIPDRQIFRQAVLRRALSPYFQLTQA 175
++ A+RKAP + ++GF Q + KL ++LL+GDIP+ F Q+ ++++L PY+ LT+A
Sbjct: 292 YIIAAIRKAPHNSKSLGFLQQSNKLHCCIQLLMGDIPELSFFHQSNMQKSLLPYYHLTKA 351
Query: 176 VRMGELQKFNEVLTTYGNQFRTDYTFKLILRLRHNVIKTAIRSIGASYSRITPTKIAEKL 235
V++G+L+KF +T Y D T++L +RLR NVIKT IR I +Y +I+ I KL
Sbjct: 352 VKLGDLKKFTSTITKYKQLLLKDDTYQLCVRLRSNVIKTGIRIISLTYKKISLRDICLKL 411
Query: 236 GLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESADIYCTVEPQLAFHQRIAFCLDL 295
L+S + E+++++AIRDGVIEA ++ E G++++ E +IY + +PQ F +RI F L
Sbjct: 412 NLDSEQTVEYMVSRAIRDGVIEAKINHEDGFIETTELLNIYDSEDPQQVFDERIKFANQL 471
Query: 296 HNQSVKAMRYP 306
H++ + +MRYP
Sbjct: 472 HDEYLVSMRYP 482
>pdb|1RZ7|H Chain H, Crystal Structure Of Human Anti-Hiv-1 Gp120-Reactive
Antibody 48d
pdb|4DVR|H Chain H, Crystal Structure Of Yu2 Gp120 Core In Complex With Fab
48d And Nbd- 557
Length = 219
Score = 35.8 bits (81), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 13/84 (15%)
Query: 211 VIKTAIRSIGASYS-------RITPTKIAEKLGLESPEDAEFIIAKAIRDGV-IEATLDR 262
+K + ++ G ++S R P K E +GL PEDA+ + A+ R V I A
Sbjct: 17 TVKISCKASGYTFSDFYMYWVRQAPGKGLEWMGLIDPEDADTMYAEKFRGRVTITADTST 76
Query: 263 EKGYMQ-----SKESADIYCTVEP 281
+ GY++ S+++A YC +P
Sbjct: 77 DTGYLELSSLRSEDTAVYYCAADP 100
>pdb|3JWD|H Chain H, Structure Of Hiv-1 Gp120 With Gp41-Interactive Region:
Layered Architecture And Basis Of Conformational
Mobility
pdb|3JWD|P Chain P, Structure Of Hiv-1 Gp120 With Gp41-Interactive Region:
Layered Architecture And Basis Of Conformational
Mobility
pdb|3JWO|H Chain H, Structure Of Hiv-1 Gp120 With Gp41-Interactive Region:
Layered Architecture And Basis Of Conformational
Mobility
Length = 220
Score = 35.8 bits (81), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 13/84 (15%)
Query: 211 VIKTAIRSIGASYS-------RITPTKIAEKLGLESPEDAEFIIAKAIRDGV-IEATLDR 262
+K + ++ G ++S R P K E +GL PEDA+ + A+ R V I A
Sbjct: 17 TVKISCKASGYTFSDFYMYWVRQAPGKGLEWMGLIDPEDADTMYAEKFRGRVTITADTST 76
Query: 263 EKGYMQ-----SKESADIYCTVEP 281
+ GY++ S+++A YC +P
Sbjct: 77 DTGYLELSSLRSEDTAVYYCAADP 100
>pdb|3IZS|EE Chain e, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|G Chain G, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|G Chain G, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|F Chain F, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|F Chain F, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|F Chain F, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 244
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 32/96 (33%), Positives = 47/96 (48%), Gaps = 7/96 (7%)
Query: 101 LGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELL-LGDIP--DRQIF 157
L R A + EY TA +N++QA R A + A + + KL VV + + IP R++
Sbjct: 45 LERNAAYQKEYETAERNIIQAKRDA-KAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVL 103
Query: 158 RQAVLRRALSPYF-QLTQAVRMGELQKFNEVLTTYG 192
+ L R S F ++T+A EL K E YG
Sbjct: 104 QLLRLTRINSGTFVKVTKATL--ELLKLIEPYVAYG 137
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 0.135 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,739,054
Number of Sequences: 62578
Number of extensions: 316357
Number of successful extensions: 922
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 913
Number of HSP's gapped (non-prelim): 11
length of query: 343
length of database: 14,973,337
effective HSP length: 100
effective length of query: 243
effective length of database: 8,715,537
effective search space: 2117875491
effective search space used: 2117875491
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: 52 (24.6 bits)