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= 006516
(642 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3LAT|A Chain A, Crystal Structure Of Staphylococcus Peptidoglycan
Hydrolase Amie
pdb|3LAT|B Chain B, Crystal Structure Of Staphylococcus Peptidoglycan
Hydrolase Amie
Length = 213
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 24/66 (36%), Positives = 33/66 (50%), Gaps = 7/66 (10%)
Query: 226 EVDGTVTTQPVLEHVGISTWPGRLTLTDHALYFEAHRVVSYEKAKIYDLAEDLKQVVKPE 285
E DG T V H IS + G TDHA + R +Y A++YDL + K ++K +
Sbjct: 155 ENDGRGT---VWTHAAISNFLGG---TDHADPHQYLRSHNYSYAELYDLIYE-KYLIKTK 207
Query: 286 LTGPWG 291
PWG
Sbjct: 208 QVAPWG 213
>pdb|4AEF|A Chain A, The Crystal Structure Of Thermostable Amylase From The
Pyrococcus
pdb|4AEF|B Chain B, The Crystal Structure Of Thermostable Amylase From The
Pyrococcus
Length = 645
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 3/46 (6%)
Query: 2 EVSSRTRNMLEGLVREGSFKWLLGSRSSFDDEFEEMERSPSAGRNW 47
E+ R + L+REGS+ +LLG ++F++ ME+ G+NW
Sbjct: 11 EIFGRVAEVEFSLIREGSYAYLLGDFNAFNEGSFRMEQE---GKNW 53
>pdb|3GV2|A Chain A, X-Ray Structure Of Hexameric Hiv-1 Ca
pdb|3GV2|B Chain B, X-Ray Structure Of Hexameric Hiv-1 Ca
pdb|3GV2|C Chain C, X-Ray Structure Of Hexameric Hiv-1 Ca
pdb|3GV2|D Chain D, X-Ray Structure Of Hexameric Hiv-1 Ca
pdb|3GV2|E Chain E, X-Ray Structure Of Hexameric Hiv-1 Ca
pdb|3GV2|F Chain F, X-Ray Structure Of Hexameric Hiv-1 Ca
Length = 342
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 48/99 (48%), Gaps = 9/99 (9%)
Query: 365 QAIQEISTANSVRCESLLMFNLCDQLPGGDLILETLANMSNLRELERTNKSVGGVG---M 421
QA QE+ A + E+LL+ N P IL+ L + L E+ + VGG M
Sbjct: 176 QASQEVKNAAT---ETLLVQNAN---PDCKTILKALGPGATLEEMMTACQGVGGTRPELM 229
Query: 422 YSISAMAMVSNLGFVFGPSSSNNSIEAGAGLVVGEIAVG 460
+ SA+ + +GF ++++ ++AG +VG I G
Sbjct: 230 SAQSAVGSIETIGFPGILAAADAMVKAGRITIVGYIRAG 268
>pdb|1VYU|A Chain A, Beta3 Subunit Of Voltage-Gated Ca2+-Channel
pdb|1VYU|B Chain B, Beta3 Subunit Of Voltage-Gated Ca2+-Channel
Length = 351
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 31/95 (32%), Positives = 43/95 (45%), Gaps = 6/95 (6%)
Query: 301 YKSVSLSEPIILEFPELKGHTRRDYWLAIIREILYAHRFINKFQITGVQRDEVLSK-AVL 359
Y V P++L P LKG+ D + + L HRF + IT V D L+K +VL
Sbjct: 156 YDVVPSXRPVVLVGPSLKGYEVTDXXQKALFDFL-KHRFDGRISITRVTADLSLAKRSVL 214
Query: 360 GILRLQAIQEISTANS----VRCESLLMFNLCDQL 390
+ I E S+A S V+ E +F L L
Sbjct: 215 NNPGKRTIIERSSARSSIAEVQSEIERIFELAKSL 249
>pdb|1VYT|A Chain A, Beta3 Subunit Complexed With Aid
pdb|1VYT|B Chain B, Beta3 Subunit Complexed With Aid
Length = 351
Score = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 31/95 (32%), Positives = 43/95 (45%), Gaps = 6/95 (6%)
Query: 301 YKSVSLSEPIILEFPELKGHTRRDYWLAIIREILYAHRFINKFQITGVQRDEVLSK-AVL 359
Y V P++L P LKG+ D + + L HRF + IT V D L+K +VL
Sbjct: 156 YDVVPSMRPVVLVGPSLKGYEVTDMMQKALFDFL-KHRFDGRISITRVTADLSLAKRSVL 214
Query: 360 GILRLQAIQEISTANS----VRCESLLMFNLCDQL 390
+ I E S+A S V+ E +F L L
Sbjct: 215 NNPGKRTIIERSSARSSIAEVQSEIERIFELAKSL 249
>pdb|1VYV|A Chain A, Beta4 Subunit Of Ca2+ Channel
pdb|1VYV|B Chain B, Beta4 Subunit Of Ca2+ Channel
Length = 359
Score = 29.6 bits (65), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 33/112 (29%), Positives = 46/112 (41%), Gaps = 6/112 (5%)
Query: 284 PELTGPWGTRLFDKAVFYKSVSLSEPIILEFPELKGHTRRDYWLAIIREILYAHRFINKF 343
P T ++ Y V P++L P LKG+ D + + L HRF +
Sbjct: 147 PTTTAKQKQKVTKHIPPYDVVPSXRPVVLVGPSLKGYEVTDXXQKALFDFL-KHRFDGRI 205
Query: 344 QITGVQRDEVLSK-AVLGILRLQAIQEISTANS----VRCESLLMFNLCDQL 390
IT V D L+K +VL +AI E S S V+ E +F L L
Sbjct: 206 SITRVTADISLAKRSVLNNPSKRAIIERSNTKSSLAEVQSEIERIFELARSL 257
>pdb|1T0J|B Chain B, Crystal Structure Of A Complex Between Voltage-Gated
Calcium Channel Beta2a Subunit And A Peptide Of The
Alpha1c Subunit
Length = 224
Score = 29.3 bits (64), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 35/80 (43%), Gaps = 2/80 (2%)
Query: 301 YKSVSLSEPIILEFPELKGHTRRDYWLAIIREILYAHRFINKFQITGVQRDEVLSK-AVL 359
Y V P++L P LKG+ D + + L HRF + IT V D L+K +VL
Sbjct: 19 YDVVPSMRPVVLVGPSLKGYEVTDMMQKALFDFL-KHRFEGRISITRVTADISLAKRSVL 77
Query: 360 GILRLQAIQEISTANSVRCE 379
AI E S S E
Sbjct: 78 NNPSKHAIIERSNTRSSLAE 97
>pdb|1T0H|B Chain B, Crystal Structure Of The Rattus Norvegicus Voltage Gated
Calcium Channel Beta Subunit Isoform 2a
Length = 224
Score = 28.9 bits (63), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 35/80 (43%), Gaps = 2/80 (2%)
Query: 301 YKSVSLSEPIILEFPELKGHTRRDYWLAIIREILYAHRFINKFQITGVQRDEVLSK-AVL 359
Y V P++L P LKG+ D + + L HRF + IT V D L+K +VL
Sbjct: 19 YDVVPSXRPVVLVGPSLKGYEVTDXXQKALFDFL-KHRFEGRISITRVTADISLAKRSVL 77
Query: 360 GILRLQAIQEISTANSVRCE 379
AI E S S E
Sbjct: 78 NNPSKHAIIERSNTRSSLAE 97
>pdb|4DEX|A Chain A, Crystal Structure Of The Voltage Dependent Calcium Channel
Beta-2 Subunit In Complex With The Cav2.2 I-Ii Linker
Length = 339
Score = 28.9 bits (63), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 35/80 (43%), Gaps = 2/80 (2%)
Query: 301 YKSVSLSEPIILEFPELKGHTRRDYWLAIIREILYAHRFINKFQITGVQRDEVLSK-AVL 359
Y V P++L P LKG+ D + + L HRF + IT V D L+K +VL
Sbjct: 138 YDVVPSMRPVVLVGPSLKGYEVTDMMQKALFDFL-KHRFEGRISITRVTADISLAKRSVL 196
Query: 360 GILRLQAIQEISTANSVRCE 379
AI E S S E
Sbjct: 197 NNPSKHAIIERSNTRSSLAE 216
>pdb|4DEY|A Chain A, Crystal Structure Of The Voltage Dependent Calcium Channel
Beta-2 Subunit In Complex With The Cav1.2 I-Ii Linker
Length = 337
Score = 28.9 bits (63), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 35/80 (43%), Gaps = 2/80 (2%)
Query: 301 YKSVSLSEPIILEFPELKGHTRRDYWLAIIREILYAHRFINKFQITGVQRDEVLSK-AVL 359
Y V P++L P LKG+ D + + L HRF + IT V D L+K +VL
Sbjct: 136 YDVVPSMRPVVLVGPSLKGYEVTDMMQKALFDFL-KHRFEGRISITRVTADISLAKRSVL 194
Query: 360 GILRLQAIQEISTANSVRCE 379
AI E S S E
Sbjct: 195 NNPSKHAIIERSNTRSSLAE 214
>pdb|1SXJ|C Chain C, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 340
Score = 28.9 bits (63), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 47/105 (44%), Gaps = 15/105 (14%)
Query: 277 DLKQVVKPELTGPWGTRLF--DKAVFYKSVSLSEPI-----ILEFPELKGHTRRDYWLAI 329
DLK V+K L WGT + +K K ++L + I ILE EL+ R + L
Sbjct: 243 DLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLLTK 302
Query: 330 IREILYAHRFINKFQITGVQRDEVLSKAVLGILRLQAIQEISTAN 374
+ +I Y+ I+ D++ AV+G ++ E AN
Sbjct: 303 LADIEYS--------ISKGGNDQIQGSAVIGAIKASFENETVKAN 339
>pdb|1T3L|A Chain A, Structural Analysis Of The Voltage-Dependent Calcium
Channel Beta Subunit Functional Core In Complex With
Alpha1 Interaction Domain
pdb|1T3S|A Chain A, Structural Analysis Of The Voltage-Dependent Calcium
Channel Beta Subunit Functional Core
Length = 337
Score = 28.9 bits (63), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 43/148 (29%), Positives = 58/148 (39%), Gaps = 23/148 (15%)
Query: 236 VLEHVGISTWPGRLTLTDHALYFEAHRVVSYEKAKIYDLAEDLKQVV---KPELTGPWGT 292
V E I P R+ L + L E ++AK + L K++ K E T P
Sbjct: 86 VKEGCEIGFIPSRVKLENMRLQHE-------QRAKEFKLHSKEKRMPFFKKTEHTPP--- 135
Query: 293 RLFDKAVFYKSVSLSEPIILEFPELKGHTRRDYWLAIIREILYAHRFINKFQITGVQRDE 352
Y V P++L P LKG+ D + + L HRF + IT V D
Sbjct: 136 --------YDVVPSMRPVVLVGPSLKGYEVTDMMQKALFDFL-KHRFEGRISITRVTADI 186
Query: 353 VLSK-AVLGILRLQAIQEISTANSVRCE 379
L+K +VL AI E S S E
Sbjct: 187 SLAKRSVLNNPSKHAIIERSNTRSSLAE 214
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
0.320 0.135 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,521,333
Number of Sequences: 62578
Number of extensions: 607927
Number of successful extensions: 1470
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1470
Number of HSP's gapped (non-prelim): 14
length of query: 642
length of database: 14,973,337
effective HSP length: 105
effective length of query: 537
effective length of database: 8,402,647
effective search space: 4512221439
effective search space used: 4512221439
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: 55 (25.8 bits)