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= 023597
(280 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2F15|A Chain A, Glycogen-Binding Domain Of The Amp-Activated Protein
Kinase Beta2 Subunit
Length = 96
Score = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 44/84 (52%)
Query: 97 AAITWSLGGKQVAVTGSWDNWENVDPLWRLGKDFVIMKMLPSGVYHYRFIVDECLRYAPD 156
I WS GGK+V ++GS++NW PL + DFV + LP G + Y+F VD + P
Sbjct: 12 TVIRWSEGGKEVFISGSFNNWSTKIPLIKSHNDFVAILDLPEGEHQYKFFVDGQWVHDPS 71
Query: 157 VPWECDDSGNAYNVLDLQEYIPEV 180
P G N++ +++ EV
Sbjct: 72 EPVVTSQLGTINNLIHVKKSDFEV 95
>pdb|1Z0M|A Chain A, The Glycogen-Binding Domain Of The Amp-Activated Protein
Kinase Beta1 Subunit
pdb|1Z0M|B Chain B, The Glycogen-Binding Domain Of The Amp-Activated Protein
Kinase Beta1 Subunit
pdb|1Z0M|C Chain C, The Glycogen-Binding Domain Of The Amp-Activated Protein
Kinase Beta1 Subunit
Length = 96
Score = 50.4 bits (119), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 101 WSLGGKQVAVTGSWDNWENVDPLWRLGKDFVIMKMLPSGVYHYRFIVDECLRYAPDVPWE 160
W+ GGK+V ++GS++NW + PL R +FV + LP G + Y+F VD + P P
Sbjct: 17 WTGGGKEVYLSGSFNNWSKL-PLTRSQNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIV 75
Query: 161 CDDSGNAYNVLDLQEYIPEV 180
G N++ +++ EV
Sbjct: 76 TSQLGTVNNIIQVKKTDFEV 95
>pdb|2QLV|B Chain B, Crystal Structure Of The Heterotrimer Core Of The S.
Cerevisiae Ampk Homolog Snf1
pdb|2QLV|E Chain E, Crystal Structure Of The Heterotrimer Core Of The S.
Cerevisiae Ampk Homolog Snf1
Length = 252
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 44/85 (51%), Gaps = 5/85 (5%)
Query: 95 VAAAITWSLGGKQVAVTGSWDNWENVDPLW----RLGKDFVIMKMLPSGVYHYRFIVDEC 150
V I W GG +V VTGS+ W + L G V +++LP G + +RFIVD
Sbjct: 4 VPVEIRWQQGGSKVYVTGSFTKWRKMIGLIPDSDNNGSFHVKLRLLP-GTHRFRFIVDNE 62
Query: 151 LRYAPDVPWECDDSGNAYNVLDLQE 175
LR + +P D GN N +++++
Sbjct: 63 LRVSDFLPTATDQMGNFVNYIEVRQ 87
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 8/82 (9%)
Query: 203 SDSDFAKL-PPELPPQLQITXXXXXXXXXXXXXXXXX------XHTVLNHLFIQNTDGRQ 255
S++D + L PP+LPPQL+ H VLNHL + ++
Sbjct: 171 SNTDTSWLTPPQLPPQLENVILNKYYATQDQFNENNSGALPIPNHVVLNHL-VTSSIKHN 229
Query: 256 PMAIGSTHRFRQKYATVVLYKP 277
+ + S R++QKY T +LY P
Sbjct: 230 TLCVASIVRYKQKYVTQILYTP 251
>pdb|1Z0N|A Chain A, The Glycogen-Binding Domain Of The Amp-Activated Protein
Kinase
pdb|1Z0N|B Chain B, The Glycogen-Binding Domain Of The Amp-Activated Protein
Kinase
pdb|1Z0N|C Chain C, The Glycogen-Binding Domain Of The Amp-Activated Protein
Kinase
Length = 96
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 43/80 (53%), Gaps = 1/80 (1%)
Query: 101 WSLGGKQVAVTGSWDNWENVDPLWRLGKDFVIMKMLPSGVYHYRFIVDECLRYAPDVPWE 160
W+ GGK+V ++GS++NW + P R +FV + LP G + Y+F VD + P P
Sbjct: 17 WTGGGKEVYLSGSFNNWSKL-PXTRSQNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIV 75
Query: 161 CDDSGNAYNVLDLQEYIPEV 180
G N++ +++ EV
Sbjct: 76 TSQLGTVNNIIQVKKTDFEV 95
>pdb|4EAK|B Chain B, Co-Crystal Structure Of An Ampk Core With Atp
pdb|4EAL|B Chain B, Co-Crystal Of Ampk Core With Atp Soaked With Amp
Length = 72
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 209 KLPPELPPQL-QITXXXXXXXXXXXXXXXXXXHTVLNHLF-IQNTDGRQPMAIGSTHRFR 266
K PP LPP L Q+ H +LNHL+ + DG M + +THR++
Sbjct: 3 KAPPILPPHLLQVILNKDTGISCDPALLPEPNHVMLNHLYALSIKDG--VMVLSATHRYK 60
Query: 267 QKYATVVLYKP 277
+KY T +LYKP
Sbjct: 61 KKYVTTLLYKP 71
>pdb|2V8Q|B Chain B, Crystal Structure Of The Regulatory Fragment Of Mammalian
Ampk In Complexes With Amp
pdb|2V92|B Chain B, Crystal Structure Of The Regulatory Fragment Of Mammalian
Ampk In Complexes With Atp-Amp
pdb|2V9J|B Chain B, Crystal Structure Of The Regulatory Fragment Of Mammalian
Ampk In Complexes With Mg.Atp-Amp
pdb|2Y8L|B Chain B, Structure Of The Regulatory Fragment Of Mammalian Ampk In
Complex With Two Adp
pdb|2Y8Q|B Chain B, Structure Of The Regulatory Fragment Of Mammalian Ampk In
Complex With One Adp
pdb|2Y94|B Chain B, Structure Of An Active Form Of Mammalian Ampk
pdb|2YA3|B Chain B, Structure Of The Regulatory Fragment Of Mammalian Ampk In
Complex With Coumarin Adp
Length = 87
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 209 KLPPELPPQL-QITXXXXXXXXXXXXXXXXXXHTVLNHLFIQNTDGRQPMAIGSTHRFRQ 267
K PP LPP L Q+ H +LNHL+ + M + +THR+++
Sbjct: 18 KSPPILPPHLLQVILNKDTNISCDPALLPEPNHVMLNHLYALSIKDSV-MVLSATHRYKK 76
Query: 268 KYATVVLYKP 277
KY T +LYKP
Sbjct: 77 KYVTTLLYKP 86
>pdb|4EAI|B Chain B, Co-Crystal Structure Of An Ampk Core With Amp
pdb|4EAJ|B Chain B, Co-Crystal Of Ampk Core With Amp Soaked With Atp
Length = 85
Score = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 209 KLPPELPPQL-QITXXXXXXXXXXXXXXXXXXHTVLNHLFIQNTDGRQPMAIGSTHRFRQ 267
K PP LPP L Q+ H +LNHL+ + M + +THR+++
Sbjct: 16 KSPPILPPHLLQVILNKDTNISCDPALLPEPNHVMLNHLYALSIKD-SVMVLSATHRYKK 74
Query: 268 KYATVVLYKP 277
KY T +LYKP
Sbjct: 75 KYVTTLLYKP 84
>pdb|4EAG|B Chain B, Co-Crystal Structure Of An Chimeric Ampk Core With Atp
Length = 85
Score = 41.2 bits (95), Expect = 7e-04, Method: Composition-based stats.
Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 209 KLPPELPPQL-QITXXXXXXXXXXXXXXXXXXHTVLNHLF-IQNTDGRQPMAIGSTHRFR 266
K PP LPP L Q+ H +LNHL+ + DG M + +THR++
Sbjct: 16 KAPPILPPHLLQVILNKDTGISCDPALLPEPNHVMLNHLYALSIKDG--VMVLSATHRYK 73
Query: 267 QKYATVVLYKP 277
+KY T +LYKP
Sbjct: 74 KKYVTTLLYKP 84
>pdb|3T4N|B Chain B, Structure Of The Regulatory Fragment Of Saccharomyces
Cerevisiae Ampk In Complex With Adp
pdb|3TDH|B Chain B, Structure Of The Regulatory Fragment Of Sccharomyces
Cerevisiae Ampk In Complex With Amp
pdb|3TE5|B Chain B, Structure Of The Regulatory Fragment Of Sacchromyces
Cerevisiae Ampk In Complex With Nadh
Length = 113
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 8/82 (9%)
Query: 203 SDSDFAKL-PPELPPQLQITXXXXXXXXXXXXXXXXX------XHTVLNHLFIQNTDGRQ 255
S++D + L PP+LPPQL+ H VLNHL + ++
Sbjct: 29 SNTDTSWLTPPQLPPQLENVILNKYYATQDQFNENNSGALPIPNHVVLNHL-VTSSIKHN 87
Query: 256 PMAIGSTHRFRQKYATVVLYKP 277
+ + S R++QKY T +LY P
Sbjct: 88 TLCVASIVRYKQKYVTQILYTP 109
>pdb|4I79|A Chain A, Crystal Structure Of Human Nup43
pdb|4I79|B Chain B, Crystal Structure Of Human Nup43
Length = 399
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 102 SLGGKQVAVTGSWDNWENVDPLWRLGKDF 130
SL + TGSWDN EN LW +G DF
Sbjct: 44 SLQTAETFATGSWDNEENYISLWSIG-DF 71
>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 = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 18/32 (56%)
Query: 127 GKDFVIMKMLPSGVYHYRFIVDECLRYAPDVP 158
GK++ I LP GV+HY F +D PD P
Sbjct: 50 GKNWKIKIALPEGVWHYAFSIDGKFVLDPDNP 81
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
0.317 0.136 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,485,831
Number of Sequences: 62578
Number of extensions: 326635
Number of successful extensions: 581
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 565
Number of HSP's gapped (non-prelim): 16
length of query: 280
length of database: 14,973,337
effective HSP length: 98
effective length of query: 182
effective length of database: 8,840,693
effective search space: 1609006126
effective search space used: 1609006126
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)