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= psy4339
(303 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NF1|A Chain A, Crystal Structure Of The Tpr Domain Of Kinesin Light Chain
1
Length = 311
Score = 51.6 bits (122), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 45/161 (27%), Positives = 79/161 (49%), Gaps = 11/161 (6%)
Query: 44 LYVNEYSSGRFTESRRHAEKAIQTFKNLLPENHLLLTSAHRVKALILEEIALDSNELISV 103
L + S GR+ + ++A++ + +H + + + AL+ D N+
Sbjct: 33 LVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYR----DQNK---- 84
Query: 104 QFYKEAELLHQNALVLSLKHFGENNVQTAKHYGNIGRLYQSMQKFDEAERMQLKAIAIKE 163
YK+A L +AL + K G+++ A N+ LY K+ EAE + +A+ I+E
Sbjct: 85 --YKDAANLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIRE 142
Query: 164 KVLGKDDYEVGLSVGHLASLYNYHMLEYHKAEKLYFRSIEI 204
KVLGKD +V + +LA L + +Y + E Y R++EI
Sbjct: 143 KVLGKDHPDVAKQLNNLALLCQ-NQGKYEEVEYYYQRALEI 182
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 33/93 (35%), Positives = 50/93 (53%), Gaps = 1/93 (1%)
Query: 106 YKEAELLHQNALVLSLKHFGENNVQTAKHYGNIGRLYQSMQKFDEAERMQLKAIAIKEKV 165
YKEAE L + AL + K G+++ AK N+ L Q+ K++E E +A+ I +
Sbjct: 127 YKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTK 186
Query: 166 LGKDDYEVGLSVGHLASLYNYHMLEYHKAEKLY 198
LG DD V + +LAS Y ++ +AE LY
Sbjct: 187 LGPDDPNVAKTKNNLASCY-LKQGKFKQAETLY 218
>pdb|3CEQ|A Chain A, The Tpr Domain Of Human Kinesin Light Chain 2 (Hklc2)
pdb|3CEQ|B Chain B, The Tpr Domain Of Human Kinesin Light Chain 2 (Hklc2)
Length = 283
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 34/99 (34%), Positives = 53/99 (53%), Gaps = 1/99 (1%)
Query: 106 YKEAELLHQNALVLSLKHFGENNVQTAKHYGNIGRLYQSMQKFDEAERMQLKAIAIKEKV 165
YKEA L +AL + K G+++ A N+ LY K+ EAE + +A+ I+EKV
Sbjct: 59 YKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKV 118
Query: 166 LGKDDYEVGLSVGHLASLYNYHMLEYHKAEKLYFRSIEI 204
LGK +V + +LA L + + + E Y R++EI
Sbjct: 119 LGKFHPDVAKQLSNLALLCQ-NQGKAEEVEYYYRRALEI 156
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 34/93 (36%), Positives = 46/93 (49%), Gaps = 1/93 (1%)
Query: 106 YKEAELLHQNALVLSLKHFGENNVQTAKHYGNIGRLYQSMQKFDEAERMQLKAIAIKEKV 165
YKEAE L + AL + K G+ + AK N+ L Q+ K +E E +A+ I
Sbjct: 101 YKEAEPLCKRALEIREKVLGKFHPDVAKQLSNLALLCQNQGKAEEVEYYYRRALEIYATR 160
Query: 166 LGKDDYEVGLSVGHLASLYNYHMLEYHKAEKLY 198
LG DD V + +LAS Y +Y AE LY
Sbjct: 161 LGPDDPNVAKTKNNLASCY-LKQGKYQDAETLY 192
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 33/109 (30%), Positives = 55/109 (50%), Gaps = 6/109 (5%)
Query: 141 LYQSMQKFDEAERMQLKAIAIKEKVLGKDDYEVGLSVGHLASLYNYHMLEYHKAEKLYFR 200
+Y+ K+ EA + A+AI+EK LGKD V ++ +LA LY +Y +AE L R
Sbjct: 52 VYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRG-KYKEAEPLCKR 110
Query: 201 SIEINDNLKLFSASYSGLEYHYRDLKLFSASYSG---LEYDYRGLIHVY 246
++EI + K+ + + +L L + +EY YR + +Y
Sbjct: 111 ALEIRE--KVLGKFHPDVAKQLSNLALLCQNQGKAEEVEYYYRRALEIY 157
>pdb|3EDT|B Chain B, Crystal Structure Of The Mutated S328n Hklc2 Tpr Domain
pdb|3EDT|D Chain D, Crystal Structure Of The Mutated S328n Hklc2 Tpr Domain
pdb|3EDT|F Chain F, Crystal Structure Of The Mutated S328n Hklc2 Tpr Domain
pdb|3EDT|H Chain H, Crystal Structure Of The Mutated S328n Hklc2 Tpr Domain
Length = 283
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 34/99 (34%), Positives = 53/99 (53%), Gaps = 1/99 (1%)
Query: 106 YKEAELLHQNALVLSLKHFGENNVQTAKHYGNIGRLYQSMQKFDEAERMQLKAIAIKEKV 165
YKEA L +AL + K G+++ A N+ LY K+ EAE + +A+ I+EKV
Sbjct: 59 YKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKV 118
Query: 166 LGKDDYEVGLSVGHLASLYNYHMLEYHKAEKLYFRSIEI 204
LGK +V + +LA L + + + E Y R++EI
Sbjct: 119 LGKFHPDVAKQLNNLALLCQ-NQGKAEEVEYYYRRALEI 156
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 34/93 (36%), Positives = 46/93 (49%), Gaps = 1/93 (1%)
Query: 106 YKEAELLHQNALVLSLKHFGENNVQTAKHYGNIGRLYQSMQKFDEAERMQLKAIAIKEKV 165
YKEAE L + AL + K G+ + AK N+ L Q+ K +E E +A+ I
Sbjct: 101 YKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATR 160
Query: 166 LGKDDYEVGLSVGHLASLYNYHMLEYHKAEKLY 198
LG DD V + +LAS Y +Y AE LY
Sbjct: 161 LGPDDPNVAKTKNNLASCY-LKQGKYQDAETLY 192
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 33/109 (30%), Positives = 55/109 (50%), Gaps = 6/109 (5%)
Query: 141 LYQSMQKFDEAERMQLKAIAIKEKVLGKDDYEVGLSVGHLASLYNYHMLEYHKAEKLYFR 200
+Y+ K+ EA + A+AI+EK LGKD V ++ +LA LY +Y +AE L R
Sbjct: 52 VYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRG-KYKEAEPLCKR 110
Query: 201 SIEINDNLKLFSASYSGLEYHYRDLKLFSASYSG---LEYDYRGLIHVY 246
++EI + K+ + + +L L + +EY YR + +Y
Sbjct: 111 ALEIRE--KVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIY 157
>pdb|3B5X|A Chain A, Crystal Structure Of Msba From Vibrio Cholerae
pdb|3B5X|B Chain B, Crystal Structure Of Msba From Vibrio Cholerae
Length = 582
Score = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 36/108 (33%), Positives = 54/108 (50%), Gaps = 12/108 (11%)
Query: 25 LFGSENLQVAIAEDEL--AYALYVNEYSSGRFTESRRHAEKAIQTFKNLLPENHLLLTSA 82
L G + +VAIA L A L ++E +S TES E+AIQ + L +N +L A
Sbjct: 481 LSGGQRQRVAIARALLRDAPVLILDEATSALDTES----ERAIQAALDELQKNKTVLVIA 536
Query: 83 HRVKAL--ILEEIALDSNELISVQFYKEAELLHQNALVLSLK--HFGE 126
HR+ + E + +D E+I + + A+LL Q+ L FGE
Sbjct: 537 HRLSTIEQADEILVVDEGEII--ERGRHADLLAQDGAYAQLHRIQFGE 582
>pdb|3QWV|A Chain A, Crystal Structure Of Histone Lysine Methyltransferase
Smyd2 In Complex With The Cofactor Product Adohcy
pdb|3QWW|A Chain A, Crystal Structure Of Histone Lysine Methyltransferase
Smyd2 In Complex With The Methyltransferase Inhibitor
Sinefungin
Length = 433
Score = 31.2 bits (69), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%)
Query: 122 KHFGENNVQTAKHYGNIGRLYQSMQKFDEAERMQLKAIAIKEKVLGKD 169
KH+ ++ A + +GRLY ++ E+ KAIAI E GKD
Sbjct: 372 KHYPVYSLNVASMWLKLGRLYMGLENKAAGEKALKKAIAIMEVAHGKD 419
>pdb|3S7B|A Chain A, Structural Basis Of Substrate Methylation And Inhibition
Of Smyd2
pdb|3S7D|A Chain A, Structural Basis Of Substrate Methylation And Inhibition
Of Smyd2
pdb|3S7F|A Chain A, Structural Basis Of Substrate Methylation And Inhibition
Of Smyd2
pdb|3S7J|A Chain A, Structural Basis Of Substrate Methylation And Inhibition
Of Smyd2
Length = 433
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%)
Query: 122 KHFGENNVQTAKHYGNIGRLYQSMQKFDEAERMQLKAIAIKEKVLGKD 169
KH+ ++ A + +GRLY ++ E+ KAIAI E GKD
Sbjct: 372 KHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKD 419
>pdb|3RIB|A Chain A, Human Lysine Methyltransferase Smyd2 In Complex With
Adohcy
pdb|3RIB|B Chain B, Human Lysine Methyltransferase Smyd2 In Complex With
Adohcy
Length = 441
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%)
Query: 122 KHFGENNVQTAKHYGNIGRLYQSMQKFDEAERMQLKAIAIKEKVLGKD 169
KH+ ++ A + +GRLY ++ E+ KAIAI E GKD
Sbjct: 372 KHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKD 419
>pdb|3TG4|A Chain A, Structure Of Smyd2 In Complex With Sam
pdb|3TG5|A Chain A, Structure Of Smyd2 In Complex With P53 And Sah
Length = 433
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%)
Query: 122 KHFGENNVQTAKHYGNIGRLYQSMQKFDEAERMQLKAIAIKEKVLGKD 169
KH+ ++ A + +GRLY ++ E+ KAIAI E GKD
Sbjct: 372 KHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKD 419
>pdb|4A3Q|A Chain A, The 2.15 Angstrom Resolution Crystal Structure Of
Staphylococcus Aureus Alanine Racemase
pdb|4A3Q|B Chain B, The 2.15 Angstrom Resolution Crystal Structure Of
Staphylococcus Aureus Alanine Racemase
Length = 382
Score = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 106 YKEAELLHQNALVLSL---KHFGENNVQTAKHYGNIGRLYQSMQKFDEAERMQLKAIAIK 162
+K LH N V+++ +G +V+ A+H G + ++ DEA +++ I K
Sbjct: 22 FKVFSTLHPNKTVMAVVKANAYGLGSVKVARHLMENGATFFAVATLDEAIELRMHGITAK 81
Query: 163 EKVLG 167
VLG
Sbjct: 82 ILVLG 86
>pdb|3OO2|A Chain A, 2.37 Angstrom Resolution Crystal Structure Of An Alanine
Racemase (Alr) From Staphylococcus Aureus Subsp. Aureus
Col
pdb|3OO2|B Chain B, 2.37 Angstrom Resolution Crystal Structure Of An Alanine
Racemase (Alr) From Staphylococcus Aureus Subsp. Aureus
Col
Length = 385
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 106 YKEAELLHQNALVLSL---KHFGENNVQTAKHYGNIGRLYQSMQKFDEAERMQLKAIAIK 162
+K LH N V+++ +G +V+ A+H G + ++ DEA +++ I K
Sbjct: 25 FKVFSTLHPNKTVMAVVKANAYGLGSVKVARHLMENGATFFAVATLDEAIELRMHGITAK 84
Query: 163 EKVLG 167
VLG
Sbjct: 85 ILVLG 89
>pdb|2HMJ|A Chain A, Crystal Structure Of The Naphthalene 1,2-Dioxygenase
Phe-352-Val Mutant.
pdb|2HML|A Chain A, Crystal Structure Of The Naphthalene 1,2-Dioxygenase F352v
Mutant Bound To Phenanthrene.
pdb|2HMN|A Chain A, Crystal Structure Of The Naphthalene 1,2-Dioxygenase F352v
Mutant Bound To Anthracene
Length = 449
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 32/81 (39%), Gaps = 18/81 (22%)
Query: 203 EINDNLKLFSASYSGLEYHYRDLKLFS-----------ASYSGL-------EYDYRGLIH 244
E +DN + +AS +G +Y RD L S A Y G+ E YRG
Sbjct: 359 ESDDNDNMETASQNGKKYQSRDSDLLSNLGFGEDVYGDAVYPGVVGKSAIGETSYRGFYR 418
Query: 245 VYECLENFEKMTEFTNKLSEW 265
Y+ + EF + S W
Sbjct: 419 AYQAHVSSSNWAEFEHASSTW 439
>pdb|1NDO|A Chain A, Napthalene 1,2-Dioxygenase
pdb|1NDO|C Chain C, Napthalene 1,2-Dioxygenase
pdb|1NDO|E Chain E, Napthalene 1,2-Dioxygenase
pdb|1EG9|A Chain A, Naphthalene 1,2-Dioxygenase With Indole Bound In The
Active Site.
pdb|1O7M|A Chain A, Naphthalene 1,2-Dioxygenase, Binary Complex With Dioxygen
pdb|1O7N|A Chain A, Naphthalene 1,2-dioxygenase, Ternary Complex With Dioxygen
And Indole
pdb|1O7P|A Chain A, Naphthalene 1,2-Dioxygenase, Product Complex
pdb|1O7W|A Chain A, Naphthalene 1,2-Dioxygenase, Fully Reduced Form
pdb|1O7G|A Chain A, Naphthalene 1,2-Dioxygenase With Naphthalene Bound In The
Active Site.
pdb|1O7H|A Chain A, Naphthalene 1,2-Dioxygenase With Oxidized Rieske Iron
Sulphur Center Site.
pdb|1UUV|A Chain A, Naphthalene 1,2-Dioxygenase With Nitric Oxide And Indole
Bound In The Active Site.
pdb|1UUW|A Chain A, Naphthalene 1,2-dioxygenase With Nitric Oxide Bound In The
Active Site.
pdb|2HMK|A Chain A, Crystal Structure Of Naphthalene 1,2-Dioxygenase Bound To
Phenanthrene
pdb|2HMM|A Chain A, Crystal Structure Of Naphthalene 1,2-Dioxygenase Bound To
Anthracene
pdb|2HMO|A Chain A, Crystal Structure Of Naphthalene 1,2-Dioxygenase Bound To
3- Nitrotoluene
Length = 449
Score = 28.1 bits (61), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 32/81 (39%), Gaps = 18/81 (22%)
Query: 203 EINDNLKLFSASYSGLEYHYRDLKLFS-----------ASYSGL-------EYDYRGLIH 244
E +DN + +AS +G +Y RD L S A Y G+ E YRG
Sbjct: 359 ESDDNDNMETASQNGKKYQSRDSDLLSNLGFGEDVYGDAVYPGVVGKSAIGETSYRGFYR 418
Query: 245 VYECLENFEKMTEFTNKLSEW 265
Y+ + EF + S W
Sbjct: 419 AYQAHVSSSNWAEFEHASSTW 439
>pdb|3F1C|A Chain A, Crystal Structure Of 2-C-Methyl-D-Erythritol 4-Phosphate
Cytidylyltransferase From Listeria Monocytogenes
pdb|3F1C|B Chain B, Crystal Structure Of 2-C-Methyl-D-Erythritol 4-Phosphate
Cytidylyltransferase From Listeria Monocytogenes
Length = 246
Score = 27.7 bits (60), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 32/64 (50%)
Query: 55 TESRRHAEKAIQTFKNLLPENHLLLTSAHRVKALILEEIALDSNELISVQFYKEAELLHQ 114
T + +K ++NL PE +LT A ++ L +++ L E+ +++ +L
Sbjct: 169 TPQSFNMKKVFNHYQNLTPEKKQILTDACKICLLAGDDVKLVKGEIFNIKITTPYDLKVA 228
Query: 115 NALV 118
NA++
Sbjct: 229 NAII 232
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 0.133 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,858,918
Number of Sequences: 62578
Number of extensions: 365164
Number of successful extensions: 1010
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 992
Number of HSP's gapped (non-prelim): 27
length of query: 303
length of database: 14,973,337
effective HSP length: 98
effective length of query: 205
effective length of database: 8,840,693
effective search space: 1812342065
effective search space used: 1812342065
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)