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= psy1723
(246 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WGM|A Chain A, Solution Structure Of The U-Box In Human Ubiquitin
Conjugation Factor E4a
Length = 98
Score = 116 bits (290), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 54/84 (64%), Positives = 70/84 (83%)
Query: 161 QSDEALLAGAPDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSDQTDPFNRSPLTM 220
Q +E A A DE+LDPIM+T+M +PV LPSSR T+D+STIARHLLSDQTDPFNRSPLTM
Sbjct: 10 QQEEETYADACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTM 69
Query: 221 EQVIPNTQLQTQIQDWIRQCRQKS 244
+Q+ PNT+L+ +IQ W+ + +Q+S
Sbjct: 70 DQIRPNTELKEKIQRWLAERKQQS 93
>pdb|3M62|A Chain A, Crystal Structure Of Ufd2 In Complex With The
Ubiquitin-Like (Ubl) Domain Of Rad23
pdb|3M63|A Chain A, Crystal Structure Of Ufd2 In Complex With The
Ubiquitin-Like (Ubl) Domain Of Dsk2
Length = 968
Score = 101 bits (251), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 66/216 (30%), Positives = 103/216 (47%), Gaps = 13/216 (6%)
Query: 42 LGNETIHTLEYLTSEIRSIFCHSTMVDRIAAMLNYFLFHLVGPKMRNFKTSRRSPGKQEG 101
L ++++ E + +I + F +V R+A+MLNY L LVGPK K
Sbjct: 747 LADKSMKLFEIYSKDIPAAFVTPEIVYRLASMLNYNLESLVGPKCGELKVKDPQSYSFNP 806
Query: 102 VGSIPAERKLKLNISTXXXXXXXXXXXX----------XXXXXARIGGASLIPDLRRVAV 151
+ A + +N+S R G + + ++
Sbjct: 807 KDLLKALTTVYINLSEQSEFISAVAKDERSFNRNLFVRAVDILGRKTGLASPEFIEKLLN 866
Query: 152 LVEKLGAQLQSDEAL---LAGAPDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSD 208
K Q ++DE PDE+LDP+M TIM +PV LP+S+ +D+STI HLLSD
Sbjct: 867 FANKAEEQRKADEEEDLEYGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSD 926
Query: 209 QTDPFNRSPLTMEQVIPNTQLQTQIQDWIRQCRQKS 244
TDPFNR PL +E V PN +L+ +I + +Q ++++
Sbjct: 927 STDPFNRMPLKLEDVTPNEELRQKILCFKKQKKEEA 962
>pdb|2QIZ|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 101 bits (251), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 66/216 (30%), Positives = 103/216 (47%), Gaps = 13/216 (6%)
Query: 42 LGNETIHTLEYLTSEIRSIFCHSTMVDRIAAMLNYFLFHLVGPKMRNFKTSRRSPGKQEG 101
L ++++ E + +I + F +V R+A+MLNY L LVGPK K
Sbjct: 761 LADKSMKLFEIYSKDIPAAFVTPEIVYRLASMLNYNLESLVGPKCGELKVKDPQSYSFNP 820
Query: 102 VGSIPAERKLKLNISTXXXXXXXXXXXX----------XXXXXARIGGASLIPDLRRVAV 151
+ A + +N+S R G + + ++
Sbjct: 821 KDLLKALTTVYINLSEQSEFISAVAKDERSFNRNLFVRAVDILGRKTGLASPEFIEKLLN 880
Query: 152 LVEKLGAQLQSDEAL---LAGAPDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSD 208
K Q ++DE PDE+LDP+M TIM +PV LP+S+ +D+STI HLLSD
Sbjct: 881 FANKAEEQRKADEEEDLEYGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSD 940
Query: 209 QTDPFNRSPLTMEQVIPNTQLQTQIQDWIRQCRQKS 244
TDPFNR PL +E V PN +L+ +I + +Q ++++
Sbjct: 941 STDPFNRMPLKLEDVTPNEELRQKILCFKKQKKEEA 976
>pdb|2QJ0|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 92.0 bits (227), Expect = 3e-19, Method: Composition-based stats.
Identities = 63/216 (29%), Positives = 99/216 (45%), Gaps = 13/216 (6%)
Query: 42 LGNETIHTLEYLTSEIRSIFCHSTMVDRIAAMLNYFLFHLVGPKMRNFKTSRRSPGKQEG 101
L +++ E + +I + F +V R+A+ LNY L LVGPK K
Sbjct: 761 LADKSXKLFEIYSKDIPAAFVTPEIVYRLASXLNYNLESLVGPKCGELKVKDPQSYSFNP 820
Query: 102 VGSIPAERKLKLNISTXXXXXXXXXX----------XXXXXXXARIGGASLIPDLRRVAV 151
+ A + +N+S R G + + ++
Sbjct: 821 KDLLKALTTVYINLSEQSEFISAVAKDERSFNRNLFVRAVDILGRKTGLASPEFIEKLLN 880
Query: 152 LVEKLGAQLQSDEAL---LAGAPDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSD 208
K Q ++DE PDE+LDP+ TI +PV LP+S+ +D+STI HLLSD
Sbjct: 881 FANKAEEQRKADEEEDLEYGDVPDEFLDPLXYTIXKDPVILPASKXNIDRSTIKAHLLSD 940
Query: 209 QTDPFNRSPLTMEQVIPNTQLQTQIQDWIRQCRQKS 244
TDPFNR PL +E V PN +L+ +I + +Q ++++
Sbjct: 941 STDPFNRXPLKLEDVTPNEELRQKILCFKKQKKEEA 976
>pdb|2KRE|A Chain A, Solution Structure Of E4bUFD2A U-Box Domain
pdb|3L1X|A Chain A, Crystal Structure Of U-Box Domain Of Human E4b Ubiquitin
Ligase
pdb|3L1Z|B Chain B, Crystal Structure Of The U-Box Domain Of Human E4b
Ubiquitin Ligase In Complex With Ubch5c E2 Ubiquitin
Conjugating Enzyme
Length = 100
Score = 77.4 bits (189), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 41/92 (44%), Positives = 59/92 (64%), Gaps = 1/92 (1%)
Query: 148 RVAVLVEKLGAQLQSDEALLAGAPDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLS 207
+ A VE++ A+ E + APDE+ DP+M+T+M +PV LPS +D+S I RHLL+
Sbjct: 4 KFAEKVEEIVAKNARAEIDYSDAPDEFRDPLMDTLMTDPVRLPSG-TIMDRSIILRHLLN 62
Query: 208 DQTDPFNRSPLTMEQVIPNTQLQTQIQDWIRQ 239
TDPFNR LT + P +L+ QIQ W+R+
Sbjct: 63 SPTDPFNRQTLTESMLEPVPELKEQIQAWMRE 94
>pdb|2KR4|A Chain A, U-Box Domain Of The E3 Ubiquitin Ligase E4b
Length = 85
Score = 72.8 bits (177), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 38/78 (48%), Positives = 52/78 (66%), Gaps = 1/78 (1%)
Query: 162 SDEALLAGAPDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSDQTDPFNRSPLTME 221
S E + APDE+ DP+M+T+M +PV LPS +D+S I RHLL+ TDPFNR LT
Sbjct: 3 SAEIDYSDAPDEFRDPLMDTLMTDPVRLPSG-TVMDRSIILRHLLNSPTDPFNRQMLTES 61
Query: 222 QVIPNTQLQTQIQDWIRQ 239
+ P +L+ QIQ W+R+
Sbjct: 62 MLEPVPELKEQIQAWMRE 79
>pdb|2OXQ|C Chain C, Structure Of The Ubch5 :chip U-Box Complex
pdb|2OXQ|D Chain D, Structure Of The Ubch5 :chip U-Box Complex
Length = 80
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 171 PDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLS-DQTDPFNRSPLTMEQVIPNTQL 229
PD I +M EP PS T D+ I HL DP RSPLT +Q+IPN +
Sbjct: 11 PDYLCGKISFELMAEPCITPSGI-TYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNLAM 69
Query: 230 QTQIQDWIRQ 239
+ I +I++
Sbjct: 70 KEVIDAFIQE 79
>pdb|2C2L|A Chain A, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
pdb|2C2L|B Chain B, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
pdb|2C2L|C Chain C, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
pdb|2C2L|D Chain D, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
Length = 281
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 33/68 (48%), Gaps = 2/68 (2%)
Query: 171 PDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLS-DQTDPFNRSPLTMEQVIPNTQL 229
PD I +M EP PS T D+ I HL +P RSPLT EQ+IPN +
Sbjct: 206 PDYLCGKISFELMREPCITPSG-ITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAM 264
Query: 230 QTQIQDWI 237
+ I +I
Sbjct: 265 KEVIDAFI 272
>pdb|2F42|A Chain A, Dimerization And U-Box Domains Of Zebrafish C-Terminal Of
Hsp70 Interacting Protein
Length = 179
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 171 PDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLS-DQTDPFNRSPLTMEQVIPNTQL 229
PD I +M EP PS T D+ I HL DP RSPLT +Q+IPN +
Sbjct: 104 PDYLCGKISFELMREPCITPSG-ITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNLAM 162
Query: 230 QTQIQDWIRQ 239
+ I +I++
Sbjct: 163 KEVIDAFIQE 172
>pdb|2C2V|S Chain S, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
pdb|2C2V|T Chain T, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
pdb|2C2V|U Chain U, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
pdb|2C2V|V Chain V, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
Length = 78
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 171 PDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLS-DQTDPFNRSPLTMEQVIPNTQL 229
PD I +M EP PS T D+ I HL +P RSPLT EQ+IPN +
Sbjct: 3 PDYLCGKISFELMREPCITPSGI-TYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAM 61
Query: 230 QTQIQDWIRQ 239
+ I +I +
Sbjct: 62 KEVIDAFISE 71
>pdb|1N87|A Chain A, Solution Structure Of The U-Box Of Prp19
Length = 56
Score = 31.6 bits (70), Expect = 0.41, Method: Composition-based stats.
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 186 PVTLPSSRQTLDKSTIARHLLSDQTDPFNRSPLTMEQVI 224
PV P SR +KS + +++ DP PL++E+++
Sbjct: 13 PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIV 51
>pdb|2BAY|A Chain A, Crystal Structure Of The Prp19 U-Box Dimer
pdb|2BAY|B Chain B, Crystal Structure Of The Prp19 U-Box Dimer
pdb|2BAY|C Chain C, Crystal Structure Of The Prp19 U-Box Dimer
pdb|2BAY|D Chain D, Crystal Structure Of The Prp19 U-Box Dimer
pdb|2BAY|E Chain E, Crystal Structure Of The Prp19 U-Box Dimer
pdb|2BAY|F Chain F, Crystal Structure Of The Prp19 U-Box Dimer
Length = 61
Score = 30.8 bits (68), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 186 PVTLPSSRQTLDKSTIARHLLSDQTDPFNRSPLTMEQVI 224
PV P SR +KS + +++ DP PL++E+++
Sbjct: 16 PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIV 54
>pdb|2NX8|A Chain A, The Crystal Structure Of The Trna-Specific Adenosine
Deaminase From Streptococcus Pyogenes
Length = 179
Score = 30.4 bits (67), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 13/61 (21%)
Query: 154 EKLGAQLQSDEALLAGAPDEYLDPIMNTIMLEPVTLPSSRQTLDKSTIARHLLSDQTDPF 213
E+L ++Q + LLA IM T RQ ++ IA+HL+ +Q+DPF
Sbjct: 132 ERLNHRVQVERGLLAAD----CANIMQTFF---------RQGRERKKIAKHLIKEQSDPF 178
Query: 214 N 214
+
Sbjct: 179 D 179
>pdb|1XDJ|A Chain A, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ And Homocysteine
pdb|1XDJ|B Chain B, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ And Homocysteine
Length = 766
Score = 28.5 bits (62), Expect = 3.9, Method: Composition-based stats.
Identities = 15/27 (55%), Positives = 17/27 (62%)
Query: 145 DLRRVAVLVEKLGAQLQSDEALLAGAP 171
DLR+VA LVEKLGA S+ L P
Sbjct: 321 DLRKVASLVEKLGASAISNSCPLFHLP 347
>pdb|1XPG|A Chain A, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ And
Methyltetrahydrofolate
pdb|1XPG|B Chain B, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ And
Methyltetrahydrofolate
Length = 765
Score = 28.5 bits (62), Expect = 3.9, Method: Composition-based stats.
Identities = 15/27 (55%), Positives = 17/27 (62%)
Query: 145 DLRRVAVLVEKLGAQLQSDEALLAGAP 171
DLR+VA LVEKLGA S+ L P
Sbjct: 321 DLRKVASLVEKLGASAISNSCPLFHLP 347
>pdb|1XR2|A Chain A, Crystal Structure Of Oxidized T. Maritima Cobalamin-
Independent Methionine Synthase Complexed With
Methyltetrahydrofolate
pdb|1XR2|B Chain B, Crystal Structure Of Oxidized T. Maritima Cobalamin-
Independent Methionine Synthase Complexed With
Methyltetrahydrofolate
Length = 766
Score = 28.1 bits (61), Expect = 4.3, Method: Composition-based stats.
Identities = 15/27 (55%), Positives = 17/27 (62%)
Query: 145 DLRRVAVLVEKLGAQLQSDEALLAGAP 171
DLR+VA LVEKLGA S+ L P
Sbjct: 321 DLRKVASLVEKLGASAISNSCPLFHLP 347
>pdb|1T7L|A Chain A, Crystal Structure Of Cobalamin-Independent Methionine
Synthase From T. Maritima
pdb|1T7L|B Chain B, Crystal Structure Of Cobalamin-Independent Methionine
Synthase From T. Maritima
pdb|3BQ5|A Chain A, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ And Homocysteine
(Monoclinic)
pdb|3BQ5|B Chain B, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ And Homocysteine
(Monoclinic)
pdb|3BQ6|A Chain A, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ (Monoclinic)
pdb|3BQ6|B Chain B, Crystal Structure Of T. Maritima Cobalamin-Independent
Methionine Synthase Complexed With Zn2+ (Monoclinic)
Length = 766
Score = 28.1 bits (61), Expect = 4.5, Method: Composition-based stats.
Identities = 15/27 (55%), Positives = 17/27 (62%)
Query: 145 DLRRVAVLVEKLGAQLQSDEALLAGAP 171
DLR+VA LVEKLGA S+ L P
Sbjct: 321 DLRKVASLVEKLGASAISNSCPLFHLP 347
>pdb|1RJP|A Chain A, Crystal Structure Of D-Aminoacylase In Complex With 100mm
Cucl2
pdb|1RK6|A Chain A, The Enzyme In Complex With 50mm Cdcl2
pdb|1V51|A Chain A, The Functional Role Of The Binuclear Metal Center In D-
Aminoacylase. One-Metal Activation And Second-Metal
Attenuation
Length = 496
Score = 27.7 bits (60), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 140 ASLIPDLRRVAVLVEKLGAQLQSDEALLAGA 170
A+++PDLRR A E Q +D+AL +GA
Sbjct: 166 AAVMPDLRREATADEIQAMQALADDALASGA 196
>pdb|1M7J|A Chain A, Crystal Structure Of D-Aminoacylase Defines A Novel Subset
Of Amidohydrolases
Length = 484
Score = 27.7 bits (60), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 140 ASLIPDLRRVAVLVEKLGAQLQSDEALLAGA 170
A+++PDLRR A E Q +D+AL +GA
Sbjct: 154 AAVMPDLRREATADEIQAMQALADDALASGA 184
>pdb|1RJQ|A Chain A, The Crystal Structure Of The D-Aminoacylase Mutant D366a
pdb|1RJR|A Chain A, The Crystal Structure Of The D-Aminoacylase D366a Mutant
In Complex With 100mm Zncl2
pdb|1RK5|A Chain A, The D-Aminoacylase Mutant D366a In Complex With 100mm
Cucl2
Length = 496
Score = 27.7 bits (60), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 140 ASLIPDLRRVAVLVEKLGAQLQSDEALLAGA 170
A+++PDLRR A E Q +D+AL +GA
Sbjct: 166 AAVMPDLRREATADEIQAMQALADDALASGA 196
>pdb|1V4Y|A Chain A, The Functional Role Of The Binuclear Metal Center In D-
Aminoacylase. One-Metal Activation And Second-Metal
Attenuation
Length = 496
Score = 27.7 bits (60), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 140 ASLIPDLRRVAVLVEKLGAQLQSDEALLAGA 170
A+++PDLRR A E Q +D+AL +GA
Sbjct: 166 AAVMPDLRREATADEIQAMQALADDALASGA 196
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 0.135 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,116,793
Number of Sequences: 62578
Number of extensions: 211633
Number of successful extensions: 431
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 404
Number of HSP's gapped (non-prelim): 25
length of query: 246
length of database: 14,973,337
effective HSP length: 96
effective length of query: 150
effective length of database: 8,965,849
effective search space: 1344877350
effective search space used: 1344877350
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: 50 (23.9 bits)