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= psy6552
(254 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZME|A Chain A, Integrated Structural And Functional Model Of The Human
Escrt-Ii Complex
Length = 258
Score = 282 bits (722), Expect = 1e-76, Method: Compositional matrix adjust.
Identities = 135/250 (54%), Positives = 187/250 (74%), Gaps = 6/250 (2%)
Query: 2 RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
RR G GAI K+KL + KYK++GT + E+QL Q+S+ L+ F+ LE FAS++K EI+K+
Sbjct: 3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62
Query: 62 QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
+FR FQ+MCA+IGVDPLAS KGFWS +LG+GDFYYEL VQI+EVCLA ++NGGLI L+
Sbjct: 63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122
Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
EL +++K RGK QD++ +DL+ A KKLK G GF IIP+G G YL+QS+P EL++D
Sbjct: 123 ELHQQVLKGRGKF--AQDVSQDDLIRAIKKLKALGTGFGIIPVG-GTYLIQSVPAELNMD 179
Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
H++VL Q+A KN +++VS + L W TERA+ L+ +++EG AW+D Q+P E YW P
Sbjct: 180 HTVVL-QLAEKN-GYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLP 237
Query: 241 SLFTECMNAE 250
+LFT+ + E
Sbjct: 238 ALFTDLYSQE 247
>pdb|3CUQ|A Chain A, Integrated Structural And Functional Model Of The Human
Escrt-Ii Complex
Length = 234
Score = 258 bits (658), Expect = 3e-69, Method: Compositional matrix adjust.
Identities = 123/228 (53%), Positives = 171/228 (75%), Gaps = 6/228 (2%)
Query: 24 GTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRK 83
GT + E+QL Q+S+ L+ F+ LE FAS++K EI+K+ +FR FQ+MCA+IGVDPLAS K
Sbjct: 1 GTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQDMCATIGVDPLASGK 60
Query: 84 GFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNE 142
GFWS +LG+GDFYYEL VQI+EVCLA ++NGGLI L+EL +++K RGK QD++ +
Sbjct: 61 GFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLEELHQQVLKGRGKF--AQDVSQD 118
Query: 143 DLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLN 202
DL+ A KKLK G GF IIP+G G YL+QS+P EL++DH++VL Q+A KN +++VS +
Sbjct: 119 DLIRAIKKLKALGTGFGIIPVG-GTYLIQSVPAELNMDHTVVL-QLAEKN-GYVTVSEIK 175
Query: 203 NELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTECMNAE 250
L W TERA+ L+ +++EG AW+D Q+P E YW P+LFT+ + E
Sbjct: 176 ASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLPALFTDLYSQE 223
>pdb|1U5T|A Chain A, Structure Of The Escrt-Ii Endosomal Trafficking Complex
pdb|1W7P|A Chain A, The Crystal Structure Of Endosomal Complex Escrt-Ii
(Vps22VPS25VPS36)
Length = 233
Score = 127 bits (319), Expect = 5e-30, Method: Compositional matrix adjust.
Identities = 79/243 (32%), Positives = 128/243 (52%), Gaps = 15/243 (6%)
Query: 3 RRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQ 62
++ G+ A + L+ KY D +I E Q +L L F+++L FA ++ +E++ +
Sbjct: 2 KQFGLAAFDE--LKDGKYNDVNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPE 59
Query: 63 FRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDEL 122
FR F MC+SIG+DPL+ L + DFYYE+ ++++E+C T NGG+I EL
Sbjct: 60 FRSKFMHMCSSIGIDPLSLFDRDKHLFTVNDFYYEVCLKVIEICRQTKDMNGGVISFQEL 119
Query: 123 RTRLVKSRGKSLQHQDITNE-DLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDH 181
V R ++ D+ D+L + + +IF +G+ ++S+P EL+ D
Sbjct: 120 EK--VHFRKLNVGLDDLEKSIDMLKSLECFEIFQI--------RGKKFLRSVPNELTSDQ 169
Query: 182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS 241
+ +L+ + + S+S+L L W R++ ALD MV G WID Q E LYW PS
Sbjct: 170 TKILEICSIL--GYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGAEALYWDPS 227
Query: 242 LFT 244
T
Sbjct: 228 WIT 230
>pdb|2ZME|B Chain B, Integrated Structural And Functional Model Of The Human
Escrt-Ii Complex
Length = 238
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 58/258 (22%), Positives = 116/258 (44%), Gaps = 44/258 (17%)
Query: 3 RRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLE---SFASEYKN---E 56
R G+ I+++ E+ K DK S E LS+ + ++ +E S A++ K+ +
Sbjct: 4 RAVGIVGIERKLEEKRKETDKNIS---EAFEDLSKLMIKAKEMVELSKSIANKIKDKQGD 60
Query: 57 IKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGL 116
I +D R F+ S+G+ +R+ + S ++ +L+ Q+ + + GG+
Sbjct: 61 ITEDETIR--FKSYLLSMGIANPVTRETYGS---GTQYHMQLAKQLAGILQVPLEERGGI 115
Query: 117 ILLDELRTRLVKSRGKSLQHQDITNEDLLAAAK---------KLKIFGNGFSIIPIG--Q 165
+ L E+ + ++RG L ++ EDL+ A K +L++F +G +I + +
Sbjct: 116 MSLTEVYCLVNRARGMEL----LSPEDLVNACKMLEALKLPLRLRVFDSGVMVIELQSHK 171
Query: 166 GQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA 225
+ +V S +S SL ++ A + +SVL + ER ++ E
Sbjct: 172 EEEMVASALETVSEKGSLTSEEFAK----LVGMSVL-----LAKER------LLLAEKMG 216
Query: 226 WIDTQSPQEHLYWFPSLF 243
+ E L ++P+LF
Sbjct: 217 HLCRDDSVEGLRFYPNLF 234
>pdb|3KCZ|A Chain A, Human Poly(Adp-Ribose) Polymerase 2, Catalytic Fragment In
Complex With An Inhibitor 3-Aminobenzamide
pdb|3KCZ|B Chain B, Human Poly(Adp-Ribose) Polymerase 2, Catalytic Fragment In
Complex With An Inhibitor 3-Aminobenzamide
pdb|3KJD|A Chain A, Human Poly(Adp-Ribose) Polymerase 2, Catalytic Fragment In
Complex With An Inhibitor Abt-888
pdb|3KJD|B Chain B, Human Poly(Adp-Ribose) Polymerase 2, Catalytic Fragment In
Complex With An Inhibitor Abt-888
Length = 368
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 31/123 (25%), Positives = 50/123 (40%), Gaps = 15/123 (12%)
Query: 13 QKLEQEKYKDKGTS--IQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRR---HF 67
+ L+ E Y+ K S +Q S + T D E K ++D R H
Sbjct: 159 RPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHG 218
Query: 68 QEMCASIGV--------DPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILL 119
M +G+ P A G+ + G G ++ ++S + C A+ KN GL+LL
Sbjct: 219 SRMSNWVGILSHGLRIAHPEAPITGY--MFGKGIYFADMSSKSANYCFASRLKNTGLLLL 276
Query: 120 DEL 122
E+
Sbjct: 277 SEV 279
>pdb|1GS0|A Chain A, Crystal Structure Of The Catalytic Fragment Of Murine Poly
(Adp-Ribose) Polymerase-2
pdb|1GS0|B Chain B, Crystal Structure Of The Catalytic Fragment Of Murine Poly
(Adp-Ribose) Polymerase-2
Length = 351
Score = 30.8 bits (68), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 78 PLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDEL 122
P A G+ + G G ++ ++S + C A+ KN GL+LL E+
Sbjct: 218 PEAPITGY--MFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEV 260
>pdb|3CUQ|B Chain B, Integrated Structural And Functional Model Of The Human
Escrt-Ii Complex
Length = 218
Score = 30.8 bits (68), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 32/147 (21%), Positives = 70/147 (47%), Gaps = 27/147 (18%)
Query: 27 IQENQLEQLSQHL-NTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGF 85
I+ ++ +LS+ + N +DK + +I +D R F+ S+G+ +R+ +
Sbjct: 18 IKAKEMVELSKSIANKIKDK--------QGDITEDETIR--FKSYLLSMGIANPVTRETY 67
Query: 86 WSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLL 145
S ++ +L+ Q+ + + GG++ L E+ + ++RG L ++ EDL+
Sbjct: 68 GS---GTQYHMQLAKQLAGILQVPLEERGGIMSLTEVYCLVNRARGMEL----LSPEDLV 120
Query: 146 AAAK---------KLKIFGNGFSIIPI 163
A K +L++F +G +I +
Sbjct: 121 NACKMLEALKLPLRLRVFDSGVMVIEL 147
>pdb|3A9G|A Chain A, Crystal Structure Of Pqq-Dependent Sugar Dehydrogenase
Apo-Form
pdb|3A9H|A Chain A, Crystal Structure Of Pqq-Dependent Sugar Dehydrogenase
Holo-Form
Length = 354
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 158 FSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHIS 197
+SI P+G G+YLV PG L L + VAS + A++
Sbjct: 32 WSIAPLGGGRYLVTERPGRLVLISPSGKKLVASFDVANVG 71
>pdb|1YX2|A Chain A, Crystal Structure Of The Probable Aminomethyltransferase
From Bacillus Subtilis
pdb|1YX2|B Chain B, Crystal Structure Of The Probable Aminomethyltransferase
From Bacillus Subtilis
Length = 365
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 24/96 (25%), Positives = 42/96 (43%), Gaps = 11/96 (11%)
Query: 138 DITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHIS 197
+++ D L+ ++L N S + G+ QY P ++D L+ Q+ ++ I+
Sbjct: 59 EVSGNDSLSFLQRLXT--NDVSALTPGRAQYTAXCYPDGGTVDDLLIYQKGENRYLLVIN 116
Query: 198 VSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQ 233
S ++ +L W E A G ID QS Q
Sbjct: 117 ASNIDKDLAWXKEHAA---------GDVQIDNQSDQ 143
>pdb|3LEW|A Chain A, Crystal Structure Of Susd-Like Carbohydrate Binding
Protein (Yp_001298396.1) From Bacteroides Vulgatus Atcc
8482 At 1.70 A Resolution
Length = 495
Score = 27.7 bits (60), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 7/55 (12%)
Query: 119 LDELRTRLVKSRGKSLQHQDITNEDLLAAA---KKLKIFGNGFSIIPIGQGQYLV 170
L++L+T +RG H +++ +DLL ++ +++G GFS+I I + Q V
Sbjct: 369 LNDLKT----ARGAKTIHTNLSQQDLLETIWLERRKELWGEGFSLIDIIRNQQTV 419
>pdb|2GAG|A Chain A, Heteroteterameric Sarcosine: Structure Of A Diflavin
Metaloenzyme At 1.85 A Resolution
Length = 965
Score = 27.3 bits (59), Expect = 9.3, Method: Composition-based stats.
Identities = 14/62 (22%), Positives = 28/62 (45%)
Query: 152 KIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTER 211
+I+ NG++ + +G G+Y V + D + L+ + H + + L+W E
Sbjct: 648 RIYTNGYTKLKVGMGRYGVMCKADGMIFDDGVTLRLAEDRFLLHTTTGGAADVLDWLEEW 707
Query: 212 AQ 213
Q
Sbjct: 708 LQ 709
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 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,220,833
Number of Sequences: 62578
Number of extensions: 278241
Number of successful extensions: 758
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 741
Number of HSP's gapped (non-prelim): 13
length of query: 254
length of database: 14,973,337
effective HSP length: 97
effective length of query: 157
effective length of database: 8,903,271
effective search space: 1397813547
effective search space used: 1397813547
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: 50 (23.9 bits)