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= 015413
(407 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1LV0|A Chain A, Crystal Structure Of The Rab Effector Guanine Nucleotide
Dissociation Inhibitor (Gdi) In Complex With A
Geranylgeranyl (Gg) Peptide
Length = 449
Score = 128 bits (322), Expect = 4e-30, Method: Compositional matrix adjust.
Identities = 100/370 (27%), Positives = 175/370 (47%), Gaps = 56/370 (15%)
Query: 23 FDLIVIGTGLPESVISAAASASGKSVLHLDPNPFYGSHFSSLSIADLTHFLNSHSTPSSV 82
+D+IV+GTGL E ++S S +GK VLH+D NP+YG SS+ TP
Sbjct: 7 YDVIVLGTGLTECILSGIMSVNGKKVLHMDRNPYYGGESSSI-------------TPL-- 51
Query: 83 CPDPLYSDVEISNYASRLLSQHPRNFNLDVSGPRVLFCADHAVDLMLKSGASHYLEFKSI 142
+ LY ++ + + R++N+D+ P+ L V ++L + + YL+FK +
Sbjct: 52 --EELYKRFQLLEGPPETMGRG-RDWNVDLI-PKFLMANGQLVKMLLYTEVTRYLDFKVV 107
Query: 143 DATFMLDADAKLCSVPDSRAAIFKDKSLGLMEKNQLMRFFKLVQGHLSLDESEENNVRIS 202
+ +F+ K+ VP + +G+ EK + +F V +EN+ +
Sbjct: 108 EGSFVYKG-GKIYKVPSTETEALASNLMGMFEKRRFRKFLVFVANF------DENDPKTF 160
Query: 203 E--EDLDSPFAEFLTKMKLPHKIKSIVLYAIAMADYDQEVSEYVLKTRDGINRLALYNSS 260
E + ++ + K L + +A+A+ D + + L+T INR+ LY+ S
Sbjct: 161 EGVDPQNTSMRDVYRKFDLGQDVIDFTGHALALYRTDDYLDQPCLET---INRIKLYSES 217
Query: 261 IGRFQNALGALIYPIYGQGELPQAFCRRAAVKGCLYVLRMPVISLLTDQNSGSYKGVRLA 320
+ R+ + +YP+YG GELPQ F R +A+ G Y+L PV ++ + +G GV+ +
Sbjct: 218 LARYGKS--PYLYPLYGLGELPQGFARLSAIYGGTYMLNKPVDDIIME--NGKVVGVK-S 272
Query: 321 SGQDILSHKLVLDPSFTVPGSLASSHQQLQESFQAFSLSDNKGKVARGICITRSSLK--P 378
G+ +L+ DPS+ VP + + G+V R ICI +K
Sbjct: 273 EGEVARCKQLICDPSY-VPDRVRKA-----------------GQVIRIICILSHPIKNTN 314
Query: 379 DLSNFLVIFP 388
D ++ +I P
Sbjct: 315 DANSCQIIIP 324
>pdb|1GND|A Chain A, Guanine Nucleotide Dissociation Inhibitor, Alpha-Isoform
Length = 447
Score = 128 bits (322), Expect = 5e-30, Method: Compositional matrix adjust.
Identities = 100/370 (27%), Positives = 175/370 (47%), Gaps = 56/370 (15%)
Query: 23 FDLIVIGTGLPESVISAAASASGKSVLHLDPNPFYGSHFSSLSIADLTHFLNSHSTPSSV 82
+D+IV+GTGL E ++S S +GK VLH+D NP+YG SS+ TP
Sbjct: 5 YDVIVLGTGLTECILSGIMSVNGKKVLHMDRNPYYGGESSSI-------------TPL-- 49
Query: 83 CPDPLYSDVEISNYASRLLSQHPRNFNLDVSGPRVLFCADHAVDLMLKSGASHYLEFKSI 142
+ LY ++ + + R++N+D+ P+ L V ++L + + YL+FK +
Sbjct: 50 --EELYKRFQLLEGPPETMGRG-RDWNVDLI-PKFLMANGQLVKMLLYTEVTRYLDFKVV 105
Query: 143 DATFMLDADAKLCSVPDSRAAIFKDKSLGLMEKNQLMRFFKLVQGHLSLDESEENNVRIS 202
+ +F+ K+ VP + +G+ EK + +F V +EN+ +
Sbjct: 106 EGSFVYKG-GKIYKVPSTETEALASNLMGMFEKRRFRKFLVFVANF------DENDPKTF 158
Query: 203 E--EDLDSPFAEFLTKMKLPHKIKSIVLYAIAMADYDQEVSEYVLKTRDGINRLALYNSS 260
E + ++ + K L + +A+A+ D + + L+T INR+ LY+ S
Sbjct: 159 EGVDPQNTSMRDVYRKFDLGQDVIDFTGHALALYRTDDYLDQPCLET---INRIKLYSES 215
Query: 261 IGRFQNALGALIYPIYGQGELPQAFCRRAAVKGCLYVLRMPVISLLTDQNSGSYKGVRLA 320
+ R+ + +YP+YG GELPQ F R +A+ G Y+L PV ++ + +G GV+ +
Sbjct: 216 LARYGKS--PYLYPLYGLGELPQGFARLSAIYGGTYMLNKPVDDIIME--NGKVVGVK-S 270
Query: 321 SGQDILSHKLVLDPSFTVPGSLASSHQQLQESFQAFSLSDNKGKVARGICITRSSLK--P 378
G+ +L+ DPS+ VP + + G+V R ICI +K
Sbjct: 271 EGEVARCKQLICDPSY-VPDRVRKA-----------------GQVIRIICILSHPIKNTN 312
Query: 379 DLSNFLVIFP 388
D ++ +I P
Sbjct: 313 DANSCQIIIP 322
>pdb|1D5T|A Chain A, Guanine Nucleotide Dissociation Inhibitor, Alpha-Isoform
Length = 433
Score = 128 bits (322), Expect = 5e-30, Method: Compositional matrix adjust.
Identities = 100/370 (27%), Positives = 175/370 (47%), Gaps = 56/370 (15%)
Query: 23 FDLIVIGTGLPESVISAAASASGKSVLHLDPNPFYGSHFSSLSIADLTHFLNSHSTPSSV 82
+D+IV+GTGL E ++S S +GK VLH+D NP+YG SS+ TP
Sbjct: 7 YDVIVLGTGLTECILSGIMSVNGKKVLHMDRNPYYGGESSSI-------------TPL-- 51
Query: 83 CPDPLYSDVEISNYASRLLSQHPRNFNLDVSGPRVLFCADHAVDLMLKSGASHYLEFKSI 142
+ LY ++ + + R++N+D+ P+ L V ++L + + YL+FK +
Sbjct: 52 --EELYKRFQLLEGPPETMGRG-RDWNVDLI-PKFLMANGQLVKMLLYTEVTRYLDFKVV 107
Query: 143 DATFMLDADAKLCSVPDSRAAIFKDKSLGLMEKNQLMRFFKLVQGHLSLDESEENNVRIS 202
+ +F+ K+ VP + +G+ EK + +F V +EN+ +
Sbjct: 108 EGSFVYKG-GKIYKVPSTETEALASNLMGMFEKRRFRKFLVFVANF------DENDPKTF 160
Query: 203 E--EDLDSPFAEFLTKMKLPHKIKSIVLYAIAMADYDQEVSEYVLKTRDGINRLALYNSS 260
E + ++ + K L + +A+A+ D + + L+T INR+ LY+ S
Sbjct: 161 EGVDPQNTSMRDVYRKFDLGQDVIDFTGHALALYRTDDYLDQPCLET---INRIKLYSES 217
Query: 261 IGRFQNALGALIYPIYGQGELPQAFCRRAAVKGCLYVLRMPVISLLTDQNSGSYKGVRLA 320
+ R+ + +YP+YG GELPQ F R +A+ G Y+L PV ++ + +G GV+ +
Sbjct: 218 LARYGKS--PYLYPLYGLGELPQGFARLSAIYGGTYMLNKPVDDIIME--NGKVVGVK-S 272
Query: 321 SGQDILSHKLVLDPSFTVPGSLASSHQQLQESFQAFSLSDNKGKVARGICITRSSLK--P 378
G+ +L+ DPS+ VP + + G+V R ICI +K
Sbjct: 273 EGEVARCKQLICDPSY-VPDRVRKA-----------------GQVIRIICILSHPIKNTN 314
Query: 379 DLSNFLVIFP 388
D ++ +I P
Sbjct: 315 DANSCQIIIP 324
>pdb|3CPH|G Chain G, Crystal Structure Of Sec4 In Complex With Rab-Gdi
pdb|3CPH|H Chain H, Crystal Structure Of Sec4 In Complex With Rab-Gdi
pdb|3CPI|G Chain G, Crystal Structure Of Yeast Rab-Gdi
pdb|3CPI|H Chain H, Crystal Structure Of Yeast Rab-Gdi
pdb|3CPJ|G Chain G, Crystal Structure Of Ypt31 In Complex With Yeast Rab-Gdi
Length = 451
Score = 124 bits (311), Expect = 8e-29, Method: Compositional matrix adjust.
Identities = 87/362 (24%), Positives = 167/362 (46%), Gaps = 45/362 (12%)
Query: 21 TAFDLIVIGTGLPESVISAAASASGKSVLHLDPNPFYGSHFSSLSIADLTHFLNSHSTPS 80
T +D+IV+GTG+ E ++S S GK VLH+D YG +S++++ L
Sbjct: 8 TDYDVIVLGTGITECILSGLLSVDGKKVLHIDKQDHYGGEAASVTLSQLYEKFKQ----- 62
Query: 81 SVCPDPLYSDVEISNYASRLLSQHPRNFNLDVSGPRVLFCADHAVDLMLKSGASHYLEFK 140
+P+ + S + R++N+D+ P+ L ++++ + + Y++FK
Sbjct: 63 ----NPISKEERESKFGKD------RDWNVDLI-PKFLMANGELTNILIHTDVTRYVDFK 111
Query: 141 SIDATFMLDADAKLCSVPDSRAAIFKDKSLGLMEKNQLMRFFKLVQGHLSLDESEENNVR 200
+ +++ K+ VP + +G+ EK ++ +F + + + D S +
Sbjct: 112 QVSGSYVF-KQGKIYKVPANEIEAISSPLMGIFEKRRMKKFLEWISSYKEDDLSTHQGLD 170
Query: 201 ISEEDLDSPFAEFLTKMKLPHKIKSIVLYAIAMADYDQEVSEYVLKTRDGINRLALYNSS 260
+ + +D E K L + K + +A+A+ D + + R R+ LY S
Sbjct: 171 LDKNTMD----EVYYKFGLGNSTKEFIGHAMALWTNDDYLQQ---PARPSFERILLYCQS 223
Query: 261 IGRFQNALGALIYPIYGQGELPQAFCRRAAVKGCLYVLRMPVISLLTDQNSGSYKGVRLA 320
+ R+ + +YP+YG GELPQ F R +A+ G Y+L P+ +L +++G ++GV+
Sbjct: 224 VARYGKS--PYLYPMYGLGELPQGFARLSAIYGGTYMLDTPIDEVLYKKDTGKFEGVKTK 281
Query: 321 SGQDILSHKLVLDPSFTVPGSLASSHQQLQESFQAFSLSDNKGKVARGICITRSSLKPDL 380
G + ++ DP++ P S+ Q +V R ICI + P+
Sbjct: 282 LGT-FKAPLVIADPTY-FPEKCKSTGQ----------------RVIRAICILNHPV-PNT 322
Query: 381 SN 382
SN
Sbjct: 323 SN 324
>pdb|1UKV|G Chain G, Structure Of Rabgdp-Dissociation Inhibitor In Complex With
Prenylated Ypt1 Gtpase
pdb|2BCG|G Chain G, Structure Of Doubly Prenylated Ypt1:gdi Complex
Length = 453
Score = 124 bits (311), Expect = 9e-29, Method: Compositional matrix adjust.
Identities = 87/362 (24%), Positives = 167/362 (46%), Gaps = 45/362 (12%)
Query: 21 TAFDLIVIGTGLPESVISAAASASGKSVLHLDPNPFYGSHFSSLSIADLTHFLNSHSTPS 80
T +D+IV+GTG+ E ++S S GK VLH+D YG +S++++ L
Sbjct: 10 TDYDVIVLGTGITECILSGLLSVDGKKVLHIDKQDHYGGEAASVTLSQLYEKFKQ----- 64
Query: 81 SVCPDPLYSDVEISNYASRLLSQHPRNFNLDVSGPRVLFCADHAVDLMLKSGASHYLEFK 140
+P+ + S + R++N+D+ P+ L ++++ + + Y++FK
Sbjct: 65 ----NPISKEERESKFGKD------RDWNVDLI-PKFLMANGELTNILIHTDVTRYVDFK 113
Query: 141 SIDATFMLDADAKLCSVPDSRAAIFKDKSLGLMEKNQLMRFFKLVQGHLSLDESEENNVR 200
+ +++ K+ VP + +G+ EK ++ +F + + + D S +
Sbjct: 114 QVSGSYVF-KQGKIYKVPANEIEAISSPLMGIFEKRRMKKFLEWISSYKEDDLSTHQGLD 172
Query: 201 ISEEDLDSPFAEFLTKMKLPHKIKSIVLYAIAMADYDQEVSEYVLKTRDGINRLALYNSS 260
+ + +D E K L + K + +A+A+ D + + R R+ LY S
Sbjct: 173 LDKNTMD----EVYYKFGLGNSTKEFIGHAMALWTNDDYLQQ---PARPSFERILLYCQS 225
Query: 261 IGRFQNALGALIYPIYGQGELPQAFCRRAAVKGCLYVLRMPVISLLTDQNSGSYKGVRLA 320
+ R+ + +YP+YG GELPQ F R +A+ G Y+L P+ +L +++G ++GV+
Sbjct: 226 VARYGKS--PYLYPMYGLGELPQGFARLSAIYGGTYMLDTPIDEVLYKKDTGKFEGVKTK 283
Query: 321 SGQDILSHKLVLDPSFTVPGSLASSHQQLQESFQAFSLSDNKGKVARGICITRSSLKPDL 380
G + ++ DP++ P S+ Q +V R ICI + P+
Sbjct: 284 LGT-FKAPLVIADPTY-FPEKCKSTGQ----------------RVIRAICILNHPV-PNT 324
Query: 381 SN 382
SN
Sbjct: 325 SN 326
>pdb|1LTX|R Chain R, Structure Of Rab Escort Protein-1 In Complex With Rab
Geranylgeranyl Transferase And Isoprenoid
Length = 650
Score = 119 bits (299), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 78/231 (33%), Positives = 117/231 (50%), Gaps = 17/231 (7%)
Query: 106 RNFNLDVSGPRVLFCADHAVDLMLKSGASHYLEFKSIDATFMLDADAKLCSVPDSRAAIF 165
R FN+D+ ++L+ +DL++KS S Y EFK+I + + VP SRA +F
Sbjct: 222 RRFNIDLVS-KLLYSRGLLIDLLIKSNVSRYAEFKNITRILAF-REGTVEQVPCSRADVF 279
Query: 166 KDKSLGLMEKNQLMRFFKLVQGHLSLDESEENNVRISEEDLDSPFAEFLTKMKLPHKIKS 225
K L ++EK LM+F + E + R E + F+E+L KL ++
Sbjct: 280 NSKQLTMVEKRMLMKFLTFCVEY----EEHPDEYRAYE---GTTFSEYLKTQKLTPNLQY 332
Query: 226 IVLYAIAMADYDQEVSEYVLKTRDGINRLALYNSSIGRFQNALGALIYPIYGQGELPQAF 285
VL++IAM SE T DG+ + +GR+ N ++P+YGQGELPQ F
Sbjct: 333 FVLHSIAM------TSETTSCTVDGLKATKKFLQCLGRYGNT--PFLFPLYGQGELPQCF 384
Query: 286 CRRAAVKGCLYVLRMPVISLLTDQNSGSYKGVRLASGQDILSHKLVLDPSF 336
CR AV G +Y LR V L+ D+ S K V GQ I+S +++ S+
Sbjct: 385 CRMCAVFGGIYCLRHSVQCLVVDKESRKCKAVIDQFGQRIISKHFIIEDSY 435
Score = 64.3 bits (155), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 29/60 (48%), Positives = 42/60 (70%)
Query: 23 FDLIVIGTGLPESVISAAASASGKSVLHLDPNPFYGSHFSSLSIADLTHFLNSHSTPSSV 82
FD+IVIGTGLPES+I+AA S SG+ VLH+D +YG +++S S + L +L + + V
Sbjct: 9 FDVIVIGTGLPESIIAAACSRSGQRVLHVDSRSYYGGNWASFSFSGLLSWLKEYQENNDV 68
>pdb|1VG0|A Chain A, The Crystal Structures Of The Rep-1 Protein In Complex
With Monoprenylated Rab7 Protein
pdb|1VG9|A Chain A, The Crystal Structures Of The Rep-1 Protein In Complex
With C-Terminally Truncated Rab7 Protein
pdb|1VG9|C Chain C, The Crystal Structures Of The Rep-1 Protein In Complex
With C-Terminally Truncated Rab7 Protein
pdb|1VG9|E Chain E, The Crystal Structures Of The Rep-1 Protein In Complex
With C-Terminally Truncated Rab7 Protein
pdb|1VG9|G Chain G, The Crystal Structures Of The Rep-1 Protein In Complex
With C-Terminally Truncated Rab7 Protein
Length = 650
Score = 119 bits (298), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 78/231 (33%), Positives = 117/231 (50%), Gaps = 17/231 (7%)
Query: 106 RNFNLDVSGPRVLFCADHAVDLMLKSGASHYLEFKSIDATFMLDADAKLCSVPDSRAAIF 165
R FN+D+ ++L+ +DL++KS S Y EFK+I + + VP SRA +F
Sbjct: 222 RRFNIDLVS-KLLYSRGLLIDLLIKSNVSRYAEFKNITRILAF-REGTVEQVPCSRADVF 279
Query: 166 KDKSLGLMEKNQLMRFFKLVQGHLSLDESEENNVRISEEDLDSPFAEFLTKMKLPHKIKS 225
K L ++EK LM+F + E + R E + F+E+L KL ++
Sbjct: 280 NSKQLTMVEKRMLMKFLTFCVEY----EEHPDEYRAYE---GTTFSEYLKTQKLTPNLQY 332
Query: 226 IVLYAIAMADYDQEVSEYVLKTRDGINRLALYNSSIGRFQNALGALIYPIYGQGELPQAF 285
VL++IAM SE T DG+ + +GR+ N ++P+YGQGELPQ F
Sbjct: 333 FVLHSIAM------TSETTSCTVDGLKATKKFLQCLGRYGNT--PFLFPLYGQGELPQCF 384
Query: 286 CRRAAVKGCLYVLRMPVISLLTDQNSGSYKGVRLASGQDILSHKLVLDPSF 336
CR AV G +Y LR V L+ D+ S K V GQ I+S +++ S+
Sbjct: 385 CRMCAVFGGIYCLRHSVQCLVVDKESRKCKAVIDQFGQRIISKHFIIEDSY 435
Score = 64.3 bits (155), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 29/60 (48%), Positives = 42/60 (70%)
Query: 23 FDLIVIGTGLPESVISAAASASGKSVLHLDPNPFYGSHFSSLSIADLTHFLNSHSTPSSV 82
FD+IVIGTGLPES+I+AA S SG+ VLH+D +YG +++S S + L +L + + V
Sbjct: 9 FDVIVIGTGLPESIIAAACSRSGQRVLHVDSRSYYGGNWASFSFSGLLSWLKEYQENNDV 68
>pdb|3P1W|A Chain A, Crystal Structure Of Rab Gdi From Plasmodium Falciparum,
Pfl2060c
Length = 475
Score = 103 bits (258), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 91/361 (25%), Positives = 163/361 (45%), Gaps = 61/361 (16%)
Query: 23 FDLIVIGTGLPESVISAAASASGKSVLHLDPNPFYGSHFSSLSIADLTHFLNSHSTPSSV 82
+D+I++GTGL E ++S S GK +L LD NP+YG +SL +LT+ N+ P
Sbjct: 21 YDVIILGTGLKECILSGLLSHYGKKILVLDRNPYYGGETASL---NLTNLYNTFK-PKEN 76
Query: 83 CPDPLYSDVEISNYASRLLSQHPRNFNLDVSGPRVLFCADHAVDLMLKSGASHYLEFKSI 142
P S Y R++N+D+ P+ + + V ++ K+ ++YLE+ +
Sbjct: 77 IP---------SKYGEN------RHWNVDLI-PKFILVGGNLVKILKKTRVTNYLEWLVV 120
Query: 143 DATFM--------LDADAKLCSVPDSRAAIFKDKSLGLMEKNQLMRFFKLVQGHLSLDES 194
+ +++ L ++ + VP + L LMEKN+ F++ V
Sbjct: 121 EGSYVYQHQKKGFLTSEKFIHKVPATDMEALVSPLLSLMEKNRCKNFYQYVS-------E 173
Query: 195 EENNVRISEEDLDSPFA----EFLTKMKLPHKIKSIVLYAIAMADYDQEVSEYVLKTRDG 250
+ N R + ++LD P+ E L + +A+A+ D + + T
Sbjct: 174 WDANKRNTWDNLD-PYKLTMLEIYKHFNLCQLTIDFLGHAVALYLNDDYLKQPAYLT--- 229
Query: 251 INRLALYNSSIGRFQNALGALIYPIYGQGELPQAFCRRAAVKGCLYVLRMPVISLLTDQN 310
+ R+ LY SI F + IYP+YG G +P+ F R A+ G ++L V+ + D +
Sbjct: 230 LERIKLYMQSISAFGKS--PFIYPLYGLGGIPEGFSRMCAINGGTFMLNKNVVDFVFDDD 287
Query: 311 SGSYKGVRLASGQDILSHKLVLDPSFTVPGSLASSHQQLQESFQAFSLSDNKGKVARGIC 370
+ G++ + G+ K++ DPS+ + L+ + G+V R IC
Sbjct: 288 N-KVCGIKSSDGEIAYCDKVICDPSYVM---------HLKNKIKKI------GQVIRCIC 331
Query: 371 I 371
I
Sbjct: 332 I 332
>pdb|3OIC|A Chain A, Crystal Structure Of Enoyl-Acp Reductases Iii (Fabl) From
B. Subtilis (Apo Form)
pdb|3OIC|D Chain D, Crystal Structure Of Enoyl-Acp Reductases Iii (Fabl) From
B. Subtilis (Apo Form)
pdb|3OID|A Chain A, Crystal Structure Of Enoyl-Acp Reductases Iii (Fabl) From
B. Subtilis (Complex With Nadp And Tcl)
pdb|3OID|B Chain B, Crystal Structure Of Enoyl-Acp Reductases Iii (Fabl) From
B. Subtilis (Complex With Nadp And Tcl)
pdb|3OID|C Chain C, Crystal Structure Of Enoyl-Acp Reductases Iii (Fabl) From
B. Subtilis (Complex With Nadp And Tcl)
pdb|3OID|D Chain D, Crystal Structure Of Enoyl-Acp Reductases Iii (Fabl) From
B. Subtilis (Complex With Nadp And Tcl)
Length = 258
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 9/81 (11%)
Query: 90 DVEISNYASRLL------SQHPRNFNLDVSGPRVLFCADHAVDLMLKSGASHYLEFKSID 143
DV ++N AS +L + ++ ++++ +LFCA A LM K+G H + S+
Sbjct: 84 DVFVNNAASGVLRPVMELEETHWDWTMNINAKALLFCAQEAAKLMEKNGGGHIVSISSLG 143
Query: 144 ATFMLDADAKLCSVPDSRAAI 164
+ L+ +V S+AA+
Sbjct: 144 SIRYLE---NYTTVGVSKAAL 161
>pdb|1ZOV|A Chain A, Crystal Structure Of Monomeric Sarcosine Oxidase From
Bacillus Sp. Ns- 129
pdb|1ZOV|B Chain B, Crystal Structure Of Monomeric Sarcosine Oxidase From
Bacillus Sp. Ns- 129
Length = 386
Score = 33.1 bits (74), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 39/171 (22%), Positives = 68/171 (39%), Gaps = 12/171 (7%)
Query: 21 TAFDLIVIGTGLPESVISAAASASGKSVL---HLDPNPFYGSHFSSLSIADLTHFLNSHS 77
T FD+IV+G G + G L DP GSH I +
Sbjct: 2 THFDVIVVGAGSMGMAAGYYLAKQGVKTLLVDSFDPPHTNGSHHGDTRIIRHAYGEGREY 61
Query: 78 TPSSVCPDPLYSDVEISNYASRLLSQHPRNFNLDVSGPRVLFCADHAVDLMLKSGASHYL 137
P ++ L+ ++E + ++ +Q + V GP+ V +++ H L
Sbjct: 62 VPFALRAQELWYELEKETH-HKIFTQ----TGVLVYGPK---GGSAFVSETMEAANIHSL 113
Query: 138 EFKSIDATFMLDADAKLCSVPDSRAAIFKDKSLGLMEKNQLMRFFKLVQGH 188
E + + + D A + VPD+ AIF+ S L +N + + +L + H
Sbjct: 114 EHELFEGKQLTDRWAGV-EVPDNYEAIFEPNSGVLFSENCIQAYRELAEAH 163
>pdb|3HDQ|A Chain A, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|B Chain B, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|C Chain C, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|D Chain D, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|E Chain E, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|F Chain F, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|G Chain G, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|H Chain H, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|I Chain I, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|J Chain J, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDY|A Chain A, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|B Chain B, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|C Chain C, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|D Chain D, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|E Chain E, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|F Chain F, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|G Chain G, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|H Chain H, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|I Chain I, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|J Chain J, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HE3|A Chain A, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|B Chain B, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|C Chain C, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|D Chain D, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|E Chain E, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|F Chain F, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|G Chain G, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|H Chain H, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|I Chain I, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|J Chain J, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3MJ4|A Chain A, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|B Chain B, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|C Chain C, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|D Chain D, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|E Chain E, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|F Chain F, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|G Chain G, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|H Chain H, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|I Chain I, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|J Chain J, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
Length = 397
Score = 31.2 bits (69), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 22 AFDLIVIGTGLPESVISAAASASGKSVLHLDPNPFYGSH 60
FD +++G G SV++ ++SG+ VL +D P G +
Sbjct: 29 GFDYLIVGAGFAGSVLAERLASSGQRVLIVDRRPHIGGN 67
>pdb|2Y0S|C Chain C, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|Y Chain Y, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|C Chain C, Rnap At 3.2ang
pdb|4B1O|C Chain C, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|Y Chain Y, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 395
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 31/90 (34%), Positives = 46/90 (51%), Gaps = 6/90 (6%)
Query: 164 IFKDKSLGLMEKNQLMRFFKLVQGHLSLDESEENNVRISEEDLDSPFAEFLTKMK-LPHK 222
+ KDK + + + + + KL G +DESE N + IS ++DS A F + K L K
Sbjct: 173 MLKDKGVTVDDVKKAINRLKL--GEFVIDESEGNTLNISFANIDSIAALFKLRDKILNTK 230
Query: 223 IKSIVLYAIAMADYDQEVSEYVLKTRDGIN 252
IK I I A ++ EY++ T DG N
Sbjct: 231 IKGI--KGIKRAIVQKKGDEYIILT-DGSN 257
>pdb|2WAC|A Chain A, Extended Tudor Domain Of Drosophila Melanogaster Tudor-Sn
( P100)
pdb|2WAC|B Chain B, Extended Tudor Domain Of Drosophila Melanogaster Tudor-Sn
( P100)
Length = 218
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 42/94 (44%), Gaps = 14/94 (14%)
Query: 257 YNSSIGRFQNALGALIYPIYGQGE---------LPQAFCRRAAVKGCLYVLRMPVISLLT 307
Y + + R Q + ++Y YG E LP AF Y L + ++L T
Sbjct: 69 YRAKVERVQGSNATVLYIDYGNKETLPTNRLAALPPAFSSEKPY-ATEYALAL--VALPT 125
Query: 308 DQNSGSYKGVRLASGQDILSHKLVLDPSFTVPGS 341
D N + +R A +D+L+HK+ L+ V GS
Sbjct: 126 D-NEDKEEALR-AFSEDVLNHKVQLNVELKVTGS 157
>pdb|3DZB|A Chain A, Crystal Structure Of Prephenate Dehydrogenase From
Streptococcus Thermophilus
pdb|3DZB|B Chain B, Crystal Structure Of Prephenate Dehydrogenase From
Streptococcus Thermophilus
Length = 317
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 44/87 (50%), Gaps = 10/87 (11%)
Query: 29 GTGLPESVISAAASASGKSVLHLDPNPFYGSHFSSLSIADLTHFLNSHS--TPSSVCPD- 85
G+ E V +A +GK+V + +P GSH S AD+T F N++ TP+S+ +
Sbjct: 100 GSTKREIVEAAERYLTGKNVQFVGSHPXAGSHKSGAIAADVTLFENAYYIFTPTSLTKET 159
Query: 86 --PLYSDVEISNYASRLL----SQHPR 106
P D+ +S SR + ++H R
Sbjct: 160 TIPELKDI-LSGLKSRYVEIDAAEHDR 185
>pdb|2KEB|A Chain A, Nmr Solution Structure Of The N-Terminal Domain Of The Dna
Polymerase Alpha P68 Subunit
Length = 101
Score = 28.9 bits (63), Expect = 5.2, Method: Composition-based stats.
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 332 LDPSFTVPGSLASSHQQLQESFQAFSL 358
L+ F PGS+++S QQL E Q F L
Sbjct: 14 LEVLFQGPGSMSASAQQLAEELQIFGL 40
>pdb|2WAQ|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|Y Chain Y, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
Length = 395
Score = 28.1 bits (61), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 45/90 (50%), Gaps = 6/90 (6%)
Query: 164 IFKDKSLGLMEKNQLMRFFKLVQGHLSLDESEENNVRISEEDLDSPFAEFLTKMK-LPHK 222
+ KDK + + + + + KL G +DESE + IS ++DS A F + K L K
Sbjct: 173 MLKDKGVTVDDVKKAINRLKL--GEFVIDESEGTTLNISFANIDSIAALFKLRDKILNTK 230
Query: 223 IKSIVLYAIAMADYDQEVSEYVLKTRDGIN 252
IK I I A ++ EY++ T DG N
Sbjct: 231 IKGI--KGIKRAIVQKKGDEYIILT-DGSN 257
>pdb|3SB4|A Chain A, Crystal Structure Of A Hypothetical Leucine Rich Repeat
Protein (Bt_1240) From Bacteroides Thetaiotaomicron
Vpi-5482 At 1.99 A Resolution
pdb|3SB4|B Chain B, Crystal Structure Of A Hypothetical Leucine Rich Repeat
Protein (Bt_1240) From Bacteroides Thetaiotaomicron
Vpi-5482 At 1.99 A Resolution
Length = 329
Score = 28.1 bits (61), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 30/51 (58%), Gaps = 10/51 (19%)
Query: 182 FKLVQGH----LSLDESEENNVRISEEDLDSPFAE--FLTKMKLPHKIKSI 226
FKL++ + +SLD S+ N I D FA+ +L K+KLPH +K+I
Sbjct: 218 FKLIRDYXPNLVSLDISKTNATTIP----DFTFAQKKYLLKIKLPHNLKTI 264
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 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,162,906
Number of Sequences: 62578
Number of extensions: 429818
Number of successful extensions: 1066
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1033
Number of HSP's gapped (non-prelim): 22
length of query: 407
length of database: 14,973,337
effective HSP length: 101
effective length of query: 306
effective length of database: 8,652,959
effective search space: 2647805454
effective search space used: 2647805454
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: 53 (25.0 bits)