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= psy4050
(472 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3DZX|A Chain A, Crystal Structure Of The Rabgap Domain Of Human Tbc1d22b
Length = 346
Score = 89.0 bits (219), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 54/190 (28%), Positives = 103/190 (54%), Gaps = 19/190 (10%)
Query: 182 EVVERLLFLYAKMNPGQGYVQGMNEIIGPIYYTFATDPVLDNREH-------------AE 228
E+ ER+LF++A +P GYVQG+N+++ P + F ++ V ++ E+ E
Sbjct: 130 EIFERILFIWAIRHPASGYVQGINDLVTPFFVVFLSEYVEEDVENFDVTNLSQDMLRSIE 189
Query: 229 ADCFFVFTNLMGEIRDFFIKSLDETESGINRLMSKLNQTMKQKDLEVWEKLYAIELHPQY 288
AD F+ + L+ I+D + + + GI + + L + + + D +V E+
Sbjct: 190 ADSFWCMSKLLDGIQDNYTFA----QPGIQKKVKALEELVSRIDEQVHNHFRRYEVEYLQ 245
Query: 289 YSFRWLTLLLSQEFPLPDVLRIWDSLFADELRFSFLN-HICCAMILLVREDIL-AGDFPS 346
++FRW+ LL +E PL +R+WD+ ++ FS + ++C A ++ R++IL DF
Sbjct: 246 FAFRWMNNLLMRELPLRCTIRLWDTYQSEPEGFSHFHLYVCAAFLIKWRKEILDEEDFQG 305
Query: 347 IVKLLQHYPS 356
++ LLQ+ P+
Sbjct: 306 LLMLLQNLPT 315
>pdb|2QFZ|A Chain A, Crystal Structure Of Human Tbc1 Domain Family Member 22a
pdb|2QFZ|B Chain B, Crystal Structure Of Human Tbc1 Domain Family Member 22a
Length = 345
Score = 81.3 bits (199), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 56/209 (26%), Positives = 110/209 (52%), Gaps = 24/209 (11%)
Query: 182 EVVERLLFLYAKMNPGQGYVQGMNEIIGPIYYTFATDPV----LDNRE----------HA 227
E+ ER+LF++A +P GYVQG+N+++ P + F + + +D + +
Sbjct: 128 EIFERILFIWAIRHPASGYVQGINDLVTPFFVVFICEYIEAEEVDTVDVSGVPAEVLCNI 187
Query: 228 EADCFFVFTNLMGEIRDFFIKSLDETESGINRLMSKLNQTMKQKDLEVWEKLYAIELHPQ 287
EAD ++ + L+ I+D + + + GI + L + + + D +V L E+
Sbjct: 188 EADTYWCMSKLLDGIQDNYTFA----QPGIQMKVKMLEELVSRIDEQVHRHLDQHEVRYL 243
Query: 288 YYSFRWLTLLLSQEFPLPDVLRIWDSLFADELRFSFLN-HICCAMILLVREDIL-AGDFP 345
++FRW+ LL +E PL +R+WD+ ++ FS + ++C A ++ R++IL DF
Sbjct: 244 QFAFRWMNNLLMREVPLRCTIRLWDTYQSEPDGFSHFHLYVCAAFLVRWRKEILEEKDFQ 303
Query: 346 SIVKLLQHYPSS----VDIPTVISKAVEL 370
++ LQ+ P++ DI ++++A L
Sbjct: 304 ELLLFLQNLPTAHWDDEDISLLLAEAYRL 332
>pdb|2G77|A Chain A, Crystal Structure Of Gyp1 Tbc Domain In Complex With Rab33
Gtpase Bound To Gdp And Alf3
Length = 410
Score = 75.9 bits (185), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 45/152 (29%), Positives = 80/152 (52%), Gaps = 22/152 (14%)
Query: 184 VERLLFLYAKMNPGQGYVQGMNEIIGPIYYTFAT--------------DP----VLDNRE 225
++R+L+L+A +P GYVQG+N+++ P + TF T DP V +
Sbjct: 133 LQRILYLWAIRHPASGYVQGINDLVTPFFETFLTEYLPPSQIDDVKIKDPSTYMVDEQIT 192
Query: 226 HAEADCFFVFTNLMGEIRDFFIKSLDETESGINRLMSKLNQTMKQKDLEVWEKLYAIELH 285
EAD F+ T L+ +I D +I + GI R + L+Q +K+ D +++ +
Sbjct: 193 DLEADTFWCLTKLLEQITDNYIHG----QPGILRQVKNLSQLVKRIDADLYNHFQNEHVE 248
Query: 286 PQYYSFRWLTLLLSQEFPLPDVLRIWDSLFAD 317
++FRW+ LL +EF + V+R+WD+ ++
Sbjct: 249 FIQFAFRWMNCLLMREFQMGTVIRMWDTYLSE 280
>pdb|1FKM|A Chain A, Crystal Structure Of The YptRAB-Gap Domain Of Gyp1p
Length = 396
Score = 72.8 bits (177), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 45/152 (29%), Positives = 77/152 (50%), Gaps = 22/152 (14%)
Query: 184 VERLLFLYAKMNPGQGYVQGMNEIIGPIYYTFAT--------------DP----VLDNRE 225
++R+L+L+A +P GYVQG+N+++ P + TF T DP V +
Sbjct: 113 LQRILYLWAIRHPASGYVQGINDLVTPFFETFLTEYLPPSQIDDVEIKDPSTYXVDEQIT 172
Query: 226 HAEADCFFVFTNLMGEIRDFFIKSLDETESGINRLMSKLNQTMKQKDLEVWEKLYAIELH 285
EAD F+ T L+ +I D +I + GI R + L+Q +K+ D +++ +
Sbjct: 173 DLEADTFWCLTKLLEQITDNYIHG----QPGILRQVKNLSQLVKRIDADLYNHFQNEHVE 228
Query: 286 PQYYSFRWLTLLLSQEFPLPDVLRIWDSLFAD 317
++FRW LL +EF V+R WD+ ++
Sbjct: 229 FIQFAFRWXNCLLXREFQXGTVIRXWDTYLSE 260
>pdb|2QQ8|A Chain A, Crystal Structure Of The Putative Rabgap Domain Of Human
Tbc1 Domain Family Member 14
Length = 334
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 52/194 (26%), Positives = 77/194 (39%), Gaps = 28/194 (14%)
Query: 173 LEEGREAHWEVVERLLFLYAKMNPGQGYVQGMNEIIGPIYYTFATDPVLDNREHAEADCF 232
++G H +++ +L Y P GYVQGM+ I + T AD F
Sbjct: 127 FQQGGPYH-DMLHSILGAYTCYRPDVGYVQGMSFIAAVLILNLDT-----------ADAF 174
Query: 233 FVFTNLMGEIRDFFIKSLDETESGINRLMSKLNQTMKQKDLEVWEKLYA----IELHPQY 288
F+NL+ + +D G+ + +++L KL+A L P
Sbjct: 175 IAFSNLLNKPCQMAFFRVDH---GLMLTYFAAFEVFFEENLP---KLFAHFKKNNLTPDI 228
Query: 289 YSFRWLTLLLSQEFPLPDVLRIWDSLFADELRFSFLNHICCAMILLVREDILAG-DFPSI 347
Y W+ L S+ PL RIWD D F F + IL + EDIL DF +
Sbjct: 229 YLIDWIFTLYSKSLPLDLACRIWDVFCRDGEEFLFRTALG---ILKLFEDILTKMDFIHM 285
Query: 348 VKLLQHYPSSVDIP 361
+ L P D+P
Sbjct: 286 AQFLTRLPE--DLP 297
>pdb|3HZJ|A Chain A, Crystal Structure Of The Rabgap Domain Of The Rabgap1l
Protein
pdb|3HZJ|B Chain B, Crystal Structure Of The Rabgap Domain Of The Rabgap1l
Protein
pdb|3HZJ|C Chain C, Crystal Structure Of The Rabgap Domain Of The Rabgap1l
Protein
Length = 310
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 38/179 (21%), Positives = 75/179 (41%), Gaps = 21/179 (11%)
Query: 175 EGREAHWEVVERLLFLYAKMNPGQGYVQGMNEIIGPIYYTFATDPVLDNREHAEADCFFV 234
+G+E+ +++ + Y+ + GY QG +F +L + +A C V
Sbjct: 93 DGQESLYKICKA----YSVYDEDIGYCQGQ---------SFLAAVLLLHXPEEQAFCVLV 139
Query: 235 FTNLMGEIRDFFIKSLDETESGINRLMSKLNQTMKQKDL-EVWEKLYAIELHPQYYSFRW 293
+RD + + ++ +L + + Q+ L ++ + L Y+ +W
Sbjct: 140 KIXYDYGLRDLYRNNFEDLHCKFYQL-----ERLXQEQLPDLHSHFSDLNLEAHXYASQW 194
Query: 294 LTLLLSQEFPLPDVLRIWDSLFADELRFSFLNHICCAMILLVREDILAGDFPSIVKLLQ 352
L + +FPL V I D L + L F H+ A++ +ED+L DF +K +
Sbjct: 195 FLTLFTAKFPLCXVFHIIDLLLCEGLNIIF--HVALALLKTSKEDLLQADFEGALKFFR 251
>pdb|2QYJ|A Chain A, Crystal Structure Of A Designed Full Consensus Ankyrin
Length = 166
Score = 32.7 bits (73), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 35/109 (32%), Positives = 47/109 (43%), Gaps = 17/109 (15%)
Query: 98 ALVVRKAAEDYAPLE-EGREAHWEVVERLLFLYAKMNP--GQGYV-------QGMNEIIG 147
A V K + Y PL RE H E+VE LL A +N GY +G EI+
Sbjct: 38 ADVNAKDKDGYTPLHLAAREGHLEIVEVLLKAGADVNAKDKDGYTPLHLAAREGHLEIV- 96
Query: 148 PIYYTFATDPVLENRVRKAAEDYAPLE-EGREAHWEVVERLLFLYAKMN 195
+ D +++ + Y PL RE H E+VE LL A +N
Sbjct: 97 EVLLKAGADVNAKDK-----DGYTPLHLAAREGHLEIVEVLLKAGADVN 140
>pdb|2XEE|A Chain A, Structural Determinants For Improved Thermal Stability Of
Designed Ankyrin Repeat Proteins With A Redesigned C-
Capping Module.
pdb|2XEE|B Chain B, Structural Determinants For Improved Thermal Stability Of
Designed Ankyrin Repeat Proteins With A Redesigned C-
Capping Module.
pdb|2XEE|C Chain C, Structural Determinants For Improved Thermal Stability Of
Designed Ankyrin Repeat Proteins With A Redesigned C-
Capping Module.
pdb|2XEE|D Chain D, Structural Determinants For Improved Thermal Stability Of
Designed Ankyrin Repeat Proteins With A Redesigned C-
Capping Module
Length = 157
Score = 31.6 bits (70), Expect = 0.92, Method: Composition-based stats.
Identities = 34/104 (32%), Positives = 44/104 (42%), Gaps = 17/104 (16%)
Query: 103 KAAEDYAPLE-EGREAHWEVVERLLFLYAKMNP--GQGYV-------QGMNEIIGPIYYT 152
K + Y PL RE H E+VE LL A +N GY +G EI+ +
Sbjct: 31 KDKDGYTPLHLAAREGHLEIVEVLLKAGADVNAKDKDGYTPLHLAAREGHLEIVEVLLKA 90
Query: 153 FATDPVLENRVRKAAEDYAPLE-EGREAHWEVVERLLFLYAKMN 195
A + K + Y PL RE H E+VE LL A +N
Sbjct: 91 GA------DVNAKDKDGYTPLHLAAREGHLEIVEVLLKAGADVN 128
>pdb|2BIB|A Chain A, Crystal Structure Of The Complete Modular Teichioic Acid
Phosphorylcholine Esterase Pce (Cbpe) From Streptococcus
Pneumoniae
Length = 547
Score = 31.6 bits (70), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 3/68 (4%)
Query: 138 YVQGMNEIIGPIYYTFATDPVLENRVRKAAEDYAPL-EEGREA-HWEVVERLLFLYAKMN 195
Y G NEI G YY T +L+N+ +K + L + G A +W+ ++ + + + K N
Sbjct: 333 YAVGWNEIEGEWYYFNQTGILLQNQWKKWNNHWFYLTDSGASAKNWKKIDGIWYYFNKEN 392
Query: 196 PGQ-GYVQ 202
+ G+VQ
Sbjct: 393 QMEIGWVQ 400
>pdb|2XEH|A Chain A, Structural Determinants For Improved Thermal Stability Of
Designed Ankyrin Repeat Proteins With A Redesigned C-
Capping Module.
pdb|2XEH|B Chain B, Structural Determinants For Improved Thermal Stability Of
Designed Ankyrin Repeat Proteins With A Redesigned C-
Capping Module.
pdb|2XEH|C Chain C, Structural Determinants For Improved Thermal Stability Of
Designed Ankyrin Repeat Proteins With A Redesigned C-
Capping Module
Length = 157
Score = 31.6 bits (70), Expect = 0.98, Method: Composition-based stats.
Identities = 34/104 (32%), Positives = 44/104 (42%), Gaps = 17/104 (16%)
Query: 103 KAAEDYAPLE-EGREAHWEVVERLLFLYAKMNP--GQGYV-------QGMNEIIGPIYYT 152
K + Y PL RE H E+VE LL A +N GY +G EI+ +
Sbjct: 31 KDKDGYTPLHLAAREGHLEIVEVLLKAGADVNAKDKDGYTPLHLAAREGHLEIVEVLLKA 90
Query: 153 FATDPVLENRVRKAAEDYAPLE-EGREAHWEVVERLLFLYAKMN 195
A + K + Y PL RE H E+VE LL A +N
Sbjct: 91 GA------DVNAKDKDGYTPLHLAAREGHLEIVEVLLKAGADVN 128
>pdb|2J4O|A Chain A, Structure Of Tab1
Length = 401
Score = 28.9 bits (63), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 42/90 (46%), Gaps = 5/90 (5%)
Query: 223 NREHAEADCFFVFTNLMGEIRDFFIKSLDETESGINRLMSKLNQTMKQKDL-----EVWE 277
N EHAEAD V + F++S+D+ + L S+L + + Q L ++ E
Sbjct: 94 NAEHAEADVRRVLLQAFDVVERSFLESIDDALAEKASLQSQLPEGVPQHQLPPQYQKILE 153
Query: 278 KLYAIELHPQYYSFRWLTLLLSQEFPLPDV 307
+L +E + + +LL+ + + +V
Sbjct: 154 RLKTLEREISGGAMAVVAVLLNNKLYVANV 183
>pdb|2POM|A Chain A, Tab1 With Manganese Ion
Length = 372
Score = 28.9 bits (63), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 30/130 (23%), Positives = 55/130 (42%), Gaps = 12/130 (9%)
Query: 185 ERLLFLYAKMNPGQGYVQGMNEIIGPIYYTFATDPVLD--NREHAEADCFFVFTNLMGEI 242
E FLY N G N + + + + +L N EHAEAD V +
Sbjct: 61 ENNCFLYGVFNGYDG-----NRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVV 115
Query: 243 RDFFIKSLDETESGINRLMSKLNQTMKQKDL-----EVWEKLYAIELHPQYYSFRWLTLL 297
F++S+D+ + L S+L + + Q L ++ E+L +E + + +L
Sbjct: 116 ERSFLESIDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVL 175
Query: 298 LSQEFPLPDV 307
L+ + + +V
Sbjct: 176 LNNKLYVANV 185
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
0.323 0.139 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,778,745
Number of Sequences: 62578
Number of extensions: 568771
Number of successful extensions: 1142
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1100
Number of HSP's gapped (non-prelim): 29
length of query: 472
length of database: 14,973,337
effective HSP length: 102
effective length of query: 370
effective length of database: 8,590,381
effective search space: 3178440970
effective search space used: 3178440970
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)