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= psy3426
(360 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QQ8|A Chain A, Crystal Structure Of The Putative Rabgap Domain Of Human
Tbc1 Domain Family Member 14
Length = 334
Score = 58.2 bits (139), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 44/165 (26%), Positives = 67/165 (40%), Gaps = 4/165 (2%)
Query: 23 HTKLKRVLKAWVTSHPQFDFVYWQGLDSLCAPFVFLNFNDEATAYACFSTFIPKYLHNFF 82
H L +L A+ P +V QG+ S A + LN D A A+ FS + K F
Sbjct: 134 HDMLHSILGAYTCYRPDVGYV--QGM-SFIAAVLILNL-DTADAFIAFSNLLNKPCQMAF 189
Query: 83 LRDNSAVVREYLSKFSHLIAFHDAELANHMSEINFIPELFAIPWFLTMFSHVLPLHKIFH 142
R + ++ Y + F + +L H + N P+++ I W T++S LPL
Sbjct: 190 FRVDHGLMLTYFAAFEVFFEENLPKLFAHFKKNNLTPDIYLIDWIFTLYSKSLPLDLACR 249
Query: 143 LWDKLLLGDASFPLFIGVSILKQLRETLLSSGFNECILLFSDLPE 187
+WD F + ILK + L F + LPE
Sbjct: 250 IWDVFCRDGEEFLFRTALGILKLFEDILTKMDFIHMAQFLTRLPE 294
>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 = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 42/165 (25%), Positives = 67/165 (40%), Gaps = 4/165 (2%)
Query: 18 SSKTGHTKLKRVLKAWVTSHPQFDFVYWQGLDSLCAPFVFLNFNDEATAYACFSTFIPKY 77
+ G L ++ KA+ D Y QG L A V L E A+ Y
Sbjct: 90 TGGDGQESLYKICKAYSVYDE--DIGYCQGQSFLAA--VLLLHXPEEQAFCVLVKIXYDY 145
Query: 78 LHNFFLRDNSAVVREYLSKFSHLIAFHDAELANHMSEINFIPELFAIPWFLTMFSHVLPL 137
R+N + + L +L +H S++N +A WFLT+F+ PL
Sbjct: 146 GLRDLYRNNFEDLHCKFYQLERLXQEQLPDLHSHFSDLNLEAHXYASQWFLTLFTAKFPL 205
Query: 138 HKIFHLWDKLLLGDASFPLFIGVSILKQLRETLLSSGFNECILLF 182
+FH+ D LL + + +++LK +E LL + F + F
Sbjct: 206 CXVFHIIDLLLCEGLNIIFHVALALLKTSKEDLLQADFEGALKFF 250
>pdb|3QYE|A Chain A, Crystal Structure Of Human Tbc1d1 Rabgap Domain
pdb|3QYE|B Chain B, Crystal Structure Of Human Tbc1d1 Rabgap Domain
Length = 331
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 47/178 (26%), Positives = 80/178 (44%), Gaps = 14/178 (7%)
Query: 21 TGHTKLKRVLKAWVTSHPQFDFVYWQGLDSLCAPFVFLNFNDEAT----AYACFSTFIPK 76
G L +LKA+ S + Y QGL S A + L+ ++E + F + K
Sbjct: 127 AGQLSLYNILKAY--SLLDQEVGYCQGL-SFVAGILLLHMSEEEAFKMLKFLMFDMGLRK 183
Query: 77 YLHNFFLRDNSAVVREYLSKFSHLIAFHDAELANHMSEINFIPELFAIPWFLTMFSHVLP 136
R + +++ + + S L+ + +L NH+ E P L+A PWFLTMF+ P
Sbjct: 184 QY-----RPDMIILQIQMYQLSRLLHDYHRDLYNHLEEHEIGPSLYAAPWFLTMFASQFP 238
Query: 137 LHKIFHLWDKLLLGDASFPLFIGVSILKQLRETLLSSGFNECILLF--SDLPEVDIEQ 192
L + ++D + L + +S+L + +L E I+ F S LP + + Q
Sbjct: 239 LGFVARVFDMIFLQGTEVIFKVALSLLGSHKPLILQHENLETIVDFIKSTLPNLGLVQ 296
>pdb|3QWL|A Chain A, Crystal Structure Of Human Tbc1 Domain Family Member 7
Length = 294
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 29/113 (25%), Positives = 52/113 (46%), Gaps = 4/113 (3%)
Query: 97 FSHLIAFHDAELANHMSEINFIPELFAIPWFLTMFSHVLPLHKIFHLWDKLLLGDASFPL 156
F + D L H+ + P+L WF F+ LP + +WDK++ G +
Sbjct: 178 FEQYLNLEDGRLLTHLRMCSAAPKLPYDLWFKRCFAGCLPESSLQRVWDKVVSGSCKILV 237
Query: 157 FIGVSILKQLRETLLSSGFNECILLF-SDLPEVDIEQSVTDSIDIY---CVTP 205
F+ V IL + +++ E I F ++P+ + V+ +ID++ C TP
Sbjct: 238 FVAVEILLTFKIKVMALNSAEKITKFLENIPQDSSDAIVSKAIDLWHKHCGTP 290
>pdb|3DZX|A Chain A, Crystal Structure Of The Rabgap Domain Of Human Tbc1d22b
Length = 346
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 44/188 (23%), Positives = 74/188 (39%), Gaps = 30/188 (15%)
Query: 27 KRVLKAWVTSHPQFDFVYWQGLDSLCAPF--VFL---------NFND-----------EA 64
+R+L W HP +V QG++ L PF VFL NF+ EA
Sbjct: 133 ERILFIWAIRHPASGYV--QGINDLVTPFFVVFLSEYVEEDVENFDVTNLSQDMLRSIEA 190
Query: 65 TAYACFSTFIPKYLHNFFLRDNSAVVREYLSKFSHLIAFHDAELANHMSEINFIPELFAI 124
++ C S + N+ +++ + L++ D ++ NH FA
Sbjct: 191 DSFWCMSKLLDGIQDNYTF--AQPGIQKKVKALEELVSRIDEQVHNHFRRYEVEYLQFAF 248
Query: 125 PWFLTMFSHVLPLHKIFHLWDKLLL---GDASFPLFIGVSILKQLRETLL-SSGFNECIL 180
W + LPL LWD G + F L++ + L + R+ +L F ++
Sbjct: 249 RWMNNLLMRELPLRCTIRLWDTYQSEPEGFSHFHLYVCAAFLIKWRKEILDEEDFQGLLM 308
Query: 181 LFSDLPEV 188
L +LP +
Sbjct: 309 LLQNLPTI 316
>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 = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 42/188 (22%), Positives = 70/188 (37%), Gaps = 33/188 (17%)
Query: 27 KRVLKAWVTSHPQFDFVYWQGLDSLCAPFVFLNF------------------------ND 62
+R+L W HP +V QG++ L PF F+ F N
Sbjct: 131 ERILFIWAIRHPASGYV--QGINDLVTPF-FVVFICEYIEAEEVDTVDVSGVPAEVLCNI 187
Query: 63 EATAYACFSTFIPKYLHNFFLRDNSAVVREYLSKFSHLIAFHDAELANHMSEINFIPELF 122
EA Y C S + N+ ++ + L++ D ++ H+ + F
Sbjct: 188 EADTYWCMSKLLDGIQDNYTFAQPGIQMK--VKMLEELVSRIDEQVHRHLDQHEVRYLQF 245
Query: 123 AIPWFLTMFSHVLPLHKIFHLWDKLLL---GDASFPLFIGVSILKQLRETLL-SSGFNEC 178
A W + +PL LWD G + F L++ + L + R+ +L F E
Sbjct: 246 AFRWMNNLLMREVPLRCTIRLWDTYQSEPDGFSHFHLYVCAAFLVRWRKEILEEKDFQEL 305
Query: 179 ILLFSDLP 186
+L +LP
Sbjct: 306 LLFLQNLP 313
>pdb|3QYB|A Chain A, X-Ray Crystal Structure Of Human Tbc1d4 (As160) Rabgap
Domain
Length = 301
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 96 KFSHLIAFHDAELANHMSEINFIPELFAIPWFLTMFSHVLPLHKIFHLWDKLLLGDASFP 155
+ S L+ + +L NH+ E P L+A PWFLT+F+ L + ++D + L
Sbjct: 188 QLSRLLHDYHRDLYNHLEENEISPSLYAAPWFLTLFASQFSLGFVARVFDIIFLQGTEVI 247
Query: 156 LFIGVSILKQLRETLL 171
+ +S+L +ETL+
Sbjct: 248 FKVALSLLSS-QETLI 262
>pdb|2G77|A Chain A, Crystal Structure Of Gyp1 Tbc Domain In Complex With Rab33
Gtpase Bound To Gdp And Alf3
Length = 410
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 36/158 (22%), Positives = 60/158 (37%), Gaps = 35/158 (22%)
Query: 20 KTGHTKLKRVLKAWVTSHPQFDFVYWQGLDSLCAPF--VFL-------NFND-------- 62
K+ L+R+L W HP +V QG++ L PF FL +D
Sbjct: 127 KSVQNSLQRILYLWAIRHPASGYV--QGINDLVTPFFETFLTEYLPPSQIDDVKIKDPST 184
Query: 63 ----------EATAYACFSTFIPKYLHNFFLRDNSAVVREYLSKFSHLIAFHDAELANHM 112
EA + C + + + N ++ ++R+ + S L+ DA+L NH
Sbjct: 185 YMVDEQITDLEADTFWCLTKLLEQITDN-YIHGQPGILRQ-VKNLSQLVKRIDADLYNHF 242
Query: 113 SE--INFIPELFAIPWFLTMFSHVLPLHKIFHLWDKLL 148
+ FI FA W + + + +WD L
Sbjct: 243 QNEHVEFI--QFAFRWMNCLLMREFQMGTVIRMWDTYL 278
>pdb|1FKM|A Chain A, Crystal Structure Of The YptRAB-Gap Domain Of Gyp1p
Length = 396
Score = 35.0 bits (79), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 36/158 (22%), Positives = 58/158 (36%), Gaps = 35/158 (22%)
Query: 20 KTGHTKLKRVLKAWVTSHPQFDFVYWQGLDSLCAPF--VFL-------NFND-------- 62
K+ L+R+L W HP +V QG++ L PF FL +D
Sbjct: 107 KSVQNSLQRILYLWAIRHPASGYV--QGINDLVTPFFETFLTEYLPPSQIDDVEIKDPST 164
Query: 63 ----------EATAYACFSTFIPKYLHNFFLRDNSAVVREYLSKFSHLIAFHDAELANHM 112
EA + C + + + N ++ ++R+ + S L+ DA+L NH
Sbjct: 165 YXVDEQITDLEADTFWCLTKLLEQITDN-YIHGQPGILRQ-VKNLSQLVKRIDADLYNHF 222
Query: 113 SE--INFIPELFAIPWFLTMFSHVLPLHKIFHLWDKLL 148
+ FI FA W + + WD L
Sbjct: 223 QNEHVEFI--QFAFRWXNCLLXREFQXGTVIRXWDTYL 258
>pdb|2JTQ|A Chain A, Rhodanese From E.Coli
pdb|2JTR|A Chain A, Rhodanese Persulfide From E. Coli
pdb|2JTS|A Chain A, Rhodanese With Anions From E. Coli
Length = 85
Score = 30.0 bits (66), Expect = 1.9, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 260 IDIRDNEEYVAESIIGSINIPLARIPDLEST 290
ID+R E+Y E + G+INIPL + + +T
Sbjct: 5 IDVRVPEQYQQEHVQGAINIPLKEVKERIAT 35
>pdb|3D1P|A Chain A, Atomic Resolution Structure Of Uncharacterized Protein
From Saccharomyces Cerevisiae
Length = 139
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 255 PKVLVIDIRDNEEYVAESIIGSINIPLARIPD 286
P V+++D+R+ EY I SIN+P PD
Sbjct: 39 PNVVLVDVREPSEYSIVHIPASINVPYRSHPD 70
>pdb|3G5J|A Chain A, Crystal Structure Of N-Terminal Domain Of Putative AtpGTP
BINDING Protein From Clostridium Difficile 630
pdb|3G5J|B Chain B, Crystal Structure Of N-Terminal Domain Of Putative AtpGTP
BINDING Protein From Clostridium Difficile 630
Length = 134
Score = 28.1 bits (61), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 248 INTRFKKPKVLVIDIRDNEEYVAESIIGSINIPLARIPDLESTDLGSM 295
I K KV+ +D+R EY + I+ +IN PL + E ++G++
Sbjct: 9 IEKALKLDKVIFVDVRTEGEYEEDHILNAINXPL--FKNNEHNEVGTI 54
>pdb|4HL4|A Chain A, Crystal Structure Of The Human Tbc1d20 Rabgap Domain
Length = 292
Score = 28.1 bits (61), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 33/131 (25%), Positives = 55/131 (41%), Gaps = 10/131 (7%)
Query: 44 YWQGLDSLCAPFVFLNFNDEATAYACFSTFIPKYLHNFF--LRDNSAVVREYLSKFSHLI 101
Y+QG + F+ + E A + +L +F DN+ + YL +I
Sbjct: 129 YYQGYHDIVVTFLLVV--GERLATSLVEKLSTHHLRDFMDPTMDNTKHILNYLMP---II 183
Query: 102 AFHDAELANHMSEINFIPELFAIPWFLTMFSHVLP-LHKIFHLWDKLLLGDASFPL-FIG 159
+ EL + M + +FA+ W +T F HVL + L+D L P+ F
Sbjct: 184 DQVNPELHDFMQSAE-VGTIFALSWLITWFGHVLSDFRHVVRLYDFFLACHPLMPIYFAA 242
Query: 160 VSILKQLRETL 170
V +L + +E L
Sbjct: 243 VIVLYREQEVL 253
>pdb|4HLQ|A Chain A, Crystal Structure Of Human Rab1b Bound To Gdp And Bef3 In
Complex With The Gap Domain Of Tbc1d20 From Homo Sapiens
pdb|4HLQ|C Chain C, Crystal Structure Of Human Rab1b Bound To Gdp And Bef3 In
Complex With The Gap Domain Of Tbc1d20 From Homo Sapiens
pdb|4HLQ|E Chain E, Crystal Structure Of Human Rab1b Bound To Gdp And Bef3 In
Complex With The Gap Domain Of Tbc1d20 From Homo Sapiens
pdb|4HLQ|G Chain G, Crystal Structure Of Human Rab1b Bound To Gdp And Bef3 In
Complex With The Gap Domain Of Tbc1d20 From Homo Sapiens
pdb|4HLQ|I Chain I, Crystal Structure Of Human Rab1b Bound To Gdp And Bef3 In
Complex With The Gap Domain Of Tbc1d20 From Homo Sapiens
Length = 305
Score = 27.7 bits (60), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 33/131 (25%), Positives = 55/131 (41%), Gaps = 10/131 (7%)
Query: 44 YWQGLDSLCAPFVFLNFNDEATAYACFSTFIPKYLHNFF--LRDNSAVVREYLSKFSHLI 101
Y+QG + F+ + E A + +L +F DN+ + YL +I
Sbjct: 142 YYQGYHDIVVTFLLVV--GERLATSLVEKLSTHHLRDFMDPTMDNTKHILNYLMP---II 196
Query: 102 AFHDAELANHMSEINFIPELFAIPWFLTMFSHVLP-LHKIFHLWDKLLLGDASFPL-FIG 159
+ EL + M + +FA+ W +T F HVL + L+D L P+ F
Sbjct: 197 DQVNPELHDFMQSAE-VGTIFALSWLITWFGHVLSDFRHVVRLYDFFLACHPLMPIYFAA 255
Query: 160 VSILKQLRETL 170
V +L + +E L
Sbjct: 256 VIVLYREQEVL 266
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
0.326 0.141 0.433
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,053,071
Number of Sequences: 62578
Number of extensions: 388144
Number of successful extensions: 1370
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1361
Number of HSP's gapped (non-prelim): 15
length of query: 360
length of database: 14,973,337
effective HSP length: 100
effective length of query: 260
effective length of database: 8,715,537
effective search space: 2266039620
effective search space used: 2266039620
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)