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= psy16628
(107 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3EH1|A Chain A, Crystal Structure Of The Human Copii-Coat Protein Sec24b
Length = 751
Score = 74.3 bits (181), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 33/75 (44%), Positives = 48/75 (64%)
Query: 33 LYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAEGQTQPS 92
L+ + V A Y + + LL L +PGD RT I +T+DS +HFY+L EG +QP
Sbjct: 164 LFVLDVSHNAVEAGYLTILCQSLLENLDKLPGDSRTRIGFMTFDSTIHFYNLQEGLSQPQ 223
Query: 93 QMILTDIDDIFLPSP 107
+I++DIDD+FLP+P
Sbjct: 224 MLIVSDIDDVFLPTP 238
>pdb|3EGD|B Chain B, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec23a24A COMPLEXED WITH THE SNARE PROTEIN SEC22 AND
BOUND To The Transport Signal Sequence Of Vesicular
Stomatitis Virus Glycoprotein
pdb|3EGX|B Chain B, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec23a24A COMPLEXED WITH THE SNARE PROTEIN SEC22B AND
Bound To The Transport Signal Sequence Of The Snare
Protein Bet1
Length = 748
Score = 64.3 bits (155), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 39/55 (70%)
Query: 53 EVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAEGQTQPSQMILTDIDDIFLPSP 107
+ LL+ L +PG+ RT I IT+DS +HFY L E +QP +I++DI+D+F+P P
Sbjct: 182 QSLLDNLDLLPGNTRTKIGFITFDSTIHFYGLQESLSQPQMLIVSDIEDVFIPMP 236
>pdb|2NUP|B Chain B, Crystal Structure Of The Human Sec23a24A HETERODIMER,
Complexed With The Snare Protein Sec22b
pdb|2NUT|B Chain B, Crystal Structure Of The Human Sec23a24A HETERODIMER,
Complexed With The Snare Protein Sec22b
Length = 753
Score = 64.3 bits (155), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 39/55 (70%)
Query: 53 EVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAEGQTQPSQMILTDIDDIFLPSP 107
+ LL+ L +PG+ RT I IT+DS +HFY L E +QP +I++DI+D+F+P P
Sbjct: 187 QSLLDNLDLLPGNTRTKIGFITFDSTIHFYGLQESLSQPQMLIVSDIEDVFIPMP 241
>pdb|3EFO|B Chain B, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec2324 BOUND TO THE TRANSPORT SIGNAL SEQUENCE OF
SYNTAXIN 5
pdb|3EG9|B Chain B, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec2324 BOUND TO THE TRANSPORT SIGNAL SEQUENCE OF
MEMBRIN
Length = 770
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 53 EVLLNQLKSMPGDRRTS-----IAIITYDSAVHFYSLAEGQTQPSQMILTDIDDIFLP 105
E L L+ +P + + + ITY+ +HF+++ QP M++TD+ ++F+P
Sbjct: 201 EELKTMLEKIPKEEQEETSAIRVGFITYNKVLHFFNVKSNLAQPQMMVVTDVGEVFVP 258
>pdb|1PCX|A Chain A, Crystal Structure Of The Copii Coat Subunit, Sec24,
Complexed With A Peptide From The Snare Protein Bet1
pdb|1PD0|A Chain A, Crystal Structure Of The Copii Coat Subunit, Sec24,
Complexed With A Peptide From The Snare Protein Sed5
(Yeast Syntaxin-5)
pdb|1PD1|A Chain A, Crystal Structure Of The Copii Coat Subunit, Sec24,
Complexed With A Peptide Containing The Dxe Cargo
Sorting Signal Of Yeast Sys1 Protein
Length = 810
Score = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 8/63 (12%)
Query: 53 EVLLNQLKSMPG-DRRTSIAIITYDSAVHFYSL-------AEGQTQPSQMILTDIDDIFL 104
LL L S+P D RT I+I+ D+A+H++ + E Q + M + D+++ FL
Sbjct: 211 NTLLQNLDSIPNHDERTRISILCVDNAIHYFKIPLDSENNEESADQINMMDIADLEEPFL 270
Query: 105 PSP 107
P P
Sbjct: 271 PRP 273
>pdb|1M2V|B Chain B, Crystal Structure Of The Yeast Sec2324 HETERODIMER
Length = 926
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 8/63 (12%)
Query: 53 EVLLNQLKSMPG-DRRTSIAIITYDSAVHFYSLA-------EGQTQPSQMILTDIDDIFL 104
LL L S+P D RT I+I+ D+A+H++ + E Q + M + D+++ FL
Sbjct: 327 NTLLQNLDSIPNHDERTRISILCVDNAIHYFKIPLDSENNEESADQINMMDIADLEEPFL 386
Query: 105 PSP 107
P P
Sbjct: 387 PRP 389
>pdb|3EH2|A Chain A, Crystal Structure Of The Human Copii-Coat Protein Sec24c
pdb|3EH2|B Chain B, Crystal Structure Of The Human Copii-Coat Protein Sec24c
pdb|3EH2|C Chain C, Crystal Structure Of The Human Copii-Coat Protein Sec24c
Length = 766
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 55 LLNQLKSMPGDRRTSIAI--ITYDSAVHFYSLAEGQTQPSQMILTDIDDIFLP 105
LL+ L G ++I + +TY+ +HFY++ QP M+++D+ D+F+P
Sbjct: 202 LLDFLPREGGAEESAIRVGFVTYNKVLHFYNVKSSLAQPQMMVVSDVADMFVP 254
>pdb|3LL9|A Chain A, X-Ray Structures Of Isopentenyl Phosphate Kinase
pdb|3LL9|B Chain B, X-Ray Structures Of Isopentenyl Phosphate Kinase
Length = 269
Score = 28.5 bits (62), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 27/44 (61%), Gaps = 4/44 (9%)
Query: 65 DRRTSIAIITYDSAVHFYSLAEGQTQPSQMIL-TDIDDIFLPSP 107
DRR ++I+ D ++ +SL + P ++IL TD+D ++ +P
Sbjct: 150 DRRLKFSVISGDQLINHFSL---RLXPERVILGTDVDGVYTRNP 190
>pdb|1QZU|A Chain A, Crystal Structure Of Human Phosphopantothenoylcysteine
Decarboxylase
pdb|1QZU|B Chain B, Crystal Structure Of Human Phosphopantothenoylcysteine
Decarboxylase
pdb|1QZU|C Chain C, Crystal Structure Of Human Phosphopantothenoylcysteine
Decarboxylase
pdb|1QZU|D Chain D, Crystal Structure Of Human Phosphopantothenoylcysteine
Decarboxylase
Length = 206
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%), Gaps = 3/35 (8%)
Query: 49 ALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYS 83
AL+ +L+++L +PG +A++T + A HFYS
Sbjct: 32 ALKLPLLVSKLLDIPG---LEVAVVTTERAKHFYS 63
>pdb|2GTH|A Chain A, Crystal Structure Of The Wildtype Mhv Coronavirus
Non-Structural Protein Nsp15
Length = 370
Score = 26.6 bits (57), Expect = 3.8, Method: Composition-based stats.
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 73 ITYDSAVHFYSLAEGQTQPSQMILTDID 100
+TYDS++H Y + + + S+ + T ID
Sbjct: 298 VTYDSSIHSYFITDENSGSSKSVCTVID 325
>pdb|2GTI|A Chain A, Mutation Of Mhv Coronavirus Non-Structural Protein Nsp15
(F307l)
Length = 370
Score = 26.6 bits (57), Expect = 3.8, Method: Composition-based stats.
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 73 ITYDSAVHFYSLAEGQTQPSQMILTDID 100
+TYDS++H Y + + + S+ + T ID
Sbjct: 298 VTYDSSIHSYLITDENSGSSKSVCTVID 325
>pdb|4ESX|A Chain A, Crystal Structure Of C. Albicans Thi5 Complexed With Plp
pdb|4ESX|B Chain B, Crystal Structure Of C. Albicans Thi5 Complexed With Plp
Length = 342
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 12 HLSNSHAYYTIVWELGIFKCPLYFMVVKGY 41
H+S + + + WE + P+Y +KGY
Sbjct: 3 HMSTNKITFLLNWEAAPYHIPVYLANIKGY 32
>pdb|4ESW|A Chain A, Crystal Structure Of C. Albicans Thi5 H66g Mutant
pdb|4ESW|B Chain B, Crystal Structure Of C. Albicans Thi5 H66g Mutant
Length = 342
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 12 HLSNSHAYYTIVWELGIFKCPLYFMVVKGY 41
H+S + + + WE + P+Y +KGY
Sbjct: 3 HMSTNKITFLLNWEAAPYHIPVYLANIKGY 32
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 0.140 0.435
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,047,833
Number of Sequences: 62578
Number of extensions: 95570
Number of successful extensions: 265
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 254
Number of HSP's gapped (non-prelim): 13
length of query: 107
length of database: 14,973,337
effective HSP length: 72
effective length of query: 35
effective length of database: 10,467,721
effective search space: 366370235
effective search space used: 366370235
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: 45 (21.9 bits)