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= 041442
(230 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4DL0|J Chain J, Crystal Structure Of The Heterotrimeric Egchead Peripheral
Stalk Complex Of The Yeast Vacuolar Atpase
pdb|4DL0|E Chain E, Crystal Structure Of The Heterotrimeric Egchead Peripheral
Stalk Complex Of The Yeast Vacuolar Atpase
pdb|4EFA|E Chain E, Crystal Structure Of The Heterotrimeric Egchead Peripheral
Stalk Complex Of The Yeast Vacuolar Atpase - Second
Conformation
Length = 233
Score = 100 bits (248), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 69/223 (30%), Positives = 122/223 (54%), Gaps = 13/223 (5%)
Query: 6 VSRQIQQMVRFIRQEAEEKANEISVSAEEEFNIEKMQLFEAEKKKIKQEYERKSKQAEAR 65
V+ ++ +M FIR+EAEEKA EI + A++E+ IEK + E I ++ K K+A
Sbjct: 13 VNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKAMLS 72
Query: 66 RKIEYSMQLNAARIKFLQAQDDAVNAMKEAASKELLNVSNDKNKYRTVLKGLIVQSMLRL 125
++I S N R+K L A++ +++ + E ++L ++N++++Y+ +L+ LIV+++L+L
Sbjct: 73 QQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPILQSLIVEALLKL 132
Query: 126 NEKAVLLRCREMDRKLVESIVXXXXXXXXXXXXRQAP--KITMDDKVFLPPPPKSADSHE 183
E +++ E D L+ES+ R AP +I + + ++
Sbjct: 133 LEPKAIVKALERDVDLIESMKDDIMREYGEKAQR-APLEEIVISNDYL----------NK 181
Query: 184 PSCSGGVVVASQDGKIVLENTLDARLNVAFRQNLPEIRKRLLG 226
SGGVVV++ KI + NTL+ RL + + LP IR L G
Sbjct: 182 DLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYG 224
>pdb|2KZ9|A Chain A, Structure Of E1-69 Of Yeast V-Atpase
Length = 69
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 36/57 (63%)
Query: 6 VSRQIQQMVRFIRQEAEEKANEISVSAEEEFNIEKMQLFEAEKKKIKQEYERKSKQA 62
V+ ++ +M FIR+EAEEKA EI + A++E+ IEK + E I ++ K K+A
Sbjct: 13 VNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKA 69
>pdb|2DM9|A Chain A, Crystal Structure Of Ph1978 From Pyrococcus Horikoshii Ot3
pdb|2DM9|B Chain B, Crystal Structure Of Ph1978 From Pyrococcus Horikoshii Ot3
Length = 198
Score = 34.3 bits (77), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 33/132 (25%), Positives = 63/132 (47%), Gaps = 22/132 (16%)
Query: 78 RIKFLQAQDDAVNAMKEAASKELLNVSNDKNKYRTVLKGLIVQSMLRLNEKAVLLRCREM 137
R K L Q++ ++++ E + L +S D+ Y +K L+ +++ LNEK V + E
Sbjct: 72 RRKRLAIQEEIISSVLEEVKRRLETMSEDE--YFESVKALLKEAIKELNEKKVRVMSNEK 129
Query: 138 DRKLVESIVXXXXXXXXXXXXRQAPKITMDDKVFLPPPPKSADSHEPSCSGGVVVASQDG 197
L+ S + + K + D ++ D+ GGV+V ++DG
Sbjct: 130 TLGLIASRI-------------EEIKSELGD--VSIELGETVDTM-----GGVIVETEDG 169
Query: 198 KIVLENTLDARL 209
+I ++NT +AR+
Sbjct: 170 RIRIDNTFEARM 181
>pdb|4DT0|A Chain A, The Structure Of The Peripheral Stalk Subunit E From
Pyrococcus Horikoshii
Length = 208
Score = 34.3 bits (77), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 33/132 (25%), Positives = 63/132 (47%), Gaps = 22/132 (16%)
Query: 78 RIKFLQAQDDAVNAMKEAASKELLNVSNDKNKYRTVLKGLIVQSMLRLNEKAVLLRCREM 137
R K L Q++ ++++ E + L +S D+ Y +K L+ +++ LNEK V + E
Sbjct: 82 RRKRLAIQEEIISSVLEEVKRRLETMSEDE--YFESVKALLKEAIKELNEKKVRVMSNEK 139
Query: 138 DRKLVESIVXXXXXXXXXXXXRQAPKITMDDKVFLPPPPKSADSHEPSCSGGVVVASQDG 197
L+ S + + K + D ++ D+ GGV+V ++DG
Sbjct: 140 TLGLIASRI-------------EEIKSELGDVSI--ELGETVDTM-----GGVIVETEDG 179
Query: 198 KIVLENTLDARL 209
+I ++NT +AR+
Sbjct: 180 RIRIDNTFEARM 191
>pdb|2DMA|A Chain A, Crystal Structure Of Ph1978 From Pyrococcus Horikoshii Ot3
(Form Ii)
Length = 198
Score = 33.5 bits (75), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 33/131 (25%), Positives = 61/131 (46%), Gaps = 22/131 (16%)
Query: 78 RIKFLQAQDDAVNAMKEAASKELLNVSNDKNKYRTVLKGLIVQSMLRLNEKAVLLRCREM 137
R K L Q++ ++++ E + L S D+ Y +K L+ +++ LNEK V + E
Sbjct: 72 RRKRLAIQEEIISSVLEEVKRRLETXSEDE--YFESVKALLKEAIKELNEKKVRVXSNEK 129
Query: 138 DRKLVESIVXXXXXXXXXXXXRQAPKITMDDKVFLPPPPKSADSHEPSCSGGVVVASQDG 197
L+ S + + K + D ++ D+ GGV+V ++DG
Sbjct: 130 TLGLIASRI-------------EEIKSELGD--VSIELGETVDTX-----GGVIVETEDG 169
Query: 198 KIVLENTLDAR 208
+I ++NT +AR
Sbjct: 170 RIRIDNTFEAR 180
>pdb|3DGE|A Chain A, Structure Of A Histidine Kinase-response Regulator Complex
Reveals Insights Into Two-component Signaling And A
Novel Cis- Autophosphorylation Mechanism
pdb|3DGE|B Chain B, Structure Of A Histidine Kinase-response Regulator Complex
Reveals Insights Into Two-component Signaling And A
Novel Cis- Autophosphorylation Mechanism
Length = 258
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 71 SMQLNAARIKFLQAQDDAVNAMKEAASKELLNVSNDKN 108
S+Q+N ++ + AVNA+KE AS +NV + N
Sbjct: 88 SLQINREKVDLCDLVESAVNAIKEFASSHNVNVLFESN 125
>pdb|2C2A|A Chain A, Structure Of The Entire Cytoplasmic Portion Of A Sensor
Histidine Kinase Protein
Length = 258
Score = 27.7 bits (60), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 71 SMQLNAARIKFLQAQDDAVNAMKEAASKELLNVSNDKN 108
S+Q+N ++ + AVNA+KE AS +NV + N
Sbjct: 88 SLQINREKVDLCDLVESAVNAIKEFASSHNVNVLFESN 125
>pdb|3LG8|A Chain A, Crystal Structure Of The C-Terminal Part Of Subunit E
(E101-206) From Methanocaldococcus Jannaschii Of A1ao
Atp Synthase
pdb|3LG8|B Chain B, Crystal Structure Of The C-Terminal Part Of Subunit E
(E101-206) From Methanocaldococcus Jannaschii Of A1ao
Atp Synthase
Length = 106
Score = 27.3 bits (59), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 5/43 (11%)
Query: 183 EP-SCSGGVVVASQDGKIVLENTLDARLNVAFRQNLPEIRKRL 224
EP +GG ++ + DG L+N+L+A F +NL IR R+
Sbjct: 63 EPVDIAGGCIIETADGLKSLDNSLEA----IFNRNLNVIRARI 101
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
0.314 0.129 0.338
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,054,461
Number of Sequences: 62578
Number of extensions: 158800
Number of successful extensions: 425
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 406
Number of HSP's gapped (non-prelim): 28
length of query: 230
length of database: 14,973,337
effective HSP length: 96
effective length of query: 134
effective length of database: 8,965,849
effective search space: 1201423766
effective search space used: 1201423766
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)