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= 008254
(572 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1IRZ|A Chain A, Solution Structure Of Arr10-B Belonging To The Garp Family
Of Plant Myb-Related Dna Binding Motifs Of The
Arabidopsis Response Regulators
Length = 64
Score = 75.1 bits (183), Expect = 9e-14, Method: Composition-based stats.
Identities = 34/61 (55%), Positives = 48/61 (78%)
Query: 328 RKKMKVDWTPELHKKFVQAVEQLGVDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRH 387
+KK +V WT ELH KF+ AV+ LGV++A+P +IL+LM V+ LTR NVASHLQK+R+ +
Sbjct: 3 QKKPRVLWTHELHNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVALKK 62
Query: 388 I 388
+
Sbjct: 63 V 63
>pdb|1L5Y|A Chain A, Crystal Structure Of Mg2+ / Bef3-bound Receiver Domain Of
Sinorhizobium Meliloti Dctd
pdb|1L5Y|B Chain B, Crystal Structure Of Mg2+ / Bef3-bound Receiver Domain Of
Sinorhizobium Meliloti Dctd
pdb|1L5Z|A Chain A, Crystal Structure Of The E121k Substitution Of The
Receiver Domain Of Sinorhizobium Meliloti Dctd
Length = 155
Score = 36.6 bits (83), Expect = 0.043, Method: Composition-based stats.
Identities = 31/121 (25%), Positives = 51/121 (42%), Gaps = 18/121 (14%)
Query: 20 VLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDKPENFHVAIVEVTTSNTDGS 79
V L+D D ++ LE + VS+F + EAL+ S + + I ++ DG
Sbjct: 6 VFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLS--ADFAGIVISDIRMPGMDGL 63
Query: 80 F---KFLETAKDLPTIITSNIHCLSTMMKCIAIMVMNQLFDNNFQLGAVEFLRKPLSEDK 136
K L DLP I+ + + ++ I Q GA +F+ KP + D+
Sbjct: 64 ALFRKILALDPDLPMILVTGHGDIPMAVQAI-------------QDGAYDFIAKPFAADR 110
Query: 137 L 137
L
Sbjct: 111 L 111
>pdb|1QKK|A Chain A, Crystal Structure Of The Receiver Domain And Linker Region
Of Dctd From Sinorhizobium Meliloti
Length = 155
Score = 36.6 bits (83), Expect = 0.043, Method: Composition-based stats.
Identities = 31/121 (25%), Positives = 51/121 (42%), Gaps = 18/121 (14%)
Query: 20 VLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDKPENFHVAIVEVTTSNTDGS 79
V L+D D ++ LE + VS+F + EAL+ S + + I ++ DG
Sbjct: 6 VFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLS--ADFAGIVISDIRMPGMDGL 63
Query: 80 F---KFLETAKDLPTIITSNIHCLSTMMKCIAIMVMNQLFDNNFQLGAVEFLRKPLSEDK 136
K L DLP I+ + + ++ I Q GA +F+ KP + D+
Sbjct: 64 ALFRKILALDPDLPMILVTGHGDIPMAVQAI-------------QDGAYDFIAKPFAADR 110
Query: 137 L 137
L
Sbjct: 111 L 111
>pdb|1NXO|A Chain A, Micarec Ph7.0
pdb|1NXP|A Chain A, Micarec Ph4.5
pdb|1NXS|A Chain A, Micarec Ph4.9
pdb|1NXV|A Chain A, Micarec Ph 4.2
pdb|1NXW|A Chain A, Micarec Ph 5.1
pdb|1NXX|A Chain A, Micarec Ph 5.5
pdb|2A9O|A Chain A, Crystal Structures Of An Activated Yycf Homologue, The
Essential Response Regulator From S.Pneumoniae In
Complex With Bef3 And The Effect Of Ph On Bef3 Binding,
Possible Phosphate In The Active Site
pdb|2A9P|A Chain A, Medium Resolution Bef3 Bound Rr02-Rec
pdb|2A9Q|A Chain A, Low Resolution Structure Rr02-rec On Bef3 Bound
Length = 120
Score = 35.4 bits (80), Expect = 0.090, Method: Composition-based stats.
Identities = 33/123 (26%), Positives = 60/123 (48%), Gaps = 19/123 (15%)
Query: 19 RVLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAF-SDKPENFHVAIVEVTTSNTD 77
++L++D + + +KF + Y V T +N EAL F +++P+ + I+++ D
Sbjct: 3 KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAEQPD---IIILDLMLPEID 59
Query: 78 GSFKFLETAKDLPTIITSNIHCLSTMMKCIAIMVMNQLFDN--NFQLGAVEFLRKPLSED 135
G LE AK + TS++ L K + FD +LGA +++ KP S
Sbjct: 60 G----LEVAKTIRK--TSSVPILMLSAK-------DSEFDKVIGLELGADDYVTKPFSNR 106
Query: 136 KLR 138
+L+
Sbjct: 107 ELQ 109
>pdb|1NXT|A Chain A, Micarec Ph 4.0
pdb|2A9R|A Chain A, Rr02-Rec Phosphate In The Active Site
Length = 120
Score = 34.7 bits (78), Expect = 0.15, Method: Composition-based stats.
Identities = 33/123 (26%), Positives = 59/123 (47%), Gaps = 19/123 (15%)
Query: 19 RVLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAF-SDKPENFHVAIVEVTTSNTD 77
++L++D + + +KF + Y V T +N EAL F +++P+ + I+ + D
Sbjct: 3 KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAEQPD---IIILXLMLPEID 59
Query: 78 GSFKFLETAKDLPTIITSNIHCLSTMMKCIAIMVMNQLFDN--NFQLGAVEFLRKPLSED 135
G LE AK + TS++ L K + FD +LGA +++ KP S
Sbjct: 60 G----LEVAKTIRK--TSSVPILMLSAK-------DSEFDKVIGLELGADDYVTKPFSNR 106
Query: 136 KLR 138
+L+
Sbjct: 107 ELQ 109
>pdb|3JTE|A Chain A, Crystal Structure Of Response Regulator Receiver Domain
Protein From Clostridium Thermocellum
Length = 143
Score = 34.3 bits (77), Expect = 0.22, Method: Composition-based stats.
Identities = 32/122 (26%), Positives = 51/122 (41%), Gaps = 16/122 (13%)
Query: 19 RVLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDKPENFHVAIVEVTTSNTDG 78
++L++D +S+ +KF LE V T + E L F++ + V I ++ G
Sbjct: 5 KILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTENCNSIDVVITDMKMPKLSG 64
Query: 79 SFKFLETAKDLP---TIITSNIHCLSTMMKCIAIMVMNQLFDNNFQLGAVEFLRKPLSED 135
E K P II + L AI+ M + GA E+LRKP++
Sbjct: 65 MDILREIKKITPHMAVIILTGHGDLDN-----AILAMKE--------GAFEYLRKPVTAQ 111
Query: 136 KL 137
L
Sbjct: 112 DL 113
>pdb|3CJN|A Chain A, Crystal Structure Of Transcriptional Regulator, Marr
Family, From Silicibacter Pomeroyi
Length = 162
Score = 33.5 bits (75), Expect = 0.34, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 352 VDQAIPSRILELMKVEGLTRHNVASHLQKYRMHRRHILPKED---DRKWPHARDQMLRNY 408
V+Q+ SR L+ ++ +GL R V S Q R R ++ P DR WPH R R +
Sbjct: 78 VEQSTLSRALDGLQADGLVRREVDSDDQ--RSSRVYLTPAGRAVYDRLWPHXRASHDRXF 135
>pdb|2C4X|A Chain A, Structural Basis For The Promiscuous Specificity Of The
Carbohydrate-Binding Modules From The Beta-Sandwich
Super Family
Length = 260
Score = 32.0 bits (71), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 27/97 (27%), Positives = 45/97 (46%), Gaps = 11/97 (11%)
Query: 425 LVP-TGPVYPVW---GAPSNHLAAVQMWAPPGYPPWQQAESWN--WKPYPGMPADAWGCP 478
+VP T + +W GAP +AA+Q + P P W + WN WK Y + D W
Sbjct: 160 VVPGTTXTFRIWIPSGAP---IAAIQPYIXPHTPDWSEV-LWNSTWKGYTXVKTDDWNEI 215
Query: 479 VMPLPNGPYSSFPQGASGYHNSGVDDNSYAMPQNSVD 515
+ LP ++PQ G +D+ + + +++D
Sbjct: 216 TLTLPEDVDPTWPQ-QXGIQVQTIDEGEFTIYVDAID 251
>pdb|1KRW|A Chain A, Solution Structure And Backbone Dynamics Of
Beryllofluoride- Activated Ntrc Receiver Domain
Length = 124
Score = 30.4 bits (67), Expect = 2.7, Method: Composition-based stats.
Identities = 32/121 (26%), Positives = 49/121 (40%), Gaps = 20/121 (16%)
Query: 20 VLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDKPENFHVAIVEVTTSNTDGS 79
V ++D DSS L+ L +TF N NE L+A + K + V + ++ DG
Sbjct: 6 VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKTPD--VLLSDIRMPGMDG- 62
Query: 80 FKFLETAKD----LPTIITSNIHCLSTMMKCIAIMVMNQLFDNNFQLGAVEFLRKPLSED 135
L+ K LP II + L + +Q GA ++L KP D
Sbjct: 63 LALLKQIKQRHPMLPVIIMTAHSDLDAAVSA-------------YQQGAFDYLPKPFDID 109
Query: 136 K 136
+
Sbjct: 110 E 110
>pdb|1J56|A Chain A, Minimized Average Structure Of Beryllofluoride-Activated
Ntrc Receiver Domain: Model Structure Incorporating
Active Site Contacts
pdb|1KRX|A Chain A, Solution Structure Of Beryllofluoride-Activated Ntrc
Receiver Domain: Model Structures Incorporating Active
Site Contacts
pdb|1NTR|A Chain A, Solution Structure Of The N-Terminal Receiver Domain Of
Ntrc
Length = 124
Score = 30.4 bits (67), Expect = 3.1, Method: Composition-based stats.
Identities = 32/121 (26%), Positives = 49/121 (40%), Gaps = 20/121 (16%)
Query: 20 VLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDKPENFHVAIVEVTTSNTDGS 79
V ++D DSS L+ L +TF N NE L+A + K + V + ++ DG
Sbjct: 6 VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKTPD--VLLSDIRMPGMDG- 62
Query: 80 FKFLETAKD----LPTIITSNIHCLSTMMKCIAIMVMNQLFDNNFQLGAVEFLRKPLSED 135
L+ K LP II + L + +Q GA ++L KP D
Sbjct: 63 LALLKQIKQRHPMLPVIIMTAHSDLDAAVSA-------------YQQGAFDYLPKPFDID 109
Query: 136 K 136
+
Sbjct: 110 E 110
>pdb|1DC7|A Chain A, Structure Of A Transiently Phosphorylated "switch" In
Bacterial Signal Transduction
Length = 124
Score = 30.4 bits (67), Expect = 3.2, Method: Composition-based stats.
Identities = 32/121 (26%), Positives = 49/121 (40%), Gaps = 20/121 (16%)
Query: 20 VLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDKPENFHVAIVEVTTSNTDGS 79
V ++D DSS L+ L +TF N NE L+A + K + V + ++ DG
Sbjct: 6 VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKTPD--VLLSDIRMPGMDG- 62
Query: 80 FKFLETAKD----LPTIITSNIHCLSTMMKCIAIMVMNQLFDNNFQLGAVEFLRKPLSED 135
L+ K LP II + L + +Q GA ++L KP D
Sbjct: 63 LALLKQIKQRHPMLPVIIMTAHSDLDAAVSA-------------YQQGAFDYLPKPFDID 109
Query: 136 K 136
+
Sbjct: 110 E 110
>pdb|2C26|A Chain A, Structural Basis For The Promiscuous Specificity Of The
Carbohydrate-Binding Modules From The Beta-Sandwich
Super Family
Length = 260
Score = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 10/89 (11%)
Query: 432 YPVW---GAPSNHLAAVQMWAPPGYPPWQQAESWN--WKPYPGMPADAWGCPVMPLPNGP 486
+ +W GAP +AA+Q + P P W + WN WK Y + D W + LP
Sbjct: 168 FRIWIPSGAP---IAAIQPYIMPHTPDWSEV-LWNSTWKGYTMVKTDDWNEITLTLPEDV 223
Query: 487 YSSFPQGASGYHNSGVDDNSYAMPQNSVD 515
++PQ G +D+ + + +++D
Sbjct: 224 DPTWPQ-QMGIQVQTIDEGEFTIYVDAID 251
>pdb|1WY5|A Chain A, Crystal Structure Of Isoluecyl-Trna Lysidine Synthetase
pdb|1WY5|B Chain B, Crystal Structure Of Isoluecyl-Trna Lysidine Synthetase
pdb|2E21|A Chain A, Crystal Structure Of Tils In A Complex With Amppnp From
Aquifex Aeolicus.
pdb|2E21|B Chain B, Crystal Structure Of Tils In A Complex With Amppnp From
Aquifex Aeolicus.
pdb|2E21|C Chain C, Crystal Structure Of Tils In A Complex With Amppnp From
Aquifex Aeolicus.
pdb|2E21|D Chain D, Crystal Structure Of Tils In A Complex With Amppnp From
Aquifex Aeolicus.
pdb|2E89|A Chain A, Crystal Structure Of Aquifex Aeolicus Tils In A Complex
With Atp, Magnesium Ion, And L-Lysine
pdb|2E89|C Chain C, Crystal Structure Of Aquifex Aeolicus Tils In A Complex
With Atp, Magnesium Ion, And L-Lysine
pdb|2E89|D Chain D, Crystal Structure Of Aquifex Aeolicus Tils In A Complex
With Atp, Magnesium Ion, And L-Lysine
pdb|2E89|B Chain B, Crystal Structure Of Aquifex Aeolicus Tils In A Complex
With Atp, Magnesium Ion, And L-Lysine
Length = 317
Score = 29.6 bits (65), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 37/85 (43%)
Query: 193 VPQQSDNEQSVPNDKYPAPSTPQLKQGGRLLDDIDCQDNTNFSTEKESAEQDGESKFVET 252
V +++ E S+P ++ P+LK+ L+D + E+E E++ + + E
Sbjct: 189 VEDETNYEVSIPRNRIRHRVIPELKRINENLEDTFLKMVKVLRAEREFLEEEAQKLYKEV 248
Query: 253 TCGNSIAEGTLQEDKPQRPRETIVK 277
GN + L+E R I K
Sbjct: 249 KKGNCLDVKKLKEKPLALQRRVIRK 273
>pdb|1DC8|A Chain A, Structure Of A Transiently Phosphorylated "switch" In
Bacterial Signal Transduction
Length = 124
Score = 29.3 bits (64), Expect = 6.0, Method: Composition-based stats.
Identities = 32/121 (26%), Positives = 48/121 (39%), Gaps = 20/121 (16%)
Query: 20 VLLLDQDSSAAAELKFKLEAMDYIVSTFYNENEALSAFSDKPENFHVAIVEVTTSNTDGS 79
V ++D DSS L+ L +TF N NE L+A + K + V + + DG
Sbjct: 6 VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKTPD--VLLSXIRMPGMDG- 62
Query: 80 FKFLETAKD----LPTIITSNIHCLSTMMKCIAIMVMNQLFDNNFQLGAVEFLRKPLSED 135
L+ K LP II + L + +Q GA ++L KP D
Sbjct: 63 LALLKQIKQRHPMLPVIIMTAHSDLDAAVSA-------------YQQGAFDYLPKPFDID 109
Query: 136 K 136
+
Sbjct: 110 E 110
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 0.131 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,593,272
Number of Sequences: 62578
Number of extensions: 762917
Number of successful extensions: 1261
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1256
Number of HSP's gapped (non-prelim): 16
length of query: 572
length of database: 14,973,337
effective HSP length: 104
effective length of query: 468
effective length of database: 8,465,225
effective search space: 3961725300
effective search space used: 3961725300
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: 54 (25.4 bits)