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= 004814
(729 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 44/149 (29%), Positives = 62/149 (41%), Gaps = 26/149 (17%)
Query: 500 KLGDTSEAYRLQEEMLAKGFPPDLITYNVLVHGLCKLGSLEEANELLRKMVGDGFIPDHI 559
K GD EA RL +E G YNVL++ +C L E A E
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSLA--EAATE--------------- 79
Query: 560 TYTSIIHASLEMGDLRRGRDLFNNMLRKGLSPTLVTYTVLIHAHAARGRLELAFMYFSEM 619
+S G L RG D+F M+ + P T+T A+ E+AF +M
Sbjct: 80 -------SSPNPG-LSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQM 131
Query: 620 QVKGIRPNVITYNALINGLCRLRRIDQAY 648
+ GI+P + +Y + G CR D+AY
Sbjct: 132 KAFGIQPRLRSYGPALFGFCRKGDADKAY 160
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 28/128 (21%), Positives = 59/128 (46%), Gaps = 17/128 (13%)
Query: 289 SRNGELEQARGLIRDMLKLGLKVSAHSYNPI--ICGYSEKGL-------LVEALNLEEEM 339
S+ G++ +A L + + G+++S + YN + +C +E L ++ ++M
Sbjct: 37 SKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQM 96
Query: 340 VTRGVAPTLATYNILIYGLCKWGRVSDARHRFFEMLRK----NVIPDIISYNTLLYGYCR 395
+ V P AT+ + D F+M+++ + P + SY L+G+CR
Sbjct: 97 IVDKVVPNEATFT----NGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCR 152
Query: 396 SGNIGEAF 403
G+ +A+
Sbjct: 153 KGDADKAY 160
Score = 39.7 bits (91), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 43/193 (22%), Positives = 80/193 (41%), Gaps = 33/193 (17%)
Query: 395 RSGNIGEAFLLFDELRSRNLVPTVVTYNTLIDGLCRYGDLEVAQQLKENMINQGILPDVI 454
+ G++ EA L+DE R + + YN L+ +C +A+ E+ N G
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLL-YVC-----SLAEAATESSPNPG------ 85
Query: 455 TYTIMVNGSCKMGNLSMAREFFNEMLRKGLQPDRFAYTTQIAGELKLGDTSEAYRLQEEM 514
LS + F +M+ + P+ +T + D A+ + ++M
Sbjct: 86 --------------LSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQM 131
Query: 515 LAKGFPPDLITYNVLVHGLCKLGSLEEANELLRKMVGDGFIPDHITYTSIIHASLEMGD- 573
A G P L +Y + G C+ G ++A E+ MV +P+ +++ S++ +
Sbjct: 132 KAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNA 191
Query: 574 ------LRRGRDL 580
L+R RDL
Sbjct: 192 DKVYKTLQRLRDL 204
Score = 33.9 bits (76), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 36/71 (50%)
Query: 195 VFNKMLRNGLLPDVKNCNRIIKVLRDNGFSVKAREVYRMMGEFGIKPSIVTYNTMLDSFC 254
+F +M+ + ++P+ ++ A ++ + M FGI+P + +Y L FC
Sbjct: 92 IFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFC 151
Query: 255 KEGEMQEALEL 265
++G+ +A E+
Sbjct: 152 RKGDADKAYEV 162
Score = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 30/127 (23%), Positives = 53/127 (41%), Gaps = 9/127 (7%)
Query: 250 LDSFCKEGEMQEALELLWEMQGRGCSPNGVTYNVLI---------TGFSRNGELEQARGL 300
LD K+G++ EAL L E + G + YNVL+ T S N L + +
Sbjct: 33 LDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92
Query: 301 IRDMLKLGLKVSAHSYNPIICGYSEKGLLVEALNLEEEMVTRGVAPTLATYNILIYGLCK 360
+ M+ + + ++ K A ++ ++M G+ P L +Y ++G C+
Sbjct: 93 FKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCR 152
Query: 361 WGRVSDA 367
G A
Sbjct: 153 KGDADKA 159
>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana, Semet Substituted Form With Sr
Length = 501
Score = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 42/149 (28%), Positives = 59/149 (39%), Gaps = 26/149 (17%)
Query: 500 KLGDTSEAYRLQEEMLAKGFPPDLITYNVLVHGLCKLGSLEEANELLRKMVGDGFIPDHI 559
K GD EA RL +E G YNVL++ +C L E A E
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSLA--EAATE--------------- 79
Query: 560 TYTSIIHASLEMGDLRRGRDLFNNMLRKGLSPTLVTYTVLIHAHAARGRLELAFMYFSEM 619
+S G L RG D+F + + P T+T A+ E AF +
Sbjct: 80 -------SSPNPG-LSRGFDIFKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQX 131
Query: 620 QVKGIRPNVITYNALINGLCRLRRIDQAY 648
+ GI+P + +Y + G CR D+AY
Sbjct: 132 KAFGIQPRLRSYGPALFGFCRKGDADKAY 160
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 28/124 (22%), Positives = 54/124 (43%), Gaps = 11/124 (8%)
Query: 324 SEKGLLVEALNLEEEMVTRGVAPTLATYNILIYGLCKWGRVSDAR------HRFFEMLRK 377
S+KG ++EAL L +E GV + YN+L+Y +C + R F++ ++
Sbjct: 37 SKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSLAEAATESSPNPGLSRGFDIFKQ 95
Query: 378 NVIPDIISYNTLLYGYCR----SGNIGEAFLLFDELRSRNLVPTVVTYNTLIDGLCRYGD 433
++ ++ R + AF + ++ + P + +Y + G CR GD
Sbjct: 96 XIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGD 155
Query: 434 LEVA 437
+ A
Sbjct: 156 ADKA 159
Score = 33.9 bits (76), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 32/151 (21%), Positives = 59/151 (39%), Gaps = 26/151 (17%)
Query: 395 RSGNIGEAFLLFDELRSRNLVPTVVTYNTLIDGLCRYGDLEVAQQLKENMINQGILPDVI 454
+ G++ EA L+DE R + + YN L+ +C +A+ E+ N G
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLL-YVC-----SLAEAATESSPNPG------ 85
Query: 455 TYTIMVNGSCKMGNLSMAREFFNEMLRKGLQPDRFAYTTQIAGELKLGDTSEAYRLQEEM 514
LS + F + + + P+ +T + D A+ ++
Sbjct: 86 --------------LSRGFDIFKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQX 131
Query: 515 LAKGFPPDLITYNVLVHGLCKLGSLEEANEL 545
A G P L +Y + G C+ G ++A E+
Sbjct: 132 KAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 227 AREVYRMMGEFGIKPSIVTYNTMLDSFCKEGEMQEALEL 265
A + + FGI+P + +Y L FC++G+ +A E+
Sbjct: 124 AFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162
>pdb|1WWM|A Chain A, Crystal Structure Of Conserved Hypothetical Protein Tt2028
From An Extremely Thermophilic Bacterium Thermus
Thermophilus Hb8
pdb|1WWM|B Chain B, Crystal Structure Of Conserved Hypothetical Protein Tt2028
From An Extremely Thermophilic Bacterium Thermus
Thermophilus Hb8
Length = 190
Score = 34.3 bits (77), Expect = 0.24, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 19/31 (61%)
Query: 67 EEKPWAFCNNRWVSDHFQAVVSDPELLVRVL 97
EE PWA + W + FQAV+ D E+L R L
Sbjct: 132 EEGPWAELSQHWFAPEFQAVLYDLEVLARGL 162
>pdb|3OM3|A Chain A, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With K362m Mutation In The
Reduced State
pdb|3OM3|C Chain C, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With K362m Mutation In The
Reduced State
pdb|3OMA|A Chain A, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With K362m Mutation
pdb|3OMA|C Chain C, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With K362m Mutation
Length = 535
Score = 30.0 bits (66), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 255 KEGEMQEALELLWEMQGRGCSPNGVTYNVLITG 287
+ G ++ + LW C+PNG +NV+ITG
Sbjct: 53 ESGLVKGFFQSLWPSAVENCTPNGHLWNVMITG 85
>pdb|1M56|A Chain A, Structure Of Cytochrome C Oxidase From Rhodobactor
Sphaeroides (Wild Type)
pdb|1M56|G Chain G, Structure Of Cytochrome C Oxidase From Rhodobactor
Sphaeroides (Wild Type)
pdb|2GSM|A Chain A, Catalytic Core (Subunits I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides
pdb|2GSM|C Chain C, Catalytic Core (Subunits I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides
pdb|3DTU|A Chain A, Catalytic Core Subunits (i And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides Complexed With Deoxycholic
Acid
pdb|3DTU|C Chain C, Catalytic Core Subunits (i And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides Complexed With Deoxycholic
Acid
pdb|3FYE|A Chain A, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides In The Reduced State
pdb|3FYE|C Chain C, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides In The Reduced State
pdb|3FYI|A Chain A, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides In The Reduced State Bound
With Cyanide
pdb|3FYI|C Chain C, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides In The Reduced State Bound
With Cyanide
Length = 566
Score = 30.0 bits (66), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 255 KEGEMQEALELLWEMQGRGCSPNGVTYNVLITG 287
+ G ++ + LW C+PNG +NV+ITG
Sbjct: 69 ESGLVKGFFQSLWPSAVENCTPNGHLWNVMITG 101
>pdb|1M57|A Chain A, Structure Of Cytochrome C Oxidase From Rhodobacter
Sphaeroides (Eq(I-286) Mutant))
pdb|1M57|G Chain G, Structure Of Cytochrome C Oxidase From Rhodobacter
Sphaeroides (Eq(I-286) Mutant))
Length = 566
Score = 30.0 bits (66), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 255 KEGEMQEALELLWEMQGRGCSPNGVTYNVLITG 287
+ G ++ + LW C+PNG +NV+ITG
Sbjct: 69 ESGLVKGFFQSLWPSAVENCTPNGHLWNVMITG 101
>pdb|3OMI|A Chain A, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With D132a Mutation
pdb|3OMI|C Chain C, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With D132a Mutation
pdb|3OMN|A Chain A, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With D132a Mutation In The
Reduced State
pdb|3OMN|C Chain C, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With D132a Mutation In The
Reduced State
Length = 535
Score = 30.0 bits (66), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 255 KEGEMQEALELLWEMQGRGCSPNGVTYNVLITG 287
+ G ++ + LW C+PNG +NV+ITG
Sbjct: 53 ESGLVKGFFQSLWPSAVENCTPNGHLWNVMITG 85
>pdb|3M84|A Chain A, Crystal Structure Of Phosphoribosylaminoimidazole
Synthetase From Francisella Tularensis
pdb|3M84|B Chain B, Crystal Structure Of Phosphoribosylaminoimidazole
Synthetase From Francisella Tularensis
pdb|3QTY|A Chain A, Crystal Structure Of Phosphoribosylaminoimidazole
Synthetase From Francisella Tularensis Complexed With
Pyrophosphate
pdb|3QTY|B Chain B, Crystal Structure Of Phosphoribosylaminoimidazole
Synthetase From Francisella Tularensis Complexed With
Pyrophosphate
Length = 350
Score = 29.3 bits (64), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 544 ELLRKMVGDGFIPDHITYTSIIHASLEMG 572
EL K +GD + HI YT+IIH L+ G
Sbjct: 218 ELEGKTIGDVLLEPHINYTNIIHDFLDNG 246
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 0.140 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,731,478
Number of Sequences: 62578
Number of extensions: 916893
Number of successful extensions: 1850
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1816
Number of HSP's gapped (non-prelim): 23
length of query: 729
length of database: 14,973,337
effective HSP length: 106
effective length of query: 623
effective length of database: 8,340,069
effective search space: 5195862987
effective search space used: 5195862987
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: 55 (25.8 bits)