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= 020181
(330 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WW1|A Chain A, Crystal Structure Of Trnase Z From Thermotoga Maritima
pdb|1WW1|B Chain B, Crystal Structure Of Trnase Z From Thermotoga Maritima
pdb|2E7Y|A Chain A, High Resolution Structure Of T. Maritima Trnase Z
pdb|2E7Y|B Chain B, High Resolution Structure Of T. Maritima Trnase Z
Length = 280
Score = 68.9 bits (167), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 66/217 (30%), Positives = 104/217 (47%), Gaps = 21/217 (9%)
Query: 82 TIEGVSIGGHETCVIIPELKCAFDIGR-----CPTRAIQQNFVFITHGHLDHIGGLPMYV 136
I G S T + + FD G ++ +VF+THGH+DHI GL V
Sbjct: 2 NIIGFSKALFSTWIYYSPERILFDAGEGVSTTLGSKVYAFKYVFLTHGHVDHIAGLWGVV 61
Query: 137 ASR--GLYNLKPPTIFVPPSIKEDVEKLFE-IHRSLGNVELNLDLVALDVGETYEMRN-- 191
R G+ + + P P VE+ E I R+ ++ + ++ L GE +RN
Sbjct: 62 NIRNNGMGDREKPLDVFYPEGNRAVEEYTEFIKRANPDLRFSFNVHPLKEGERVFLRNAG 121
Query: 192 --DIVVRPFKTHHVIP--SQGYVIYLLRKKLKKQYIHLKGKQIEKL-KKSGVE-ITDIIL 245
V+PF+T HV S GY I+ +R+KLKK++ L K+I +L K+ G + +T+
Sbjct: 122 GFKRYVQPFRTKHVSSEVSFGYHIFEVRRKLKKEFQGLDSKEISRLVKEKGRDFVTEEYH 181
Query: 246 SPEVAFTGDTTSEFMLNPRNADALRAKILITEATFLD 282
+ +GD+ + L+P ++LI E TFLD
Sbjct: 182 KKVLTISGDSLA---LDPEEIRG--TELLIHECTFLD 213
>pdb|2CBN|A Chain A, Crystal Structure Of Zipd From Escherichia Coli
Length = 306
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 48/96 (50%), Gaps = 8/96 (8%)
Query: 119 VFITHGHLDHIGGLPMYVASRGLYN-LKPPTIFVPPSIKEDVEKLFEIHRSLGNVELNLD 177
+FI+H H DH+ GLP + SR + ++P TI+ P I+E VE I S + L+
Sbjct: 61 IFISHLHGDHLFGLPGLLCSRSMSGIIQPLTIYGPQGIREFVETALRISGSW--TDYPLE 118
Query: 178 LVALDVGETYE--MRNDIVVRPFKTHHVIPSQGYVI 211
+V + GE + +R V + H + GY I
Sbjct: 119 IVEIGAGEILDDGLRK---VTAYPLEHPLECYGYRI 151
>pdb|4GCW|A Chain A, Crystal Structure Of Rnase Z In Complex With Precursor
Trna(Thr)
Length = 320
Score = 35.4 bits (80), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 47/199 (23%), Positives = 84/199 (42%), Gaps = 28/199 (14%)
Query: 119 VFITHGHLDHIGGLPMYVASRGLYNLKPP-TIFVPPSIKEDVEKLFEIHRSLGNVELNLD 177
+FITH H DH+ GLP + SR + T++ P IK +E + ++ ++ L
Sbjct: 59 IFITHMHGDHVYGLPGLLGSRSFQGGEDELTVYGPKGIKAFIETSLAVTKT--HLTYPLA 116
Query: 178 LVALDVGETYEMRNDIVVRPFKTHHVIPSQGYVIY------LLRKKLKKQYIHLKGKQIE 231
+ ++ G +E + +V H + + GY + L+ + K+ G +
Sbjct: 117 IQEIEEGIVFE-DDQFIVTAVSVIHGVEAFGYRVQEKDVPGSLKADVLKEMNIPPGPVYQ 175
Query: 232 KLKKSGVEIT----------DIILSPE----VAFTGDTTSEFMLNPRNADALRAKILITE 277
K+KK G +T D + P+ V F+GDT L D +++ E
Sbjct: 176 KIKK-GETVTLEDGRIINGNDFLEPPKKGRSVVFSGDTRVSDKLKELARD---CDVMVHE 231
Query: 278 ATFLDDEMSIEHAQQHGHT 296
ATF ++ + + H T
Sbjct: 232 ATFAKEDRKLAYDYYHSTT 250
>pdb|1Y44|A Chain A, Crystal Structure Of Rnase Z
pdb|1Y44|B Chain B, Crystal Structure Of Rnase Z
Length = 320
Score = 34.7 bits (78), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 47/199 (23%), Positives = 83/199 (41%), Gaps = 28/199 (14%)
Query: 119 VFITHGHLDHIGGLPMYVASRGLYNLKPP-TIFVPPSIKEDVEKLFEIHRSLGNVELNLD 177
+FITH H DH+ GLP + SR + T++ P IK +E + ++ ++ L
Sbjct: 59 IFITHXHGDHVYGLPGLLGSRSFQGGEDELTVYGPKGIKAFIETSLAVTKT--HLTYPLA 116
Query: 178 LVALDVGETYEMRNDIVVRPFKTHHVIPSQGYVIY------LLRKKLKKQYIHLKGKQIE 231
+ ++ G +E + +V H + + GY + L+ + K+ G +
Sbjct: 117 IQEIEEGIVFE-DDQFIVTAVSVIHGVEAFGYRVQEKDVPGSLKADVLKEXNIPPGPVYQ 175
Query: 232 KLKKSGVEIT----------DIILSPE----VAFTGDTTSEFMLNPRNADALRAKILITE 277
K+KK G +T D + P+ V F+GDT L D + + E
Sbjct: 176 KIKK-GETVTLEDGRIINGNDFLEPPKKGRSVVFSGDTRVSDKLKELARD---CDVXVHE 231
Query: 278 ATFLDDEMSIEHAQQHGHT 296
ATF ++ + + H T
Sbjct: 232 ATFAKEDRKLAYDYYHSTT 250
>pdb|3ZWF|A Chain A, Crystal Structure Of Human Trnase Z, Short Form (Elac1).
pdb|3ZWF|B Chain B, Crystal Structure Of Human Trnase Z, Short Form (Elac1)
Length = 368
Score = 34.7 bits (78), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 57/238 (23%), Positives = 97/238 (40%), Gaps = 63/238 (26%)
Query: 119 VFITHGHLDHIGGLP-----MYVASRGLYNLKPPTIFVPPSIKEDVEKLFEIH------- 166
+FITH H DH GLP + + S + + +P I+ P +++ + + E+
Sbjct: 56 IFITHLHGDHFFGLPGLLCTISLQSGSMVSKQPIEIYGPVGLRDFIWRTMELSHTELVFH 115
Query: 167 ------------------RSLGNV--------ELNLDLVALDVGE-TYEMRND--IVVRP 197
+ +V E + LD E +Y + +D VV+
Sbjct: 116 YVVHELVPTADQCPAEELKEFAHVNRADSPPKEEQGRTILLDSEENSYLLFDDEQFVVKA 175
Query: 198 FKTHHVIPSQGYVIYLLRKKLKKQYIHLK------GKQIEKLK-------KSGVEIT--D 242
F+ H IPS G+ + ++ K LK G KLK ++GV I+ D
Sbjct: 176 FRLFHRIPSFGFSVVEKKRPGKLNAQKLKDLGVPPGPAYGKLKNGISVVLENGVTISPQD 235
Query: 243 IILSP----EVAFTGDTTSEFMLNPRNADALRAKILITEATFLDDEMSIEHAQQHGHT 296
++ P ++ GD S + + A +LI EAT D +M + A++HGH+
Sbjct: 236 VLKKPIVGRKICILGD-CSGVVGDGGVKLCFEADLLIHEATLDDAQM--DKAKEHGHS 290
>pdb|2C4N|A Chain A, Nagd From E.Coli K-12 Strain
Length = 250
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 212 YLLRKKLKKQYIHLKGKQIEKLKKSGVEITDIILSPEVAFTGDTTS 257
+L R++ KK Y+ +G I +L K+G ITD+ +P+ G+T S
Sbjct: 78 FLRRQEGKKAYVVGEGALIHELYKAGFTITDV--NPDFVIVGETRS 121
>pdb|3ZQ4|A Chain A, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
pdb|3ZQ4|C Chain C, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
pdb|3ZQ4|D Chain D, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
pdb|3ZQ4|E Chain E, Unusual, Dual Endo- And Exo-Nuclease Activity In The
Degradosome Explained By Crystal Structure Analysis Of
Rnase J1
Length = 555
Score = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 12/15 (80%), Positives = 14/15 (93%)
Query: 119 VFITHGHLDHIGGLP 133
+FITHGH DHIGG+P
Sbjct: 70 LFITHGHEDHIGGIP 84
>pdb|2FK6|A Chain A, Crystal Structure Of Rnase ZTRNA(THR) COMPLEX
Length = 320
Score = 32.3 bits (72), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 46/199 (23%), Positives = 83/199 (41%), Gaps = 28/199 (14%)
Query: 119 VFITHGHLDHIGGLPMYVASRGLYNLKPP-TIFVPPSIKEDVEKLFEIHRSLGNVELNLD 177
+FITH DH+ GLP + SR + T++ P IK +E + ++ ++ L
Sbjct: 59 IFITHMAGDHVYGLPGLLGSRSFQGGEDELTVYGPKGIKAFIETSLAVTKT--HLTYPLA 116
Query: 178 LVALDVGETYEMRNDIVVRPFKTHHVIPSQGYVIY------LLRKKLKKQYIHLKGKQIE 231
+ ++ G +E + +V H + + GY + L+ + K+ G +
Sbjct: 117 IQEIEEGIVFE-DDQFIVTAVSVIHGVEAFGYRVQEKDVPGSLKADVLKEMNIPPGPVYQ 175
Query: 232 KLKKSGVEIT----------DIILSPE----VAFTGDTTSEFMLNPRNADALRAKILITE 277
K+KK G +T D + P+ V F+GDT L D +++ E
Sbjct: 176 KIKK-GETVTLEDGRIINGNDFLEPPKKGRSVVFSGDTRVSDKLKELARD---CDVMVHE 231
Query: 278 ATFLDDEMSIEHAQQHGHT 296
ATF ++ + + H T
Sbjct: 232 ATFAKEDRKLAYDYYHSTT 250
>pdb|2CFU|A Chain A, Crystal Structure Of Sdsa1, An Alkylsulfatase From
Pseudomonas Aeruginosa, In Complex With
1-Decane-Sulfonic- Acid.
pdb|2CFZ|A Chain A, Crystal Structure Of Sdsa1, An Alkylsulfatase From
Pseudomonas Aeruginosa, In Complex With 1-Dodecanol
pdb|2CG2|A Chain A, Crystal Structure Of Sdsa1, An Alkylsulfatase From
Pseudomonas Aeruginosa, In Complex With Sulfate
Length = 658
Score = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 43/102 (42%), Gaps = 26/102 (25%)
Query: 74 KGIDLEGYTIEGVSIGGHETCVIIPEL------KCAFDI-----GRCPTRAIQQNFVFIT 122
+G DL T I G +++ L + A+++ G P R V +
Sbjct: 118 RGFDLANITF----IRGDSGWIVVDTLTTPATARAAYELVSRELGERPIRT-----VIYS 168
Query: 123 HGHLDHIGGL-----PMYVASRGLYNLKPPTIFVPPSIKEDV 159
H H DH GG+ P VAS G + P F+ +IKE+V
Sbjct: 169 HAHADHFGGVRGLVEPQQVAS-GAVQIIAPAGFMEAAIKENV 209
>pdb|3AF5|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
From Pyrococcus Horikoshii
pdb|3AF6|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
From Pyrococcus Horikoshii Complexed With Rna-Analog
Length = 651
Score = 31.6 bits (70), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 28/101 (27%), Positives = 42/101 (41%), Gaps = 17/101 (16%)
Query: 119 VFITHGHLDHIGGLPMYVASRGLYNLKPPTIFVPPSIKEDV----EKLFEIHRSLGN--- 171
+ ITH HLDH G LP YNL I+ P ++ + + EI +S G
Sbjct: 252 IIITHAHLDHCGMLPYLFR----YNLFDGPIYTTPPTRDLMVLLQKDFIEIQQSNGQDPL 307
Query: 172 ------VELNLDLVALDVGETYEMRNDIVVRPFKTHHVIPS 206
E+ + LD GE ++ DI + H++ S
Sbjct: 308 YRPRDIKEVIKHTITLDYGEVRDISPDIRLTLHNAGHILGS 348
>pdb|2CG3|A Chain A, Crystal Structure Of Sdsa1, An Alkylsulfatase From
Pseudomonas Aeruginosa
Length = 658
Score = 31.2 bits (69), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 42/102 (41%), Gaps = 26/102 (25%)
Query: 74 KGIDLEGYTIEGVSIGGHETCVIIPEL------KCAFDI-----GRCPTRAIQQNFVFIT 122
+G DL T I G +++ L + A+++ G P R V +
Sbjct: 118 RGFDLANITF----IRGDSGWIVVDTLTTPATARAAYELVSRELGERPIRT-----VIYS 168
Query: 123 HGHLDHIGGL-----PMYVASRGLYNLKPPTIFVPPSIKEDV 159
H H DH GG+ P VAS G + P F +IKE+V
Sbjct: 169 HAHADHFGGVRGLVEPQQVAS-GAVQIIAPAGFXEAAIKENV 209
>pdb|2P4Z|A Chain A, A Ferredoxin-Like Metallo-Beta-Lactamase Superfamily
Protein From Thermoanaerobacter Tengcongensis
pdb|2P4Z|B Chain B, A Ferredoxin-Like Metallo-Beta-Lactamase Superfamily
Protein From Thermoanaerobacter Tengcongensis
Length = 284
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 16/31 (51%), Gaps = 7/31 (22%)
Query: 103 AFDIGRCPTRAIQQNFVFITHGHLDHIGGLP 133
D+GR V +THGH DHIGGL
Sbjct: 63 GIDVGRIKK-------VVLTHGHYDHIGGLK 86
>pdb|3BK1|A Chain A, Crystal Structure Analysis Of Rnase J
pdb|3BK2|A Chain A, Crystal Structure Analysis Of The Rnase JUMP COMPLEX
Length = 562
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 11/14 (78%), Positives = 12/14 (85%)
Query: 121 ITHGHLDHIGGLPM 134
+THGH DHIGGLP
Sbjct: 80 LTHGHEDHIGGLPF 93
>pdb|2XR1|A Chain A, Dimeric Archaeal Cleavage And Polyadenylation Specificity
Factor With N-Terminal Kh Domains (Kh-Cpsf) From
Methanosarcina Mazei
pdb|2XR1|B Chain B, Dimeric Archaeal Cleavage And Polyadenylation Specificity
Factor With N-Terminal Kh Domains (Kh-Cpsf) From
Methanosarcina Mazei
Length = 640
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 50/199 (25%), Positives = 80/199 (40%), Gaps = 34/199 (17%)
Query: 115 QQNFVFITHGHLDHIGGLPMYVASRGLYNLKPPTIFVPPSIKEDVEKLFEIHRSLGNVEL 174
Q + V +TH HLDH G +P+ Y + P PP+ R L V L
Sbjct: 237 QIDAVIVTHAHLDHQGLVPLLFK----YGYEGPVYCTPPT------------RDL-MVLL 279
Query: 175 NLDL--VALDVGETYEMRNDIVVRPFKTHHVIPSQGYVIYLLRKKLKKQY---IHLKGKQ 229
LD VA G+ + +V + K H IP + + +K + H+ G
Sbjct: 280 QLDYIDVAAKEGKKIPYESGMVAKTLK--HTIPLDYEEVTDIAPDIKLTFHNAGHILGSA 337
Query: 230 IEKLKKSGVEITDIILSPEVAFTGDTTSE--FMLNPRNADALRAKILITEATFLDDEMSI 287
I S I D + + V FTGD E + +P R + +I+EAT+ + +
Sbjct: 338 I-----SHFHIGDGLHN--VVFTGDYKYEKTRLFDPAVNKFPRVETVISEATY-GNANAF 389
Query: 288 EHAQQHGHTHLSEDIRQAV 306
+ A + HL ++ +
Sbjct: 390 QPALKDAEKHLQMVVKNTI 408
>pdb|2B3Z|A Chain A, Crystal Structure Of A Bifunctional Deaminase And
Reductase Involved In Riboflavin Biosynthesis
pdb|2B3Z|B Chain B, Crystal Structure Of A Bifunctional Deaminase And
Reductase Involved In Riboflavin Biosynthesis
pdb|2B3Z|C Chain C, Crystal Structure Of A Bifunctional Deaminase And
Reductase Involved In Riboflavin Biosynthesis
pdb|2B3Z|D Chain D, Crystal Structure Of A Bifunctional Deaminase And
Reductase Involved In Riboflavin Biosynthesis
pdb|2D5N|A Chain A, Crystal Structure Of A Bifunctional Deaminase And
Reductase Involved In Riboflavin Biosynthesis
pdb|2D5N|B Chain B, Crystal Structure Of A Bifunctional Deaminase And
Reductase Involved In Riboflavin Biosynthesis
pdb|2D5N|C Chain C, Crystal Structure Of A Bifunctional Deaminase And
Reductase Involved In Riboflavin Biosynthesis
pdb|2D5N|D Chain D, Crystal Structure Of A Bifunctional Deaminase And
Reductase Involved In Riboflavin Biosynthesis
pdb|3EX8|A Chain A, Complex Structure Of Bacillus Subtilis Ribg Reduction
Mechanism In Riboflavin Biosynthesis
pdb|3EX8|B Chain B, Complex Structure Of Bacillus Subtilis Ribg Reduction
Mechanism In Riboflavin Biosynthesis
pdb|3EX8|C Chain C, Complex Structure Of Bacillus Subtilis Ribg Reduction
Mechanism In Riboflavin Biosynthesis
pdb|3EX8|D Chain D, Complex Structure Of Bacillus Subtilis Ribg Reduction
Mechanism In Riboflavin Biosynthesis
pdb|4G3M|A Chain A, Complex Structure Of Bacillus Subtilis Ribg: The
Deamination Process In Riboflavin Biosynthesis
pdb|4G3M|B Chain B, Complex Structure Of Bacillus Subtilis Ribg: The
Deamination Process In Riboflavin Biosynthesis
pdb|4G3M|C Chain C, Complex Structure Of Bacillus Subtilis Ribg: The
Deamination Process In Riboflavin Biosynthesis
pdb|4G3M|D Chain D, Complex Structure Of Bacillus Subtilis Ribg: The
Deamination Process In Riboflavin Biosynthesis
Length = 373
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 8/83 (9%)
Query: 225 LKGKQIEKLKKSGVEITDIILSPEVAFTGDTTSEFM------LNPRNADALRAKILIT-- 276
+ G+ I +K++G+E+ + IL+ + + FM + + A +L KI +
Sbjct: 118 VAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTLKAAASLDGKIATSTG 177
Query: 277 EATFLDDEMSIEHAQQHGHTHLS 299
++ ++ E + + AQQ+ TH S
Sbjct: 178 DSKWITSEAARQDAQQYRKTHQS 200
>pdb|3H3E|A Chain A, Crystal Structure Of Tm1679, A Metal-Dependent Hydrolase
Of The Beta-Lactamase Superfamily
Length = 267
Score = 28.5 bits (62), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 18/24 (75%), Gaps = 1/24 (4%)
Query: 119 VFITHGHLDHIGGLPMYVASRGLY 142
V I+HGH DH GGL +Y++ + ++
Sbjct: 65 VLISHGHYDHAGGL-LYLSGKRVW 87
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
0.319 0.136 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,922,170
Number of Sequences: 62578
Number of extensions: 397769
Number of successful extensions: 1409
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1384
Number of HSP's gapped (non-prelim): 36
length of query: 330
length of database: 14,973,337
effective HSP length: 99
effective length of query: 231
effective length of database: 8,778,115
effective search space: 2027744565
effective search space used: 2027744565
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)