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= psy11424
(245 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1YPN|A Chain A, Reduced Form Hydroxymethylbilane Synthase (K59q Mutant)
Crystal Structure After 2 Hours In A Flow Cell
Determined By Time-Resolved Laue Diffraction
Length = 313
Score = 218 bits (554), Expect = 3e-57, Method: Compositional matrix adjust.
Identities = 112/239 (46%), Positives = 153/239 (64%), Gaps = 3/239 (1%)
Query: 1 MAIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGT 60
+A+++ +AD+AVHS+KD+P+ P G L I +REDPRDAF+SN+Y SL LP ++VGT
Sbjct: 68 VALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGT 127
Query: 61 NSLRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLF 120
+SLRR+ + P LII+SLRGN+ TRL+KLD GEY AIILA AGLKRL L+ RIR
Sbjct: 128 SSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAAL 187
Query: 121 SPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKISLA 180
P LPA GQGA+ IE + E+L LNH+ + V AERA++ G C++ +
Sbjct: 188 PPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRLEGGCQVPIG 247
Query: 181 AFAMVNNFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKKKGAIEII 239
++A + EI LRA++ P+G +II E G E +G+ AE L GA EI+
Sbjct: 248 SYA---ELIDGEIWLRALVGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNGAREIL 303
>pdb|2YPN|A Chain A, Hydroxymethylbilane Synthase
pdb|1GTK|A Chain A, Time-Resolved And Static-Ensemble Structural Chemistry Of
Hydroxymethylbilane Synthase
Length = 313
Score = 218 bits (554), Expect = 3e-57, Method: Compositional matrix adjust.
Identities = 112/239 (46%), Positives = 153/239 (64%), Gaps = 3/239 (1%)
Query: 1 MAIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGT 60
+A+++ +AD+AVHS+KD+P+ P G L I +REDPRDAF+SN+Y SL LP ++VGT
Sbjct: 68 VALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGT 127
Query: 61 NSLRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLF 120
+SLRR+ + P LII+SLRGN+ TRL+KLD GEY AIILA AGLKRL L+ RIR
Sbjct: 128 SSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAAL 187
Query: 121 SPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKISLA 180
P LPA GQGA+ IE + E+L LNH+ + V AERA++ G C++ +
Sbjct: 188 PPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRLEGGCQVPIG 247
Query: 181 AFAMVNNFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKKKGAIEII 239
++A + EI LRA++ P+G +II E G E +G+ AE L GA EI+
Sbjct: 248 SYA---ELIDGEIWLRALVGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNGAREIL 303
>pdb|1PDA|A Chain A, Structure Of Porphobilinogen Deaminase Reveals A Flexible
Multidomain Polymerase With A Single Catalytic Site
Length = 313
Score = 216 bits (551), Expect = 7e-57, Method: Compositional matrix adjust.
Identities = 111/239 (46%), Positives = 153/239 (64%), Gaps = 3/239 (1%)
Query: 1 MAIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGT 60
+A+++ +AD+AVHS+KD+P+ P G L I +REDPRDAF+SN+Y SL LP ++VGT
Sbjct: 68 VALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGT 127
Query: 61 NSLRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLF 120
+SLRR+ + P LII+SLRGN+ TRL+KLD GEY AIILA AGLKRL L+ RIR
Sbjct: 128 SSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAAL 187
Query: 121 SPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKISLA 180
P LPA GQGA+ IE + E+L LNH+ + V AERA++ G+C++ +
Sbjct: 188 PPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRLEGACQVPIG 247
Query: 181 AFAMVNNFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKKKGAIEII 239
++A + EI LR ++ P+G +II E G E +G+ AE L GA EI+
Sbjct: 248 SYA---ELIDGEIWLRGLVGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNGAREIL 303
>pdb|1AH5|A Chain A, Reduced Form Selenomethionine-Labelled Hydroxymethylbilane
Synthase Determined By Mad
Length = 313
Score = 215 bits (548), Expect = 1e-56, Method: Compositional matrix adjust.
Identities = 112/239 (46%), Positives = 150/239 (62%), Gaps = 3/239 (1%)
Query: 1 MAIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGT 60
+A+++ +AD+AVHS KD+P+ P G L I +REDPRDAF+SN+Y SL LP ++VGT
Sbjct: 68 VALLENRADIAVHSXKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGT 127
Query: 61 NSLRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLF 120
+SLRR+ + P LII+SLRGN+ TRL+KLD GEY AIILA AGLKRL L+ RIR
Sbjct: 128 SSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAAL 187
Query: 121 SPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKISLA 180
P LPA GQGA+ IE + E+L LNH+ + V AERA + G C++ +
Sbjct: 188 PPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAXNTRLEGGCQVPIG 247
Query: 181 AFAMVNNFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKKKGAIEII 239
++A + EI LRA++ P+G +II E G E G+ AE L GA EI+
Sbjct: 248 SYA---ELIDGEIWLRALVGAPDGSQIIRGERRGAPQDAEQXGISLAEELLNNGAREIL 303
>pdb|4HTG|A Chain A, Porphobilinogen Deaminase From Arabidopsis Thaliana
Length = 320
Score = 157 bits (396), Expect = 7e-39, Method: Compositional matrix adjust.
Identities = 90/237 (37%), Positives = 133/237 (56%), Gaps = 6/237 (2%)
Query: 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTN 61
A+I G D+AVHS+KD+P LP IL L RED RDAFI +L+ LP +VVGT
Sbjct: 80 ALINGHIDIAVHSMKDVPTYLPEKTILPCNLPREDVRDAFICLTAATLAELPAGSVVGTA 139
Query: 62 SLRRKVLIKSFFPSLIIK-SLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLF 120
SLRRK I +P+L ++ + RGN+ TRL+KL G+ A +LA AGLKRL++ + + +
Sbjct: 140 SLRRKSQILHKYPALHVEENFRGNVQTRLSKLQGGKVQATLLALAGLKRLSMTENVASIL 199
Query: 121 SPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKISLA 180
S +++LPA QGAI I + ++ L LNH + + ERA +GSC+ +A
Sbjct: 200 SLDEMLPAVAQGAIGIACRTDDDKMATYLASLNHEETRLAISCERAFLETLDGSCRTPIA 259
Query: 181 AFAMVNNFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGL---YAAELLKKKG 234
+A + E R ++ +P+G K++ GP + V + ELL + G
Sbjct: 260 GYA--SKDEEGNCIFRGLVASPDGTKVLETSRKGPYVYEDMVKMGKDAGQELLSRAG 314
>pdb|3ECR|A Chain A, Structure Of Human Porphobilinogen Deaminase
pdb|3ECR|B Chain B, Structure Of Human Porphobilinogen Deaminase
Length = 364
Score = 150 bits (378), Expect = 8e-37, Method: Compositional matrix adjust.
Identities = 84/240 (35%), Positives = 137/240 (57%), Gaps = 18/240 (7%)
Query: 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYI---SLSTLPKNAVV 58
A+ K + DL VHSLKD+P LP GF + AI KRE+P DA + + +L TLP+ +VV
Sbjct: 87 ALEKNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLETLPEKSVV 146
Query: 59 GTNSLRRKVLIKSFFPSLIIKSLRGNIDTRLNKLD-KGEYAAIILAAAGLKRLNLQKRIR 117
GT+SLRR ++ FP L +S+RGN++TRL KLD + E++AIILA AGL+R+ R+
Sbjct: 147 GTSSLRRAAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQEFSAIILATAGLQRMGWHNRVG 206
Query: 118 MLFSPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKI 177
+ P + + A GQGA+ +E+ +++++++ L+ + AERA R+ G C +
Sbjct: 207 QILHPEECMYAVGQGALGVEVRAKDQDILDLVGVLHDPETLLRCIAERAFLRHLEGGCSV 266
Query: 178 SLAAFAMVNNFNESEINLRAIITNPNG-----------LKIITAEVNGPIDTPETVGLYA 226
+A + + ++ L + + +G + + +GP D P+ VG+ A
Sbjct: 267 PVAVHTAMKD---GQLYLTGGVWSLDGSDSIQETMQATIHVPAQHEDGPEDDPQLVGITA 323
>pdb|3EQ1|A Chain A, The Crystal Structure Of Human Porphobilinogen Deaminase
At 2.8a Resolution
pdb|3EQ1|B Chain B, The Crystal Structure Of Human Porphobilinogen Deaminase
At 2.8a Resolution
Length = 361
Score = 148 bits (373), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 83/240 (34%), Positives = 137/240 (57%), Gaps = 18/240 (7%)
Query: 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYI---SLSTLPKNAVV 58
A+ K + DL VHSLKD+P LP GF + AI KRE+P DA + + +L TLP+ +VV
Sbjct: 84 ALEKNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLETLPEKSVV 143
Query: 59 GTNSLRRKVLIKSFFPSLIIKSLRGNIDTRLNKLD-KGEYAAIILAAAGLKRLNLQKRIR 117
GT+SLRR ++ FP L +S++GN++TRL KLD + E++AIILA AGL+R+ R+
Sbjct: 144 GTSSLRRAAQLQRKFPHLEFRSIQGNLNTRLRKLDEQQEFSAIILATAGLQRMGWHNRVG 203
Query: 118 MLFSPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKI 177
+ P + + A GQGA+ +E+ +++++++ L+ + AERA R+ G C +
Sbjct: 204 QILHPEECMYAVGQGALGVEVRAKDQDILDLVGVLHDPETLLRCIAERAFLRHLEGGCSV 263
Query: 178 SLAAFAMVNNFNESEINLRAIITNPNG-----------LKIITAEVNGPIDTPETVGLYA 226
+A + + ++ L + + +G + + +GP D P+ VG+ A
Sbjct: 264 PVAVHTAMKD---GQLYLTGGVWSLDGSDSIQETMQATIHVPAQHEDGPEDDPQLVGITA 320
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 0.137 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,625,037
Number of Sequences: 62578
Number of extensions: 253305
Number of successful extensions: 662
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 641
Number of HSP's gapped (non-prelim): 11
length of query: 245
length of database: 14,973,337
effective HSP length: 96
effective length of query: 149
effective length of database: 8,965,849
effective search space: 1335911501
effective search space used: 1335911501
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)