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= 026500
(237 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4HTG|A Chain A, Porphobilinogen Deaminase From Arabidopsis Thaliana
Length = 320
Score = 310 bits (794), Expect = 5e-85, Method: Compositional matrix adjust.
Identities = 152/190 (80%), Positives = 164/190 (86%)
Query: 4 HPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMKDVP 63
HPEL ++GAI I IIKTTGDKILSQPLADIGGKGLFTKEIDEALIN IDIAVHSMKDVP
Sbjct: 38 HPELVEDGAIHIEIIKTTGDKILSQPLADIGGKGLFTKEIDEALINGHIDIAVHSMKDVP 97
Query: 64 TYLPEKTILPCNLQREDVRDAFIXXXXXXXXXXPAGSIVGTASLRRKSQILHRYPSLKVM 123
TYLPEKTILPCNL REDVRDAFI PAGS+VGTASLRRKSQILH+YP+L V
Sbjct: 98 TYLPEKTILPCNLPREDVRDAFICLTAATLAELPAGSVVGTASLRRKSQILHKYPALHVE 157
Query: 124 ENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIAC 183
ENFRGNVQTRL KL VQATLLALAGLKRLSMTENV +ILS+D+MLPAVAQGAIGIAC
Sbjct: 158 ENFRGNVQTRLSKLQGGKVQATLLALAGLKRLSMTENVASILSLDEMLPAVAQGAIGIAC 217
Query: 184 RSNDEKMVPF 193
R++D+KM +
Sbjct: 218 RTDDDKMATY 227
>pdb|1PDA|A Chain A, Structure Of Porphobilinogen Deaminase Reveals A Flexible
Multidomain Polymerase With A Single Catalytic Site
Length = 313
Score = 166 bits (421), Expect = 9e-42, Method: Compositional matrix adjust.
Identities = 91/189 (48%), Positives = 119/189 (62%), Gaps = 5/189 (2%)
Query: 1 MALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMK 60
MA HP L +++V + T GD IL PLA +GGKGLF KE++ AL+ ++ DIAVHSMK
Sbjct: 28 MASHPGLV----VELVPMVTRGDVILDTPLAKVGGKGLFVKELEVALLENRADIAVHSMK 83
Query: 61 DVPTYLPEKTILPCNLQREDVRDAFIXXXXXXXXXXPAGSIVGTASLRRKSQILHRYPSL 120
DVP P+ L +RED RDAF+ PAGSIVGT+SLRR+ Q+ R P L
Sbjct: 84 DVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGTSSLRRQCQLAERRPDL 143
Query: 121 KVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIG 180
++ + RGNV TRL KL+ A +LA+AGLKRL + + L + LPAV QGA+G
Sbjct: 144 -IIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVG 202
Query: 181 IACRSNDEK 189
I CR +D +
Sbjct: 203 IECRLDDSR 211
>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 = 166 bits (421), Expect = 9e-42, Method: Compositional matrix adjust.
Identities = 91/189 (48%), Positives = 119/189 (62%), Gaps = 5/189 (2%)
Query: 1 MALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMK 60
MA HP L +++V + T GD IL PLA +GGKGLF KE++ AL+ ++ DIAVHSMK
Sbjct: 28 MASHPGLV----VELVPMVTRGDVILDTPLAKVGGKGLFVKELEVALLENRADIAVHSMK 83
Query: 61 DVPTYLPEKTILPCNLQREDVRDAFIXXXXXXXXXXPAGSIVGTASLRRKSQILHRYPSL 120
DVP P+ L +RED RDAF+ PAGSIVGT+SLRR+ Q+ R P L
Sbjct: 84 DVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGTSSLRRQCQLAERRPDL 143
Query: 121 KVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIG 180
++ + RGNV TRL KL+ A +LA+AGLKRL + + L + LPAV QGA+G
Sbjct: 144 -IIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVG 202
Query: 181 IACRSNDEK 189
I CR +D +
Sbjct: 203 IECRLDDSR 211
>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 = 165 bits (417), Expect = 2e-41, Method: Compositional matrix adjust.
Identities = 90/189 (47%), Positives = 119/189 (62%), Gaps = 5/189 (2%)
Query: 1 MALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMK 60
MA HP L +++V + T GD IL PLA +GG+GLF KE++ AL+ ++ DIAVHSMK
Sbjct: 28 MASHPGLV----VELVPMVTRGDVILDTPLAKVGGQGLFVKELEVALLENRADIAVHSMK 83
Query: 61 DVPTYLPEKTILPCNLQREDVRDAFIXXXXXXXXXXPAGSIVGTASLRRKSQILHRYPSL 120
DVP P+ L +RED RDAF+ PAGSIVGT+SLRR+ Q+ R P L
Sbjct: 84 DVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGTSSLRRQCQLAERRPDL 143
Query: 121 KVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIG 180
++ + RGNV TRL KL+ A +LA+AGLKRL + + L + LPAV QGA+G
Sbjct: 144 -IIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVG 202
Query: 181 IACRSNDEK 189
I CR +D +
Sbjct: 203 IECRLDDSR 211
>pdb|1AH5|A Chain A, Reduced Form Selenomethionine-Labelled Hydroxymethylbilane
Synthase Determined By Mad
Length = 313
Score = 160 bits (406), Expect = 5e-40, Method: Compositional matrix adjust.
Identities = 89/188 (47%), Positives = 116/188 (61%), Gaps = 5/188 (2%)
Query: 2 ALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMKD 61
A HP L +++V T GD IL PLA +GGKGLF KE++ AL+ ++ DIAVHS KD
Sbjct: 29 ASHPGLV----VELVPXVTRGDVILDTPLAKVGGKGLFVKELEVALLENRADIAVHSXKD 84
Query: 62 VPTYLPEKTILPCNLQREDVRDAFIXXXXXXXXXXPAGSIVGTASLRRKSQILHRYPSLK 121
VP P+ L +RED RDAF+ PAGSIVGT+SLRR+ Q+ R P L
Sbjct: 85 VPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGTSSLRRQCQLAERRPDL- 143
Query: 122 VMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGI 181
++ + RGNV TRL KL+ A +LA+AGLKRL + + L + LPAV QGA+GI
Sbjct: 144 IIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVGI 203
Query: 182 ACRSNDEK 189
CR +D +
Sbjct: 204 ECRLDDSR 211
>pdb|3ECR|A Chain A, Structure Of Human Porphobilinogen Deaminase
pdb|3ECR|B Chain B, Structure Of Human Porphobilinogen Deaminase
Length = 364
Score = 133 bits (335), Expect = 7e-32, Method: Compositional matrix adjust.
Identities = 73/183 (39%), Positives = 112/183 (61%), Gaps = 5/183 (2%)
Query: 13 IQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTIL 72
+I+ + TTGDKIL L+ IG K LFTKE++ AL +++D+ VHS+KD+PT LP +
Sbjct: 54 FEIIAMSTTGDKILDTALSKIGEKSLFTKELEHALEKNEVDLVVHSLKDLPTVLPPGFTI 113
Query: 73 PCNLQREDVRDAFI---XXXXXXXXXXPAGSIVGTASLRRKSQILHRYPSLKVMENFRGN 129
+RE+ DA + P S+VGT+SLRR +Q+ ++P L+ + RGN
Sbjct: 114 GAICKRENPHDAVVFHPKFVGKTLETLPEKSVVGTSSLRRAAQLQRKFPHLE-FRSIRGN 172
Query: 130 VQTRLRKLNERV-VQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDE 188
+ TRLRKL+E+ A +LA AGL+R+ V IL ++ + AV QGA+G+ R+ D+
Sbjct: 173 LNTRLRKLDEQQEFSAIILATAGLQRMGWHNRVGQILHPEECMYAVGQGALGVEVRAKDQ 232
Query: 189 KMV 191
++
Sbjct: 233 DIL 235
>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 = 131 bits (329), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 72/183 (39%), Positives = 112/183 (61%), Gaps = 5/183 (2%)
Query: 13 IQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTIL 72
+I+ + TTGDKIL L+ IG K LFTKE++ AL +++D+ VHS+KD+PT LP +
Sbjct: 51 FEIIAMSTTGDKILDTALSKIGEKSLFTKELEHALEKNEVDLVVHSLKDLPTVLPPGFTI 110
Query: 73 PCNLQREDVRDAFI---XXXXXXXXXXPAGSIVGTASLRRKSQILHRYPSLKVMENFRGN 129
+RE+ DA + P S+VGT+SLRR +Q+ ++P L+ + +GN
Sbjct: 111 GAICKRENPHDAVVFHPKFVGKTLETLPEKSVVGTSSLRRAAQLQRKFPHLE-FRSIQGN 169
Query: 130 VQTRLRKLNERV-VQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDE 188
+ TRLRKL+E+ A +LA AGL+R+ V IL ++ + AV QGA+G+ R+ D+
Sbjct: 170 LNTRLRKLDEQQEFSAIILATAGLQRMGWHNRVGQILHPEECMYAVGQGALGVEVRAKDQ 229
Query: 189 KMV 191
++
Sbjct: 230 DIL 232
>pdb|3OPB|A Chain A, Crystal Structure Of She4p
pdb|3OPB|B Chain B, Crystal Structure Of She4p
Length = 778
Score = 26.9 bits (58), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 10/34 (29%), Positives = 22/34 (64%)
Query: 5 PELAQEGAIQIVIIKTTGDKILSQPLADIGGKGL 38
P+LAQ+GA++I++ + + +P+ +G + L
Sbjct: 492 PQLAQQGAVKIILEYLANKQDIGEPIRILGCRAL 525
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
0.322 0.136 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,863,156
Number of Sequences: 62578
Number of extensions: 206671
Number of successful extensions: 444
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 426
Number of HSP's gapped (non-prelim): 8
length of query: 237
length of database: 14,973,337
effective HSP length: 96
effective length of query: 141
effective length of database: 8,965,849
effective search space: 1264184709
effective search space used: 1264184709
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)