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= 020472
(326 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 = 352 bits (904), Expect = 1e-97, Method: Compositional matrix adjust.
Identities = 175/221 (79%), Positives = 190/221 (85%)
Query: 62 ETKVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLAD 121
+T+ AIIRIGTRGSPLALAQA+ETR KL HPEL ++GAI I IIKTTGDKILSQPLAD
Sbjct: 7 KTRTAIIRIGTRGSPLALAQAYETREKLKKKHPELVEDGAIHIEIIKTTGDKILSQPLAD 66
Query: 122 IGGKGLFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFIXXXXXX 181
IGGKGLFTKEIDEALIN IDIAVHSMKDVPTYLPEKTILPCNL REDVRDAFI
Sbjct: 67 IGGKGLFTKEIDEALINGHIDIAVHSMKDVPTYLPEKTILPCNLPREDVRDAFICLTAAT 126
Query: 182 XXXXPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGL 241
PAGS+VGTASLRRKSQILH+YP+L V ENFRGNVQTRL KL VQATLLALAGL
Sbjct: 127 LAELPAGSVVGTASLRRKSQILHKYPALHVEENFRGNVQTRLSKLQGGKVQATLLALAGL 186
Query: 242 KRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMVPF 282
KRLSMTENV +ILS+D+MLPAVAQGAIGIACR++D+KM +
Sbjct: 187 KRLSMTENVASILSLDEMLPAVAQGAIGIACRTDDDKMATY 227
>pdb|1PDA|A Chain A, Structure Of Porphobilinogen Deaminase Reveals A Flexible
Multidomain Polymerase With A Single Catalytic Site
Length = 313
Score = 193 bits (491), Expect = 9e-50, Method: Compositional matrix adjust.
Identities = 105/212 (49%), Positives = 137/212 (64%), Gaps = 5/212 (2%)
Query: 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKG 126
++RI TR SPLAL QAH ++KLMA HP L +++V + T GD IL PLA +GGKG
Sbjct: 5 VLRIATRQSPLALWQAHYVKDKLMASHPGLV----VELVPMVTRGDVILDTPLAKVGGKG 60
Query: 127 LFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFIXXXXXXXXXXP 186
LF KE++ AL+ ++ DIAVHSMKDVP P+ L +RED RDAF+ P
Sbjct: 61 LFVKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALP 120
Query: 187 AGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSM 246
AGSIVGT+SLRR+ Q+ R P L ++ + RGNV TRL KL+ A +LA+AGLKRL +
Sbjct: 121 AGSIVGTSSLRRQCQLAERRPDL-IIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGL 179
Query: 247 TENVTNILSVDDMLPAVAQGAIGIACRSNDEK 278
+ L + LPAV QGA+GI CR +D +
Sbjct: 180 ESRIRAALPPEISLPAVGQGAVGIECRLDDSR 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 = 193 bits (491), Expect = 9e-50, Method: Compositional matrix adjust.
Identities = 105/212 (49%), Positives = 137/212 (64%), Gaps = 5/212 (2%)
Query: 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKG 126
++RI TR SPLAL QAH ++KLMA HP L +++V + T GD IL PLA +GGKG
Sbjct: 5 VLRIATRQSPLALWQAHYVKDKLMASHPGLV----VELVPMVTRGDVILDTPLAKVGGKG 60
Query: 127 LFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFIXXXXXXXXXXP 186
LF KE++ AL+ ++ DIAVHSMKDVP P+ L +RED RDAF+ P
Sbjct: 61 LFVKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALP 120
Query: 187 AGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSM 246
AGSIVGT+SLRR+ Q+ R P L ++ + RGNV TRL KL+ A +LA+AGLKRL +
Sbjct: 121 AGSIVGTSSLRRQCQLAERRPDL-IIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGL 179
Query: 247 TENVTNILSVDDMLPAVAQGAIGIACRSNDEK 278
+ L + LPAV QGA+GI CR +D +
Sbjct: 180 ESRIRAALPPEISLPAVGQGAVGIECRLDDSR 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 = 192 bits (488), Expect = 2e-49, Method: Compositional matrix adjust.
Identities = 104/212 (49%), Positives = 137/212 (64%), Gaps = 5/212 (2%)
Query: 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKG 126
++RI TR SPLAL QAH ++KLMA HP L +++V + T GD IL PLA +GG+G
Sbjct: 5 VLRIATRQSPLALWQAHYVKDKLMASHPGLV----VELVPMVTRGDVILDTPLAKVGGQG 60
Query: 127 LFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFIXXXXXXXXXXP 186
LF KE++ AL+ ++ DIAVHSMKDVP P+ L +RED RDAF+ P
Sbjct: 61 LFVKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALP 120
Query: 187 AGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSM 246
AGSIVGT+SLRR+ Q+ R P L ++ + RGNV TRL KL+ A +LA+AGLKRL +
Sbjct: 121 AGSIVGTSSLRRQCQLAERRPDL-IIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGL 179
Query: 247 TENVTNILSVDDMLPAVAQGAIGIACRSNDEK 278
+ L + LPAV QGA+GI CR +D +
Sbjct: 180 ESRIRAALPPEISLPAVGQGAVGIECRLDDSR 211
>pdb|1AH5|A Chain A, Reduced Form Selenomethionine-Labelled Hydroxymethylbilane
Synthase Determined By Mad
Length = 313
Score = 187 bits (475), Expect = 6e-48, Method: Compositional matrix adjust.
Identities = 103/212 (48%), Positives = 134/212 (63%), Gaps = 5/212 (2%)
Query: 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKG 126
++RI TR SPLAL QAH ++KL A HP L +++V T GD IL PLA +GGKG
Sbjct: 5 VLRIATRQSPLALWQAHYVKDKLXASHPGLV----VELVPXVTRGDVILDTPLAKVGGKG 60
Query: 127 LFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFIXXXXXXXXXXP 186
LF KE++ AL+ ++ DIAVHS KDVP P+ L +RED RDAF+ P
Sbjct: 61 LFVKELEVALLENRADIAVHSXKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALP 120
Query: 187 AGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSM 246
AGSIVGT+SLRR+ Q+ R P L ++ + RGNV TRL KL+ A +LA+AGLKRL +
Sbjct: 121 AGSIVGTSSLRRQCQLAERRPDL-IIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGL 179
Query: 247 TENVTNILSVDDMLPAVAQGAIGIACRSNDEK 278
+ L + LPAV QGA+GI CR +D +
Sbjct: 180 ESRIRAALPPEISLPAVGQGAVGIECRLDDSR 211
>pdb|3ECR|A Chain A, Structure Of Human Porphobilinogen Deaminase
pdb|3ECR|B Chain B, Structure Of Human Porphobilinogen Deaminase
Length = 364
Score = 147 bits (370), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 87/221 (39%), Positives = 130/221 (58%), Gaps = 9/221 (4%)
Query: 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIG 123
K+ +IR+GTR S LA Q L A +P L +I+ + TTGDKIL L+ IG
Sbjct: 20 KMRVIRVGTRKSQLARIQTDSVVATLKASYPGLQ----FEIIAMSTTGDKILDTALSKIG 75
Query: 124 GKGLFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFI---XXXXX 180
K LFTKE++ AL +++D+ VHS+KD+PT LP + +RE+ DA +
Sbjct: 76 EKSLFTKELEHALEKNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGK 135
Query: 181 XXXXXPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERV-VQATLLALA 239
P S+VGT+SLRR +Q+ ++P L+ + RGN+ TRLRKL+E+ A +LA A
Sbjct: 136 TLETLPEKSVVGTSSLRRAAQLQRKFPHLE-FRSIRGNLNTRLRKLDEQQEFSAIILATA 194
Query: 240 GLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMV 280
GL+R+ V IL ++ + AV QGA+G+ R+ D+ ++
Sbjct: 195 GLQRMGWHNRVGQILHPEECMYAVGQGALGVEVRAKDQDIL 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 = 145 bits (365), Expect = 4e-35, Method: Compositional matrix adjust.
Identities = 86/221 (38%), Positives = 130/221 (58%), Gaps = 9/221 (4%)
Query: 64 KVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIG 123
K+ +IR+GTR S LA Q L A +P L +I+ + TTGDKIL L+ IG
Sbjct: 17 KMRVIRVGTRKSQLARIQTDSVVATLKASYPGLQ----FEIIAMSTTGDKILDTALSKIG 72
Query: 124 GKGLFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFI---XXXXX 180
K LFTKE++ AL +++D+ VHS+KD+PT LP + +RE+ DA +
Sbjct: 73 EKSLFTKELEHALEKNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGK 132
Query: 181 XXXXXPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERV-VQATLLALA 239
P S+VGT+SLRR +Q+ ++P L+ + +GN+ TRLRKL+E+ A +LA A
Sbjct: 133 TLETLPEKSVVGTSSLRRAAQLQRKFPHLE-FRSIQGNLNTRLRKLDEQQEFSAIILATA 191
Query: 240 GLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKMV 280
GL+R+ V IL ++ + AV QGA+G+ R+ D+ ++
Sbjct: 192 GLQRMGWHNRVGQILHPEECMYAVGQGALGVEVRAKDQDIL 232
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
0.321 0.135 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,962,500
Number of Sequences: 62578
Number of extensions: 281626
Number of successful extensions: 679
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 646
Number of HSP's gapped (non-prelim): 17
length of query: 326
length of database: 14,973,337
effective HSP length: 99
effective length of query: 227
effective length of database: 8,778,115
effective search space: 1992632105
effective search space used: 1992632105
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: 51 (24.3 bits)