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= 016027
(396 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1QH9|A Chain A, Enzyme-Product Complex Of L-2-Haloacid Dehalogenase
pdb|1JUD|A Chain A, L-2-haloacid Dehalogenase
Length = 232
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 41/101 (40%), Gaps = 2/101 (1%)
Query: 252 YNYFFRYFSKFGKVEDAMNLYRKMIESGYTPDRLTYHILLKILCKEDKLDLAIQVSKEMK 311
Y F S G+ ++A + I + + +L Y L ++ + A + +
Sbjct: 12 YGTLFDVHSVVGRCDEAFPGRGREISALWRQKQLEYTWLRSLMNRYVNFQQATEDALRFT 71
Query: 312 CR--GCDIDLDTSTMLIHLLCRMYKFDEASAEFEDMIRRGL 350
CR G D+D T + L R+ F E ++ RRGL
Sbjct: 72 CRHLGLDLDARTRSTLCDAYLRLAPFSEVPDSLRELKRRGL 112
>pdb|1ZRM|A Chain A, Crystal Structure Of The Reaction Intermediate Of
L-2-Haloacid Dehalogenase With 2-Chloro-N-Butyrate
pdb|1ZRN|A Chain A, Intermediate Structure Of L-2-haloacid Dehalogenase With
Monochloroacetate
Length = 232
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 41/101 (40%), Gaps = 2/101 (1%)
Query: 252 YNYFFRYFSKFGKVEDAMNLYRKMIESGYTPDRLTYHILLKILCKEDKLDLAIQVSKEMK 311
Y F S G+ ++A + I + + +L Y L ++ + A + +
Sbjct: 12 YGTLFDVHSVVGRCDEAFPGRGREISALWRQKQLEYTWLRSLMNRYVNFQQATEDALRFT 71
Query: 312 CR--GCDIDLDTSTMLIHLLCRMYKFDEASAEFEDMIRRGL 350
CR G D+D T + L R+ F E ++ RRGL
Sbjct: 72 CRHLGLDLDARTRSTLCDAYLRLAPFSEVPDSLRELKRRGL 112
>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 = 32.0 bits (71), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 33/148 (22%), Positives = 54/148 (36%), Gaps = 26/148 (17%)
Query: 163 AIRLVKEMRKEGIEPNAIVYNTVIDGLVEAGRFEEVSGMMERFLVCEPGPTMVTYTSLVK 222
A+RL E R+ G++ + YN ++ V + E P P L +
Sbjct: 45 ALRLYDEARRNGVQLSQYHYNVLL----------YVCSLAEAATESSPNP------GLSR 88
Query: 223 GYCKAGDLEGASKILKMMISRGFLPSPTTYNYFFRYFSKFGKVEDAMNLYRKMIESGYTP 282
G+ I K MI +P+ T+ R E A ++ ++M G P
Sbjct: 89 GF----------DIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQP 138
Query: 283 DRLTYHILLKILCKEDKLDLAIQVSKEM 310
+Y L C++ D A +V M
Sbjct: 139 RLRSYGPALFGFCRKGDADKAYEVDAHM 166
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 32.0 bits (71), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 26/123 (21%), Positives = 56/123 (45%), Gaps = 2/123 (1%)
Query: 108 TVRVYNILLNGWFRSKNVKDAERFWLEMRKENVTPNVVTYGTLVEGYCRLRRVDRAI-RL 166
T+ +YN ++ GW R K+ ++ +TP++++Y ++ R + I R
Sbjct: 164 TLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERC 223
Query: 167 VKEMRKEGIEPNAIVYNTVIDGLVEAGRFEEVSGMMERFLVCEPGPTMVTYTSLVKG-YC 225
+++M +EG++ A+ ++ A + V + F + P V + L++ Y
Sbjct: 224 LEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYA 283
Query: 226 KAG 228
K G
Sbjct: 284 KDG 286
>pdb|1H4I|A Chain A, Methylobacterium Extorquens Methanol Dehydrogenase
pdb|1H4I|C Chain C, Methylobacterium Extorquens Methanol Dehydrogenase
Length = 599
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 34/78 (43%), Gaps = 12/78 (15%)
Query: 187 DGLVEAGRFEEVSG-----MMERFLVCEPGPTMVTYTSLV-----KGYCKAGDLEGASKI 236
+GL + + ++G MERF V G TM T LV GY KA D + +
Sbjct: 450 EGLGQIKAYNAITGDYKWEKMERFAVW--GGTMATAGDLVFYGTLDGYLKARDSDTGDLL 507
Query: 237 LKMMISRGFLPSPTTYNY 254
K I G + P TY +
Sbjct: 508 WKFKIPSGAIGYPMTYTH 525
>pdb|1H4J|A Chain A, Methylobacterium Extorquens Methanol Dehydrogenase D303e
Mutant
pdb|1H4J|C Chain C, Methylobacterium Extorquens Methanol Dehydrogenase D303e
Mutant
pdb|1H4J|E Chain E, Methylobacterium Extorquens Methanol Dehydrogenase D303e
Mutant
pdb|1H4J|G Chain G, Methylobacterium Extorquens Methanol Dehydrogenase D303e
Mutant
Length = 599
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 34/78 (43%), Gaps = 12/78 (15%)
Query: 187 DGLVEAGRFEEVSG-----MMERFLVCEPGPTMVTYTSLV-----KGYCKAGDLEGASKI 236
+GL + + ++G MERF V G TM T LV GY KA D + +
Sbjct: 450 EGLGQIKAYNAITGDYKWEKMERFAVW--GGTMATAGDLVFYGTLDGYLKARDSDTGDLL 507
Query: 237 LKMMISRGFLPSPTTYNY 254
K I G + P TY +
Sbjct: 508 WKFKIPSGAIGYPMTYTH 525
>pdb|1W6S|A Chain A, The High Resolution Structure Of Methanol Dehydrogenase
From Methylobacterium Extorquens
pdb|1W6S|C Chain C, The High Resolution Structure Of Methanol Dehydrogenase
From Methylobacterium Extorquens
Length = 599
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 34/78 (43%), Gaps = 12/78 (15%)
Query: 187 DGLVEAGRFEEVSG-----MMERFLVCEPGPTMVTYTSLV-----KGYCKAGDLEGASKI 236
+GL + + ++G MERF V G TM T LV GY KA D + +
Sbjct: 450 EGLGQIKAYNAITGDYKWEKMERFAVW--GGTMATAGDLVFYGTLDGYLKARDSDTGDLL 507
Query: 237 LKMMISRGFLPSPTTYNY 254
K I G + P TY +
Sbjct: 508 WKFKIPSGAIGYPMTYTH 525
>pdb|3I6V|A Chain A, Crystal Structure Of A Periplasmic HisGLUGLNARGOPINE
FAMILY- Binding Protein From Silicibacter Pomeroyi In
Complex With Lysine
Length = 232
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 20/90 (22%), Positives = 38/90 (42%), Gaps = 6/90 (6%)
Query: 132 WLEMRKENVTPNVVT--YGTLVEGYCRLRRVDRAIRLVKEMRKEGIEPNAIVYNTVIDGL 189
W++ +++ PN+V+ Y T++ G D I + I P A Y DG
Sbjct: 48 WVKNDWDSIIPNLVSGNYDTIIAGMSITDERDEVIDFTQNY----IPPTASSYVATSDGA 103
Query: 190 VEAGRFEEVSGMMERFLVCEPGPTMVTYTS 219
+G + ++ + E G T+V + +
Sbjct: 104 DLSGIVAAQTATIQAGYIAESGATLVEFAT 133
>pdb|4GF6|B Chain B, Crystal Structure Of Gfp With Cuprum Bound At The
Incorporated Metal Chelating Amino Acid Pyz151
Length = 246
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 11/84 (13%)
Query: 212 PTMVTYTSLVKG--YCKAGDLEGASK----ILKMMISRGFLPSP-----TTYNYFFRYFS 260
P +V V G + +G+ EG + LK + + G LP P TT++Y + FS
Sbjct: 13 PILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFS 72
Query: 261 KFGKVEDAMNLYRKMIESGYTPDR 284
++ A + ++ + GY +R
Sbjct: 73 RYPDHMKAHDFFKSAMPEGYVQER 96
>pdb|2HYP|A Chain A, Crystal Structure Of Rv0805 D66a Mutant
Length = 280
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 26/45 (57%)
Query: 161 DRAIRLVKEMRKEGIEPNAIVYNTVIDGLVEAGRFEEVSGMMERF 205
DR L++++ + G+ P+AIV+ + E + ++ G++E F
Sbjct: 41 DRLGELLEQLNQSGLRPDAIVFTGDLAAKGEPAAYRKLRGLVEPF 85
>pdb|3N10|A Chain A, Product Complex Of Adenylate Cyclase Class Iv
pdb|3N10|B Chain B, Product Complex Of Adenylate Cyclase Class Iv
pdb|3N0Y|A Chain A, Adenylate Cyclase Class Iv With Active Site Ligand Apc
pdb|3N0Y|B Chain B, Adenylate Cyclase Class Iv With Active Site Ligand Apc
pdb|3N0Z|A Chain A, Adenylate Cyclase Class Iv With Active Site Ligand 3at
pdb|3N0Z|B Chain B, Adenylate Cyclase Class Iv With Active Site Ligand 3at
Length = 179
Score = 28.5 bits (62), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 36/86 (41%), Gaps = 1/86 (1%)
Query: 225 CKAGDLEGASKILKMMISRGFLPSPTTYNYFFRYF-SKFGKVEDAMNLYRKMIESGYTPD 283
C+A ++E SK+ M+ + G+ P+ T YF KF D + E D
Sbjct: 83 CEASNIEDVSKVQSMLATLGYHPAFTIEKQRSIYFVGKFHITVDHLTGLGDFAEIAIMTD 142
Query: 284 RLTYHILLKILCKEDKLDLAIQVSKE 309
T LK C++ +QV ++
Sbjct: 143 DATELDKLKAECRDFANTFGLQVDQQ 168
>pdb|2HYO|A Chain A, Crystal Structure Of Rv0805 N97a Mutant
Length = 280
Score = 28.1 bits (61), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 26/45 (57%)
Query: 161 DRAIRLVKEMRKEGIEPNAIVYNTVIDGLVEAGRFEEVSGMMERF 205
DR L++++ + G+ P+AIV+ + E + ++ G++E F
Sbjct: 41 DRLGELLEQLNQSGLRPDAIVFTGDLADKGEPAAYRKLRGLVEPF 85
>pdb|2HY1|A Chain A, Crystal Structure Of Rv0805
Length = 280
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 26/45 (57%)
Query: 161 DRAIRLVKEMRKEGIEPNAIVYNTVIDGLVEAGRFEEVSGMMERF 205
DR L++++ + G+ P+AIV+ + E + ++ G++E F
Sbjct: 41 DRLGELLEQLNQSGLRPDAIVFTGDLADKGEPAAYRKLRGLVEPF 85
>pdb|3IB7|A Chain A, Crystal Structure Of Full Length Rv0805
pdb|3IB8|A Chain A, Crystal Structure Of Full Length Rv0805 In Complex With
5'-amp
Length = 330
Score = 28.1 bits (61), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 26/45 (57%)
Query: 161 DRAIRLVKEMRKEGIEPNAIVYNTVIDGLVEAGRFEEVSGMMERF 205
DR L++++ + G+ P+AIV+ + E + ++ G++E F
Sbjct: 51 DRLGELLEQLNQSGLRPDAIVFTGDLADKGEPAAYRKLRGLVEPF 95
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
0.324 0.139 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,497,290
Number of Sequences: 62578
Number of extensions: 471492
Number of successful extensions: 1530
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1510
Number of HSP's gapped (non-prelim): 26
length of query: 396
length of database: 14,973,337
effective HSP length: 101
effective length of query: 295
effective length of database: 8,652,959
effective search space: 2552622905
effective search space used: 2552622905
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)