BLASTP 2.2.1 [Apr-13-2001]
Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
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.
Query= gi|15644840|ref|NP_207010.1| succinyl-diaminopimelate
desuccinylase (dapE) [Helicobacter pylori 26695]
(383 letters)
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
13,198 sequences; 2,899,336 total letters
Searching...........................done
Score E
Sequences producing significant alignments: (bits) Value
pdb|1LFW|A Chain A, Crystal Structure Of Pepv 49 1e-06
pdb|2FRV|B Chain B, Crystal Structure Of The Oxidized Form ... 28 1.7
pdb|1FRV|B Chain B, Crystal Structure Of The Oxidized Form ... 28 1.7
pdb|1DLJ|A Chain A, The First Structure Of Udp-Glucose Dehy... 26 8.6
pdb|1JHN|A Chain A, Crystal Structure Of The Lumenal Domain... 26 8.6
pdb|1O0U|A Chain A, Crystal Structure Of Putative Glycerate... 26 8.6
>pdb|1LFW|A Chain A, Crystal Structure Of Pepv
Length = 470
Score = 48.9 bits (115), Expect = 1e-06
Identities = 30/71 (42%), Positives = 38/71 (53%), Gaps = 8/71 (11%)
Query: 78 GHIDVVPPGNHWQSDPFKPVI-KEGFLYGRGAQDMKGG-----VGAFLSASLNFNPKTPF 131
GH+DVVP G W DPFK I +EG +YGRG+ D KG G L F PK
Sbjct: 86 GHMDVVPAGEGWTRDPFKMEIDEEGRIYGRGSADDKGPSLTAYYGMLLLKEAGFKPKKK- 144
Query: 132 LLSILLTSDEE 142
+ +L ++EE
Sbjct: 145 -IDFVLGTNEE 154
>pdb|2FRV|B Chain B, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|2FRV|D Chain D, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|2FRV|F Chain F, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|2FRV|H Chain H, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|2FRV|J Chain J, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|2FRV|L Chain L, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
Length = 536
Score = 28.1 bits (61), Expect = 1.7
Identities = 27/100 (27%), Positives = 40/100 (40%), Gaps = 6/100 (6%)
Query: 226 NLDNGDEYFDPSKLVITNLHA-----GLGANNITPASVEIIFNARHSLKTTKESLKEYLE 280
NL G +Y + +LHA A N PA + N KTT ESLK
Sbjct: 97 NLTMGAQYMHDHLVHFYHLHALDWVNVANALNADPAKAARLANDLSPKKTTTESLKAVQA 156
Query: 281 KVLKDLPYTLELESSSSPFITASHSKLTSVLKENILKTCH 320
KV K L + +L ++ + H + +++ T H
Sbjct: 157 KV-KALVESGQLGIFTNAYFLGGHPAYVLPAEVDLIATAH 195
>pdb|1FRV|B Chain B, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|1FRV|D Chain D, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
Length = 536
Score = 28.1 bits (61), Expect = 1.7
Identities = 27/100 (27%), Positives = 40/100 (40%), Gaps = 6/100 (6%)
Query: 226 NLDNGDEYFDPSKLVITNLHA-----GLGANNITPASVEIIFNARHSLKTTKESLKEYLE 280
NL G +Y + +LHA A N PA + N KTT ESLK
Sbjct: 97 NLTMGAQYMHDHLVHFYHLHALDWVNVANALNADPAKAARLANDLSPRKTTTESLKAVQA 156
Query: 281 KVLKDLPYTLELESSSSPFITASHSKLTSVLKENILKTCH 320
KV K L + +L ++ + H + +++ T H
Sbjct: 157 KV-KALVESGQLGIFTNAYFLGGHPAYVLPAEVDLIATAH 195
>pdb|1DLJ|A Chain A, The First Structure Of Udp-Glucose Dehydrogenase (Udpgdh)
Reveals The Catalytic Residues Necessary For The
Two-Fold Oxidation
Length = 402
Score = 25.8 bits (55), Expect = 8.6
Identities = 32/136 (23%), Positives = 57/136 (41%), Gaps = 20/136 (14%)
Query: 210 NPIDTLASVLPLISGVNLDNGDEYFDPSKLVITNLHAGLGANNITPASVEIIFNARHSLK 269
N +DT A L S + + G Y D + N G G ++ + +++ N + +
Sbjct: 219 NELDTYAESRKLNSHMIIQ-GISYDDRIGMHYNNPSFGYGGYSLPKDTKQLLANYNNIPQ 277
Query: 270 TTKESL-------KEYLEK----VLKDLP--------YTLELESSSSPFITASHSKLTSV 310
T E++ K Y+ K VLK+ Y L ++S+S F ++ + +
Sbjct: 278 TLIEAIVSSNNVRKSYIAKQIINVLKEQESPVKVVGVYRLIMKSNSDNFRESAIKDVIDI 337
Query: 311 LKENILKTCHTTPLLN 326
LK +K P+LN
Sbjct: 338 LKSKDIKIIIYEPMLN 353
>pdb|1JHN|A Chain A, Crystal Structure Of The Lumenal Domain Of Calnexin
Length = 424
Score = 25.8 bits (55), Expect = 8.6
Identities = 14/29 (48%), Positives = 18/29 (61%), Gaps = 1/29 (3%)
Query: 38 ECGENGVKNLFLYRIFNPPKDHAEEKHAK 66
+CGE+ K F++R NP EEKHAK
Sbjct: 150 KCGED-YKLHFIFRHKNPKTGVYEEKHAK 177
>pdb|1O0U|A Chain A, Crystal Structure Of Putative Glycerate Kinase (Tm1585)
From Thermotoga Maritima At 2.95 A Resolution
pdb|1O0U|B Chain B, Crystal Structure Of Putative Glycerate Kinase (Tm1585)
From Thermotoga Maritima At 2.95 A Resolution
Length = 429
Score = 25.8 bits (55), Expect = 8.6
Identities = 20/67 (29%), Positives = 28/67 (40%), Gaps = 7/67 (10%)
Query: 324 LLNTKGGTSDARFFSAHGIEVVEFGVINDRIHAI-------DERVSLKELELLEKVFLGV 376
L KGG R F A + +V V+ DR+ I D S L++LEK +
Sbjct: 177 LSQVKGGRFAERVFPAKVVALVLSDVLGDRLDVIASGPAWPDSSTSEDALKVLEKYGIET 236
Query: 377 LEGLSEA 383
E + A
Sbjct: 237 SESVKRA 243
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
Posted date: Dec 20, 2002 11:08 AM
Number of letters in database: 2,899,336
Number of sequences in database: 13,198
Lambda K H
0.318 0.138 0.403
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,323,337
Number of Sequences: 13198
Number of extensions: 100879
Number of successful extensions: 296
Number of sequences better than 10.0: 6
Number of HSP's better than 10.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 294
Number of HSP's gapped (non-prelim): 6
length of query: 383
length of database: 2,899,336
effective HSP length: 90
effective length of query: 293
effective length of database: 1,711,516
effective search space: 501474188
effective search space used: 501474188
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)