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|15645557|ref|NP_207733.1| alanine racemase,
biosynthetic (alr) [Helicobacter pylori 26695]
(377 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|1SFT|A Chain A, Alanine Racemase >gi|3891941|pdb|1BD0|A... 197 1e-51
pdb|1L6F|A Chain A, Alanine Racemase Bound With N-(5'-Phosp... 195 6e-51
pdb|1E42|B Chain B, Beta2-Adaptin Appendage Domain, From Cl... 28 2.2
pdb|1BH6|A Chain A, Subtilisin Dy In Complex With The Synth... 26 8.4
pdb|1B4F|B Chain B, Oligomeric Structure Of The Human Ephb2... 26 8.4
>pdb|1SFT|A Chain A, Alanine Racemase
pdb|1BD0|A Chain A, Alanine Racemase Complexed With Alanine Phosphonate
pdb|1BD0|B Chain B, Alanine Racemase Complexed With Alanine Phosphonate
pdb|1SFT|B Chain B, Alanine Racemase
Length = 388
Score = 197 bits (502), Expect = 1e-51
Identities = 122/373 (32%), Positives = 194/373 (51%), Gaps = 10/373 (2%)
Query: 4 RASFVEVDTASLRHNFSAVKSIVPKDACVMAVVKANAYGAGAIKASEIFLQEGANYLGVA 63
R ++ EVD ++ N ++ ++P D +MAVVKANAYG G ++ + L+ GA+ L VA
Sbjct: 6 RDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVA 65
Query: 64 TLDEALELRSHFSKTPILILGYSPNANASMLVDNDLSAMIFSLEQAEVFSQMALKSQKRL 123
LDEAL LR + PIL+LG S A+A++ ++ +F + E S + +
Sbjct: 66 FLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASAL-YSGPFPI 124
Query: 124 KVHIKIDTGMHRLGLEPNFKSIETIKKIRALKGLEIEGIFTHLSNADAKIKTHAKNQMKA 183
H+K+DTGM RLG++ ++ + I +EG++TH + AD + Q
Sbjct: 125 HFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTR 184
Query: 184 FNAFLEQLLDQKIEFQYRHAYNSAGILSLCNGNENRLLNLYRPGIMLYGFYPSNGMKESC 243
F LE L + H NSA L +R N+ R GI +YG PS G+K
Sbjct: 185 FLHMLEWLPSRP---PLVHCANSAASLRF----PDRTFNMVRFGIAMYGLAPSPGIKPLL 237
Query: 244 PTILKNVISLKAQIVQIRSVKKGEFIGYGEHFYTNEETLVGVLALGYADGLMRALGNRIQ 303
P LK SL +++V ++ ++ GE + YG + E +G + +GYADG +R L
Sbjct: 238 PYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRL-QHFH 296
Query: 304 VAINNQLAPLIGKVCMDQCFVKLNNIQAKEGDEVILFGDKSAKANDASEIXALLNTIAYE 363
V ++ Q AP++G++CMDQC ++L G +V L G + + ++ L TI YE
Sbjct: 297 VLVDGQKAPIVGRICMDQCMIRLPG-PLPVGTKVTLIGRQGDEVISIDDVARHLETINYE 355
Query: 364 TISTLSKRLERVY 376
T+S R+ R++
Sbjct: 356 VPCTISYRVPRIF 368
>pdb|1L6F|A Chain A, Alanine Racemase Bound With N-(5'-Phosphopyridoxyl)-L-
Alanine
pdb|1L6F|B Chain B, Alanine Racemase Bound With N-(5'-Phosphopyridoxyl)-L-
Alanine
pdb|1L6G|A Chain A, Alanine Racemase Bound With N-(5'-Phosphopyridoxyl)-D-
Alanine
pdb|1L6G|B Chain B, Alanine Racemase Bound With N-(5'-Phosphopyridoxyl)-D-
Alanine
pdb|2SFP|A Chain A, Alanine Racemase With Bound Propionate Inhibitor
pdb|2SFP|B Chain B, Alanine Racemase With Bound Propionate Inhibitor
Length = 388
Score = 195 bits (496), Expect = 6e-51
Identities = 121/373 (32%), Positives = 193/373 (51%), Gaps = 10/373 (2%)
Query: 4 RASFVEVDTASLRHNFSAVKSIVPKDACVMAVVKANAYGAGAIKASEIFLQEGANYLGVA 63
R ++ EVD ++ N ++ ++P D +MAVVKANAYG G ++ + L+ GA+ L VA
Sbjct: 6 RDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVA 65
Query: 64 TLDEALELRSHFSKTPILILGYSPNANASMLVDNDLSAMIFSLEQAEVFSQMALKSQKRL 123
LDEAL LR + PIL+LG S A+A++ ++ +F + E S + +
Sbjct: 66 FLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASAL-YSGPFPI 124
Query: 124 KVHIKIDTGMHRLGLEPNFKSIETIKKIRALKGLEIEGIFTHLSNADAKIKTHAKNQMKA 183
H+ +DTGM RLG++ ++ + I +EG++TH + AD + Q
Sbjct: 125 HFHLXMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTR 184
Query: 184 FNAFLEQLLDQKIEFQYRHAYNSAGILSLCNGNENRLLNLYRPGIMLYGFYPSNGMKESC 243
F LE L + H NSA L +R N+ R GI +YG PS G+K
Sbjct: 185 FLHMLEWLPSRP---PLVHCANSAASLRF----PDRTFNMVRFGIAMYGLAPSPGIKPLL 237
Query: 244 PTILKNVISLKAQIVQIRSVKKGEFIGYGEHFYTNEETLVGVLALGYADGLMRALGNRIQ 303
P LK SL +++V ++ ++ GE + YG + E +G + +GYADG +R L
Sbjct: 238 PYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRL-QHFH 296
Query: 304 VAINNQLAPLIGKVCMDQCFVKLNNIQAKEGDEVILFGDKSAKANDASEIXALLNTIAYE 363
V ++ Q AP++G++CMDQC ++L G +V L G + + ++ L TI YE
Sbjct: 297 VLVDGQKAPIVGRICMDQCMIRLPG-PLPVGTKVTLIGRQGDEVISIDDVARHLETINYE 355
Query: 364 TISTLSKRLERVY 376
T+S R+ R++
Sbjct: 356 VPCTISYRVPRIF 368
>pdb|1E42|B Chain B, Beta2-Adaptin Appendage Domain, From Clathrin Adaptor Ap2
pdb|1E42|A Chain A, Beta2-Adaptin Appendage Domain, From Clathrin Adaptor Ap2
Length = 258
Score = 27.7 bits (60), Expect = 2.2
Identities = 19/56 (33%), Positives = 25/56 (43%), Gaps = 11/56 (19%)
Query: 155 KGLEIEGIFTHLSNADAKIKTHAKNQMKAFNAFLEQLLDQKIEFQYRHAYNSAGIL 210
KGLEI G FTH H +M N L+ + D I+F NS G++
Sbjct: 42 KGLEISGTFTHRQG-------HIYMEMNFTNKALQHMTDFAIQFN----KNSFGVI 86
>pdb|1BH6|A Chain A, Subtilisin Dy In Complex With The Synthetic Inhibitor
N-Benzyloxycarbonyl-Ala-Pro-Phe-Chloromethyl Ketone
Length = 274
Score = 25.8 bits (55), Expect = 8.4
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 200 YRHAYNSAGILSLCNGNENRL--------LNLYRPGIMLYGFYPSN 237
Y Y+S + + N+NR L + PG+ +Y YPSN
Sbjct: 166 YPAKYDSVIAVGAVDSNKNRASFSSVGSELEVMAPGVSVYSTYPSN 211
>pdb|1B4F|B Chain B, Oligomeric Structure Of The Human Ephb2 Receptor Sam
Domain
pdb|1B4F|F Chain F, Oligomeric Structure Of The Human Ephb2 Receptor Sam
Domain
pdb|1B4F|H Chain H, Oligomeric Structure Of The Human Ephb2 Receptor Sam
Domain
pdb|1B4F|D Chain D, Oligomeric Structure Of The Human Ephb2 Receptor Sam
Domain
pdb|1B4F|A Chain A, Oligomeric Structure Of The Human Ephb2 Receptor Sam
Domain
pdb|1B4F|C Chain C, Oligomeric Structure Of The Human Ephb2 Receptor Sam
Domain
pdb|1B4F|E Chain E, Oligomeric Structure Of The Human Ephb2 Receptor Sam
Domain
pdb|1B4F|G Chain G, Oligomeric Structure Of The Human Ephb2 Receptor Sam
Domain
pdb|1F0M|A Chain A, Monomeric Structure Of The Human Ephb2 Sam (Sterile Alpha
Motif) Domain
Length = 82
Score = 25.8 bits (55), Expect = 8.4
Identities = 17/66 (25%), Positives = 34/66 (50%), Gaps = 9/66 (13%)
Query: 199 QYRHAYNSAGILSLCNGNENRLLNLYRPGIMLYGFYPSNGMKESCPTILKNVISLKAQIV 258
QY+ ++ +AG S ++ + ++ R G+ L G IL ++ ++AQ+
Sbjct: 25 QYKESFANAGFTSFDVVSQMMMEDILRVGVTLAGHQKK---------ILNSIQVMRAQMN 75
Query: 259 QIRSVK 264
QI+SV+
Sbjct: 76 QIQSVE 81
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
0.319 0.135 0.373
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,896,131
Number of Sequences: 13198
Number of extensions: 71732
Number of successful extensions: 187
Number of sequences better than 10.0: 5
Number of HSP's better than 10.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 177
Number of HSP's gapped (non-prelim): 5
length of query: 377
length of database: 2,899,336
effective HSP length: 90
effective length of query: 287
effective length of database: 1,711,516
effective search space: 491205092
effective search space used: 491205092
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: 55 (25.8 bits)