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|15644926|ref|NP_207096.1| dipeptide ABC transporter,
periplasmic dipeptide-binding protein (dppA) [Helicobacter pylori
26695]
(549 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|1DPP|A Chain A, Dipeptide Binding Protein Complex With ... 372 e-104
pdb|1DPE| Dipeptide-Binding Protein 367 e-102
pdb|1JET|A Chain A, Oligo-Peptide Binding Protein (Oppa) Co... 129 6e-31
pdb|1PVD|A Chain A, Pyruvate Decarboxylase (Pdc) (E.C.4.1.1... 28 2.6
pdb|1PYD|A Chain A, Pyruvate Decarboxylase (Pdc) (E.C.4.1.1... 28 2.6
pdb|1QPB|A Chain A, Pyruvate Decarboyxlase From Yeast (Form... 28 2.6
pdb|1E54|A Chain A, Anion-Selective Porin From Comamonas Ac... 27 5.9
pdb|1CEN| Cellulase (Celc) Mutant With Glu 140 Replaced B... 27 7.7
pdb|1CEC| Glycosyl Hydrolase, Cellulase, Family A5 OF Cel... 27 7.7
>pdb|1DPP|A Chain A, Dipeptide Binding Protein Complex With Glycyl-L-Leucine
pdb|1DPP|C Chain C, Dipeptide Binding Protein Complex With Glycyl-L-Leucine
pdb|1DPP|E Chain E, Dipeptide Binding Protein Complex With Glycyl-L-Leucine
pdb|1DPP|G Chain G, Dipeptide Binding Protein Complex With Glycyl-L-Leucine
Length = 507
Score = 372 bits (955), Expect = e-104
Identities = 200/507 (39%), Positives = 289/507 (56%), Gaps = 9/507 (1%)
Query: 49 LVFARGADGSSMDPALVTDGESYVATG-NIYDTLVQFRYGTTEVEPALATSWDISPDGLV 107
LV+ +P L T G +Y A+ +Y+ LV+F+ GTTEV P LA W++S DG
Sbjct: 3 LVYCSEGSPEGFNPQLFTSGTTYDASSVPLYNRLVEFKIGTTEVIPGLAEKWEVSEDGKT 62
Query: 108 YTFHLRKGVYFHQTKYWNKKVEFSAKDVLFSFERQMDKAKRYYSPGAKSYKYWEGMGMSH 167
YTFHLRKGV +H K + E +A DV+FSF+RQ + Y+ SY+Y+EGMG+
Sbjct: 63 YTFHLRKGVKWHDNKEFKPTRELNADDVVFSFDRQKNAQNPYHKVSGGSYEYFEGMGLPE 122
Query: 168 IIKSIEALDDYTIRFTLNGPEAPFLANLGMDFLSILSKDYADYLAQNNKKDELAKKPIGT 227
+I ++ +DD T++F L PEAPFLA+L MDF SILSK+YAD + + ++L PIGT
Sbjct: 123 LISEVKKVDDNTVQFVLTRPEAPFLADLAMDFASILSKEYADAMMKAGTPEKLDLNPIGT 182
Query: 228 GPFKFFLWNKDEKIILLKNQDYWGPKAYLDKVVVRTIPNSSTRALALRTGEIMLMTGPNL 287
GPF+ + KD +I YWG K +D +V P++S R L+ E +M PN
Sbjct: 183 GPFQLQQYQKDSRIRYKAFDGYWGTKPQIDTLVFSITPDASVRYAKLQKNECQVMPYPNP 242
Query: 288 NEVEQLEKVPNIVVDKSAGLLASWLSLNTQKKYFDNPLVRLAINHAINADDYIKVLYEGF 347
++ ++++ +I + + GL +LS N QKK D+ VR A+ +A+N D IK +Y+G
Sbjct: 243 ADIARMKQDKSINLMEMPGLNVGYLSYNVQKKPLDDVKVRQALTYAVNKDAIIKAVYQGA 302
Query: 348 AQKMVNPFPPTIWGYNYNIKPYEYDLKKAKELLKQAGYPNGFKTTIFTTATRNP------ 401
N PPT+WGYN +++ Y YD +KAK LLK+AG GF ++ + P
Sbjct: 303 GVSAKNLIPPTMWGYNDDVQDYTYDPEKAKALLKEAGLEKGFSIDLWAMPVQRPYNPNAR 362
Query: 402 KGAVFIQASLAKIGIDVKIEVYEWGAYLKRTGLGEHEMAFSGWMADIADPDNFLYTLWSE 461
+ A IQA AK+G+ KI YEWG YLKR GEH+ GW D DPDNF TL+S
Sbjct: 363 RMAEMIQADWAKVGVQAKIVTYEWGEYLKRAKDGEHQTVMMGWTGDNGDPDNFFATLFS- 421
Query: 462 QAASAIPTQNHSFYKNKEFSNLLIKAKRVSDQKEREALYLKAQEIIHKDAPYVPLAYPYS 521
A++ N+S + K F +L+ A+ D +R LY +AQ ++H AP + +A+
Sbjct: 422 -CAASEQGSNYSKWCYKPFEDLIQPARATDDHNKRVELYKQAQVVMHDQAPALIIAHSTV 480
Query: 522 VVPHLSKVKGYKTTGVSVNRFFKVYLE 548
P +VKGY + + F V +E
Sbjct: 481 FEPVRKEVKGYVVDPLGKHHFENVSIE 507
>pdb|1DPE| Dipeptide-Binding Protein
Length = 507
Score = 367 bits (942), Expect = e-102
Identities = 198/507 (39%), Positives = 287/507 (56%), Gaps = 9/507 (1%)
Query: 49 LVFARGADGSSMDPALVTDGESYVATG-NIYDTLVQFRYGTTEVEPALATSWDISPDGLV 107
LV+ +P L G +Y A+ +Y+ LV+F+ GTTEV P LA W++S DG
Sbjct: 3 LVYCSEGSPEGFNPQLFISGTTYDASSVPLYNRLVEFKIGTTEVIPGLAEKWEVSEDGKT 62
Query: 108 YTFHLRKGVYFHQTKYWNKKVEFSAKDVLFSFERQMDKAKRYYSPGAKSYKYWEGMGMSH 167
YTFHLRKGV +H K + E +A DV+FSF+RQ + Y+ SY+Y+EGMG+
Sbjct: 63 YTFHLRKGVKWHDNKEFKPTRELNADDVVFSFDRQKNAQNPYHKVSGGSYEYFEGMGLPE 122
Query: 168 IIKSIEALDDYTIRFTLNGPEAPFLANLGMDFLSILSKDYADYLAQNNKKDELAKKPIGT 227
+I ++ +DD T++F L PEAPFLA+L MDF SILSK+YAD + + ++L PIGT
Sbjct: 123 LISEVKKVDDNTVQFVLTRPEAPFLADLAMDFASILSKEYADAMMKAGTPEKLDLNPIGT 182
Query: 228 GPFKFFLWNKDEKIILLKNQDYWGPKAYLDKVVVRTIPNSSTRALALRTGEIMLMTGPNL 287
GPF+ + KD +I YWG K +D +V P++S R L+ E +M PN
Sbjct: 183 GPFQLQQYQKDSRIRYKAFDGYWGTKPQIDTLVFSITPDASVRYAKLQKNECQVMPYPNP 242
Query: 288 NEVEQLEKVPNIVVDKSAGLLASWLSLNTQKKYFDNPLVRLAINHAINADDYIKVLYEGF 347
++ ++++ +I + + GL +LS N QKK D+ VR A+ +A+N D IK +Y+G
Sbjct: 243 ADIARMKQDKSINLMEMPGLNVGYLSYNVQKKPLDDVKVRQALTYAVNKDAIIKAVYQGA 302
Query: 348 AQKMVNPFPPTIWGYNYNIKPYEYDLKKAKELLKQAGYPNGFKTTIFTTATRNP------ 401
N PPT+WGYN +++ Y YD +KAK LLK+AG GF ++ + P
Sbjct: 303 GVSAKNLIPPTMWGYNDDVQDYTYDPEKAKALLKEAGLEKGFSIDLWAMPVQRPYNPNAR 362
Query: 402 KGAVFIQASLAKIGIDVKIEVYEWGAYLKRTGLGEHEMAFSGWMADIADPDNFLYTLWSE 461
+ A IQA AK+G+ KI YEWG YLKR GEH+ GW D DPDNF T +S
Sbjct: 363 RMAEMIQADWAKVGVQAKIVTYEWGEYLKRAKDGEHQTVMMGWTGDNGDPDNFFATEFS- 421
Query: 462 QAASAIPTQNHSFYKNKEFSNLLIKAKRVSDQKEREALYLKAQEIIHKDAPYVPLAYPYS 521
A++ N+S + K F +L+ A+ D +R LY +AQ ++H AP + +A+
Sbjct: 422 -CAASEQGSNYSKWCYKPFEDLIQPARATDDHNKRVELYKQAQVVMHDQAPALIIAHSTV 480
Query: 522 VVPHLSKVKGYKTTGVSVNRFFKVYLE 548
P +VKGY + + F V +E
Sbjct: 481 FEPVRKEVKGYVVDPLGKHHFENVSIE 507
>pdb|1JET|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kak
pdb|1JEU|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kek
pdb|1JEV|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kwk
pdb|2OLB|A Chain A, Oligopeptide Binding Protein (Oppa) Complexed With
Tri-Lysine
pdb|1B32|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kmk
pdb|1B4Z|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kdk
pdb|1QKB|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kvk
pdb|1B46|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kpk
pdb|1QKA|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Krk
pdb|1B51|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Ksk
pdb|1B1H|A Chain A, Oligo-Peptide Binding ProteinTRIPEPTIDE (LYS HPE LYS)
Complex
pdb|1B3F|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Khk
pdb|1B58|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kyk
pdb|1B5J|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kqk
pdb|1B6H|A Chain A, Oligo-Peptide Binding Protein Complexed With
Lysyl-Norvalyl- Lysine
pdb|1B9J|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Klk
pdb|2RKM|A Chain A, Structure Of Oppa Complexed With Lys-Lys
pdb|1B2H|A Chain A, Oligo-Peptide Binding Protein Complexed With
Lysyl-Ornithyl- Lysine
pdb|1B0H|A Chain A, Oligo-Peptide Binding Protein Complexed With Lysyl-
Napthylalanyl-Lysine
pdb|1B4H|A Chain A, Oligo-Peptide Binding Protein Complexed With Lysyl-
Diaminobutyric Acid-Lysine
pdb|1B5H|A Chain A, Oligo-Peptide Binding Protein Complexed With Lysyl-
Diaminopropanoic Acid-Lysine
pdb|1B5I|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Knk
pdb|1B3L|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kgk
pdb|1B3L|C Chain C, Oligo-Peptide Binding Protein (Oppa) Complexed With Kgk
pdb|1B3G|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kik
pdb|1B3H|A Chain A, Oligo-Peptide Binding Protein Complexed With Lysyl-
Cyclohexylalanyl-Lysine
pdb|1B7H|A Chain A, Oligo-Peptide Binding Protein Complexed With Lysyl-
Norleucyl-Lysine
pdb|1OLC|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With
Lys-Lys-Lys-Ala
pdb|1B40|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kfk
pdb|1RKM| Structure Of Oppa
pdb|1B05|A Chain A, Structure Of Oligo-Peptide Binding Protein Complexed With
Lys-Cys-Lys
pdb|1B52|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Ktk
pdb|1OLA|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With A
Four-Residue Peptide
Length = 517
Score = 129 bits (325), Expect = 6e-31
Identities = 129/496 (26%), Positives = 227/496 (45%), Gaps = 52/496 (10%)
Query: 49 LVFARGADGSSMDPALVTDGESYVATGNIYDTLVQFRYGTTEVE----PALATSWDISPD 104
LV G++ S+DP + + ++++ L+ ++VE P +A W+ + D
Sbjct: 15 LVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLL-----ISDVEGHPSPGVAEKWE-NKD 68
Query: 105 GLVYTFHLRKGVYFHQTKYWNKKVEFSAKDVLFSFERQMDKAKRYYSPGAKSYKYWEGMG 164
V+TFHLR+ W+ +A D ++S++R D SP A +Y
Sbjct: 69 FKVWTFHLRENAK------WSDGTPVTAHDFVYSWQRLADPNTA--SPYASYLQYGHIAN 120
Query: 165 MSHIIKS--------IEALDDYTIRFTLNGPEAPFLANLGMDFLSILSKDYADYLAQNNK 216
+ II ++ALDD+T TL+ P F L +S + K +
Sbjct: 121 IDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGD--- 177
Query: 217 KDELAKKPIGTGPFKFFLWNKDEKIILLKNQDYW-GPKAYLDKVVVRTIPNSSTRALALR 275
K + G +K W +E+I+L +N YW K +++V I + T R
Sbjct: 178 KWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYR 237
Query: 276 TGEI-MLMTGPNLNEVEQLEK-VPNIV-VDKSAGLLASWLSLNTQKKYFDNPLVRLAINH 332
+GEI M + ++L+K +PN V VD L + +N QK F++ VR A+
Sbjct: 238 SGEIDMTYNNMPIELFQKLKKEIPNEVRVDPY--LCTYYYEINNQKAPFNDVRVRTALKL 295
Query: 333 AINADDYIKVLYEGFAQKMVNPFPPTIWGYNYNIKP--YEYDLKK----AKELLKQAGYP 386
A++ D + + + PP G ++P +++ +K AK+LL +AG+
Sbjct: 296 ALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKL-VEPEWFKWSQQKRNEEAKKLLAEAGFT 354
Query: 387 NGFKTT---IFTTATRNPKGAVFIQASLAK-IGIDVKIEVYEWGAYLKRTGLGEHEMAFS 442
T ++ T+ + K A+ + + K +G++V +E EW +L G ++A +
Sbjct: 355 ADKPLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQGTFDVARA 414
Query: 443 GWMADIADPDNFLYTLWSEQAASAIPTQNHSFYKNKEFSNLLIKAKRVSDQKEREALYLK 502
GW AD +P +FL T+ S+ + N + YK+ F L+ +V+D +R LY K
Sbjct: 415 GWCADYNEPTSFLNTMLSDS------SNNTAHYKSPAFDKLIADTLKVADDTQRSELYAK 468
Query: 503 AQEIIHKDAPYVPLAY 518
A++ + KD+ VP+ Y
Sbjct: 469 AEQQLDKDSAIVPVYY 484
>pdb|1PVD|A Chain A, Pyruvate Decarboxylase (Pdc) (E.C.4.1.1.1)
pdb|1PVD|B Chain B, Pyruvate Decarboxylase (Pdc) (E.C.4.1.1.1)
Length = 537
Score = 28.1 bits (61), Expect = 2.6
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 5/52 (9%)
Query: 176 DDYTIRFTLNGPEAPFLANLGMDFLSIL----SKDYADY-LAQNNKKDELAK 222
D YTI ++GP+A + G D LS+L +KDY + +A + D+L +
Sbjct: 453 DGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQ 504
>pdb|1PYD|A Chain A, Pyruvate Decarboxylase (Pdc) (E.C.4.1.1.1)
pdb|1PYD|B Chain B, Pyruvate Decarboxylase (Pdc) (E.C.4.1.1.1)
Length = 556
Score = 28.1 bits (61), Expect = 2.6
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 5/52 (9%)
Query: 176 DDYTIRFTLNGPEAPFLANLGMDFLSIL----SKDYADY-LAQNNKKDELAK 222
D YTI ++GP+A + G D LS+L +KDY + +A + D+L +
Sbjct: 472 DGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQ 523
>pdb|1QPB|A Chain A, Pyruvate Decarboyxlase From Yeast (Form B) Complexed With
Pyruvamide
pdb|1QPB|B Chain B, Pyruvate Decarboyxlase From Yeast (Form B) Complexed With
Pyruvamide
Length = 563
Score = 28.1 bits (61), Expect = 2.6
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 5/52 (9%)
Query: 176 DDYTIRFTLNGPEAPFLANLGMDFLSIL----SKDYADY-LAQNNKKDELAK 222
D YTI ++GP+A + G D LS+L +KDY + +A + D+L +
Sbjct: 472 DGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQ 523
>pdb|1E54|A Chain A, Anion-Selective Porin From Comamonas Acidovorans
Length = 332
Score = 26.9 bits (58), Expect = 5.9
Identities = 24/79 (30%), Positives = 35/79 (43%), Gaps = 2/79 (2%)
Query: 414 IGIDVKIEVYEWGAYLKRTGLGEHEMAFSGWMADIADPDNFLYTLWSEQAASAIPT--QN 471
IG D+K Y GA G+GE ++ ++ + D TL S N
Sbjct: 232 IGGDIKTNSYMLGASAPVGGVGEVKLQYALYDQKAIDSKAHQITLGYVHNLSKRTALYGN 291
Query: 472 HSFYKNKEFSNLLIKAKRV 490
+F KNK+ S L ++AK V
Sbjct: 292 LAFLKNKDASTLGLQAKGV 310
>pdb|1CEN| Cellulase (Celc) Mutant With Glu 140 Replaced By Gln Complexed
With Cellohexaose
pdb|1CEO| Cellulase (Celc) Mutant With Glu 140 Replaced By Gln
Length = 343
Score = 26.6 bits (57), Expect = 7.7
Identities = 11/28 (39%), Positives = 16/28 (56%), Gaps = 1/28 (3%)
Query: 100 DISPDGLVYTFHLRKGVYF-HQTKYWNK 126
DI D +VY FH +F HQ +W++
Sbjct: 187 DIDDDYIVYNFHFYNPFFFTHQKAHWSE 214
>pdb|1CEC| Glycosyl Hydrolase, Cellulase, Family A5 OF CellulasesGLYCOSYL
HYDROLASES, CLOSTRIDIUM THERMOCELLUM, Endoglucanase C
Mol_id: 1; Molecule: Endoglucanase Celc; Chain: Null;
Synonym: Egc, Cellulase Celc, Endo-1,4-Beta-Glucanase
Celc; Ec: 3.2.1.4; Engineered: Yes; Other_details:
Cellulase Family A5
Length = 343
Score = 26.6 bits (57), Expect = 7.7
Identities = 11/28 (39%), Positives = 16/28 (56%), Gaps = 1/28 (3%)
Query: 100 DISPDGLVYTFHLRKGVYF-HQTKYWNK 126
DI D +VY FH +F HQ +W++
Sbjct: 187 DIDDDYIVYNFHFYNPFFFTHQKAHWSE 214
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 0.136 0.406
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,403,699
Number of Sequences: 13198
Number of extensions: 149532
Number of successful extensions: 430
Number of sequences better than 10.0: 9
Number of HSP's better than 10.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 419
Number of HSP's gapped (non-prelim): 9
length of query: 549
length of database: 2,899,336
effective HSP length: 93
effective length of query: 456
effective length of database: 1,671,922
effective search space: 762396432
effective search space used: 762396432
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)