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|15645454|ref|NP_207628.1| histone-like DNA-binding
protein HU (hup) [Helicobacter pylori 26695]
(94 letters)
Database: NC_000921.faa
1491 sequences; 494,079 total letters
Searching...done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_223492.1| DNA-BINDING PROTEIN HU [Helicobacter pylor... 181 3e-48
ref|NP_223706.1| histidine kinase [Helicobacter pylori J99] 24 0.61
ref|NP_223370.1| RNA POLYMERASE SIGMA-54 FACTOR [Helicobact... 23 1.0
ref|NP_222839.1| putative [Helicobacter pylori J99] 22 1.8
ref|NP_222854.1| Cytochrome oxidase (CBB3-TYPE) [Helicobact... 22 2.3
ref|NP_223791.1| 50S RIBOSOMAL PROTEIN L19. [Helicobacter p... 22 3.0
ref|NP_223441.1| PREPROTEIN TRANSLOCASE SUBUNIT [Helicobact... 22 3.0
ref|NP_223119.1| putative co-chaperone with DnaK [Helicobac... 21 4.0
ref|NP_223044.1| FLAGELLAR M-RING PROTEIN [Helicobacter pyl... 21 5.2
ref|NP_223645.1| putative [Helicobacter pylori J99] 20 6.8
ref|NP_223662.1| putative [Helicobacter pylori J99] 20 8.8
ref|NP_223233.1| putative [Helicobacter pylori J99] 20 8.8
ref|NP_222935.1| Outer membrane protein/porin [Helicobacter... 20 8.8
>ref|NP_223492.1| DNA-BINDING PROTEIN HU [Helicobacter pylori J99]
Length = 94
Score = 181 bits (458), Expect = 3e-48
Identities = 90/94 (95%), Positives = 93/94 (98%)
Query: 1 MNKAEFIDLVKEAGKYNSKREAEEAISAFTLAVETALSKGESVELIGFGKFETAEQKGKE 60
MNKAEFIDLVK+AGKYNSKREAEEAI+AFTLAVETALSKGESVEL+GFGKFETAEQKGKE
Sbjct: 1 MNKAEFIDLVKKAGKYNSKREAEEAINAFTLAVETALSKGESVELVGFGKFETAEQKGKE 60
Query: 61 GKVPGSDKTYKTEDKRVPKFKPGKTLKQKVEEGK 94
GKVPGSDKTYKTEDKRVPKFKPGK LKQKVEEGK
Sbjct: 61 GKVPGSDKTYKTEDKRVPKFKPGKILKQKVEEGK 94
>ref|NP_223706.1| histidine kinase [Helicobacter pylori J99]
Length = 815
Score = 23.9 bits (50), Expect = 0.61
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 50 KFETAEQKGKEGKVPGSD----KTYKTEDKRVPKFKPGKTLKQKVEEGK 94
K + + K K+ P + +T KTE ++VPK + K EE K
Sbjct: 218 KKQEDQAKPKQEVAPAKETPKTETPKTETRKVPKAETKAKAKADTEENK 266
>ref|NP_223370.1| RNA POLYMERASE SIGMA-54 FACTOR [Helicobacter pylori J99]
Length = 414
Score = 23.1 bits (48), Expect = 1.0
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 66 SDKTYKTEDKRVPKFKPGKTLKQKVEEGK 94
+D++Y T +FK LK+K++E K
Sbjct: 236 NDESYPTISLEENRFKDSDYLKEKLKEAK 264
>ref|NP_222839.1| putative [Helicobacter pylori J99]
Length = 143
Score = 22.3 bits (46), Expect = 1.8
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 49 GKFETAEQKGKEGKVPGSDK 68
G F E+KG++GK P K
Sbjct: 123 GPFHDHEKKGQKGKKPSHHK 142
>ref|NP_222854.1| Cytochrome oxidase (CBB3-TYPE) [Helicobacter pylori J99]
Length = 232
Score = 21.9 bits (45), Expect = 2.3
Identities = 13/47 (27%), Positives = 20/47 (41%)
Query: 48 FGKFETAEQKGKEGKVPGSDKTYKTEDKRVPKFKPGKTLKQKVEEGK 94
FG E K G V + K Y E K++ K + + +E G+
Sbjct: 160 FGVPYDTENGVKLGNVEEAKKAYLEEAKKITADMKDKRVLEAIERGE 206
>ref|NP_223791.1| 50S RIBOSOMAL PROTEIN L19. [Helicobacter pylori J99]
Length = 118
Score = 21.6 bits (44), Expect = 3.0
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 73 EDKRVPKFKPGKTLK 87
+DK +P FK G TL+
Sbjct: 15 KDKSMPTFKAGDTLR 29
>ref|NP_223441.1| PREPROTEIN TRANSLOCASE SUBUNIT [Helicobacter pylori J99]
Length = 865
Score = 21.6 bits (44), Expect = 3.0
Identities = 13/38 (34%), Positives = 17/38 (44%)
Query: 9 LVKEAGKYNSKREAEEAISAFTLAVETALSKGESVELI 46
+V GK + E TLAV KGESV ++
Sbjct: 98 MVLNDGKIAEMKTGEGKTLVATLAVALNAMKGESVYVV 135
>ref|NP_223119.1| putative co-chaperone with DnaK [Helicobacter pylori J99]
Length = 288
Score = 21.2 bits (43), Expect = 4.0
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 19 KREAEEAISAFTLAVETALSKGE 41
+RE ++ I F L ++TAL G+
Sbjct: 198 RREKDDIIQIFDLPLKTALFGGK 220
>ref|NP_223044.1| FLAGELLAR M-RING PROTEIN [Helicobacter pylori J99]
Length = 567
Score = 20.8 bits (42), Expect = 5.2
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 9 LVKEAGKYNSKREAEEAISAF 29
LVK+A YN R + A+S F
Sbjct: 401 LVKQAIGYNQNRGDDVAVSNF 421
>ref|NP_223645.1| putative [Helicobacter pylori J99]
Length = 2231
Score = 20.4 bits (41), Expect = 6.8
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 4 AEFIDLVKEAGKYN 17
A+FI + E GKYN
Sbjct: 1693 AQFIGVALENGKYN 1706
>ref|NP_223662.1| putative [Helicobacter pylori J99]
Length = 668
Score = 20.0 bits (40), Expect = 8.8
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 67 DKTYKTEDKRVPKFKPGKTLKQKV 90
+ Y ++ +VP+ P T+K V
Sbjct: 331 ENNYSSQYCKVPELSPNNTMKLDV 354
>ref|NP_223233.1| putative [Helicobacter pylori J99]
Length = 255
Score = 20.0 bits (40), Expect = 8.8
Identities = 7/16 (43%), Positives = 13/16 (80%)
Query: 31 LAVETALSKGESVELI 46
+A++T KGE++EL+
Sbjct: 227 MAIKTHFLKGEALELL 242
>ref|NP_222935.1| Outer membrane protein/porin [Helicobacter pylori J99]
Length = 483
Score = 20.0 bits (40), Expect = 8.8
Identities = 11/43 (25%), Positives = 21/43 (48%)
Query: 39 KGESVELIGFGKFETAEQKGKEGKVPGSDKTYKTEDKRVPKFK 81
KG+++E I +T KG + V S +Y + + +F+
Sbjct: 253 KGDNLETIYNTIQKTPNSKGFQSLVSRSSYSYSLNETQYSQFQ 295
Database: NC_000921.faa
Posted date: Dec 10, 2001 4:36 PM
Number of letters in database: 494,079
Number of sequences in database: 1491
Lambda K H
0.305 0.127 0.331
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 89,269
Number of Sequences: 1491
Number of extensions: 3211
Number of successful extensions: 14
Number of sequences better than 10.0: 13
Number of HSP's better than 10.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 13
length of query: 94
length of database: 494,079
effective HSP length: 70
effective length of query: 24
effective length of database: 389,709
effective search space: 9353016
effective search space used: 9353016
T: 11
A: 40
X1: 16 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (20.5 bits)
S2: 40 (20.0 bits)