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|15644722|ref|NP_206892.1| type II restriction enzyme
M protein (hsdM) [Helicobacter pylori 26695]
(277 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|1G60|A Chain A, Crystal Structure Of Methyltransferase ... 97 2e-21
pdb|1EG2|A Chain A, Crystal Structure Of Rhodobacter Sphero... 58 1e-09
pdb|1BOO|A Chain A, Pvuii Dna Methyltransferase (Cytosine-N... 40 3e-04
pdb|1QAN|A Chain A, The Structure Of The Rrna Methyltransfe... 28 0.88
pdb|1IAR|B Chain B, Interleukin-4 RECEPTOR ALPHA CHAIN COM... 28 1.2
pdb|1AJK|A Chain A, Circularly Permuted (1-3,1-4)-Beta-D-Gl... 27 3.4
pdb|1CPM| Circularly Permuted (1-3,1-4)-Beta-D-Glucan 4-G... 27 3.4
pdb|2AYH| 1,3-1,4-Beta-D-Glucan 4 Glucanohydrolase (E.C.3... 27 3.4
pdb|1O0U|A Chain A, Crystal Structure Of Putative Glycerate... 27 3.4
pdb|1AJO|B Chain B, Circularly Permuted (1-3,1-4)-Beta-D-Gl... 27 3.4
pdb|1GBG| Bacillus Licheniformis Beta-Glucanase 26 5.7
pdb|1BSG| Beta-Lactamase From Streptomyces Albus G 25 9.8
pdb|1J7D|A Chain A, Crystal Structure Of Hmms2-Hubc13 >gi|1... 25 9.8
>pdb|1G60|A Chain A, Crystal Structure Of Methyltransferase Mboii (Moraxella
Bovis)
pdb|1G60|B Chain B, Crystal Structure Of Methyltransferase Mboii (Moraxella
Bovis)
Length = 260
Score = 97.4 bits (241), Expect = 2e-21
Identities = 80/257 (31%), Positives = 108/257 (41%), Gaps = 45/257 (17%)
Query: 23 LYQGDCNEVLPQFENQ-FDLIFADPPYFLSNDGLSIQSGKIVSVNKGDWDKEDGINGIDE 81
++Q +C + L Q EN+ L DPPY LS K DWD D N
Sbjct: 7 IHQMNCFDFLDQVENKSVQLAVIDPPYNLS---------------KADWDSFDSHNEFLA 51
Query: 82 FNYQWINNAKKALKDTGSLLISGTYHNIFSLGCVLQKLDFKILNLITWQKTNPPPNFSCR 141
F Y+WI+ L GSL I T N + L N ITW K + + R
Sbjct: 52 FTYRWIDKVLDKLDKDGSLYIFNTPFNCAFICQYLVSKGMIFQNWITWDKRDGMGSAKRR 111
Query: 142 YLTHSAEQIIWARKSRKH-----------------KHVFNYEVLKKIN------NDKQMR 178
+ T E I++ KS+ H KH +LK N +
Sbjct: 112 FST-GQETILFFSKSKNHTFNYDEVRVPYESTDRIKHASEKGILKNGKRWFPNPNGRLCG 170
Query: 179 DVWSFPAIAPWEKVNGK-----HPTQKPLALLVRLLLMASDENSLIGDPFSGSSTTGIAA 233
+VW F + EKVNGK H T KP L+ R++ +S+ N L+ D F GS TT I A
Sbjct: 171 EVWHFSSQRHKEKVNGKTVKLTHITPKPRDLIERIIRASSNPNDLVLDCFMGSGTTAIVA 230
Query: 234 NLLKREFIGIEKESEFI 250
L R FIG + +E++
Sbjct: 231 KKLGRNFIGCDMNAEYV 247
>pdb|1EG2|A Chain A, Crystal Structure Of Rhodobacter Spheroides (N6 Adenosine)
Methyltransferase (M.Rsri)
Length = 319
Score = 58.2 bits (139), Expect = 1e-09
Identities = 58/236 (24%), Positives = 93/236 (38%), Gaps = 50/236 (21%)
Query: 27 DCNEVLPQF-ENQFDLIFADPPYFLSNDGLSIQSGKIVSVNKGDWDKEDGINGIDEFNYQ 85
DC + L + ++ LI DPPY ++ DWD G + +
Sbjct: 46 DCLDTLAKLPDDSVQLIICDPPY---------------NIMLADWDDHMDYIG---WAKR 87
Query: 86 WINNAKKALKDTGSLLI---------SGTYHNIFSLGCVLQKLDFKILNLITWQKTNPPP 136
W+ A++ L TGS+ I +G+ I + + Q + NLI W N P
Sbjct: 88 WLAEAERVLSPTGSIAIFGGLQYQGEAGSGDLISIISHMRQNSKMLLANLIIW---NYPN 144
Query: 137 NFSC-RYLTHSAEQIIWARKSRKH-------KHVFNYEVLKKINNDKQMR---------- 178
S R+ + E+I W K++K+ + ++ E DK++
Sbjct: 145 GMSAQRFFANRHEEIAWFAKTKKYFFDLDAVREPYDEETKAAYMKDKRLNPESVEKGRNP 204
Query: 179 -DVWSFPAIAPWEKVNGKHPTQKPLALLVRLLLMASDENSLIGDPFSGSSTTGIAA 233
+VW + HPTQKP A++ RL+ S S + D F+GS T A
Sbjct: 205 TNVWRMSRLNGNSLERVGHPTQKPAAVIERLVRALSHPGSTVLDFFAGSGVTARVA 260
>pdb|1BOO|A Chain A, Pvuii Dna Methyltransferase (Cytosine-N4-Specific)
Length = 323
Score = 40.0 bits (92), Expect = 3e-04
Identities = 20/64 (31%), Positives = 35/64 (54%)
Query: 196 HPTQKPLALLVRLLLMASDENSLIGDPFSGSSTTGIAANLLKREFIGIEKESEFIKISMD 255
HP + P L + M ++ + L+ D F GS+TTG+ A R++I E + E++ S
Sbjct: 233 HPARFPAKLPEFFIRMLTEPDDLVVDIFGGSNTTGLVAERESRKWISFEMKPEYVAASAF 292
Query: 256 RKIE 259
R ++
Sbjct: 293 RFLD 296
>pdb|1QAN|A Chain A, The Structure Of The Rrna Methyltransferase Ermc':
Implications For The Reaction Mechanism
pdb|1QAO|A Chain A, The Structure Of The Rrna Methyltransferase Ermc':
Implications For The Reaction Mechanism
pdb|1QAQ|A Chain A, The Structure Of The Rrna Methyltransferase Ermc':
Implications For The Reaction Mechanism
pdb|1QAM|A Chain A, The Structure Of The Rrna Methyltransferase Ermc':
Implications For The Reaction Mechanism
pdb|2ERC|A Chain A, Crystal Structure Of Ermc' A Rrna-Methyl Transferase
pdb|2ERC|B Chain B, Crystal Structure Of Ermc' A Rrna-Methyl Transferase
Length = 244
Score = 28.5 bits (62), Expect = 0.88
Identities = 34/139 (24%), Positives = 62/139 (44%), Gaps = 28/139 (20%)
Query: 36 ENQFDLIFADPPYFLSNDGLSIQSGKIVSVNKGDWDKEDGINGIDEFNYQWINNAKKALK 95
+NQ IF + PY +S D + KIV + D I I E+ + AK+ L
Sbjct: 92 KNQSYKIFGNIPYNISTDIIR----KIVFDSIAD-----EIYLIVEYGF-----AKRLLN 137
Query: 96 DTGSLLISGTYHNIFSLGCVLQKLDFKILNLITWQKTNPPPNFSCRYLTHSAEQIIWARK 155
SL + ++ ++D IL+++ + +P P + + + ++ +R
Sbjct: 138 TKRSLALF-----------LMAEVDISILSMVPREYFHPKPKVNSSLIRLNRKK---SRI 183
Query: 156 SRKHKHVFNYEVLKKINND 174
S K K +NY V+K +N +
Sbjct: 184 SHKDKQKYNYFVMKWVNKE 202
>pdb|1IAR|B Chain B, Interleukin-4 RECEPTOR ALPHA CHAIN COMPLEX
Length = 207
Score = 28.1 bits (61), Expect = 1.2
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 126 LITWQKTNPPPNFSCRYLTHSAEQIIWARKSRKHKHVFNYEVLK 169
L+TW PP N+ +LT++ IW+ ++N L+
Sbjct: 115 LLTWSNPYPPDNYLYNHLTYAVN--IWSENDPADFRIYNVTYLE 156
>pdb|1AJK|A Chain A, Circularly Permuted (1-3,1-4)-Beta-D-Glucan
4-Glucanohydrolase Cpa16m-84
pdb|1AJK|B Chain B, Circularly Permuted (1-3,1-4)-Beta-D-Glucan
4-Glucanohydrolase Cpa16m-84
Length = 214
Score = 26.6 bits (57), Expect = 3.4
Identities = 11/26 (42%), Positives = 13/26 (49%)
Query: 64 SVNKGDWDKEDGINGIDEFNYQWINN 89
S N G W+K DG + FN W N
Sbjct: 143 SYNSGTWEKADGYSNGGVFNCTWRAN 168
>pdb|1CPM| Circularly Permuted (1-3,1-4)-Beta-D-Glucan 4-Glucanohydrolase
(E.C.3.2.1.73) (Cpa16m-59)
Length = 214
Score = 26.6 bits (57), Expect = 3.4
Identities = 11/26 (42%), Positives = 13/26 (49%)
Query: 64 SVNKGDWDKEDGINGIDEFNYQWINN 89
S N G W+K DG + FN W N
Sbjct: 168 SYNSGTWEKADGYSNGGVFNCTWRAN 193
>pdb|2AYH| 1,3-1,4-Beta-D-Glucan 4 Glucanohydrolase (E.C.3.2.1.73)
(Beta-Glucanase, Lichenase) Complexed With Calcium
(Synchrotron X-Ray Diffraction)
pdb|1GLH| (1,3-1,4)-Beta-D-Glucan 4-Glucanohydrolase, Hybrid Protein
(Beta-Glucanase, Lichenase) (E.C.3.2.1.73) Complexed
With Sodium
pdb|1BYH| Hybrid (1,3-1,4)-Beta-D-Glucan 4-Glucanohydrolase H (A16-M)
(E.C.3.2.1.73) (Glu 105 Covalently Modified With
3,4-Epoxybutyl-Beta-D-Cellobioside)
Length = 214
Score = 26.6 bits (57), Expect = 3.4
Identities = 11/26 (42%), Positives = 13/26 (49%)
Query: 64 SVNKGDWDKEDGINGIDEFNYQWINN 89
S N G W+K DG + FN W N
Sbjct: 12 SYNSGTWEKADGYSNGGVFNCTWRAN 37
>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 = 26.6 bits (57), Expect = 3.4
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 53 DGLSIQSGKIVSVNKGDWDKEDGINGIDEFNYQWINNAKKALKDTGSLLISG 104
DG + +G IV G K G D + Y N++ ALK +G+LLI+G
Sbjct: 366 DGPTDAAGGIVD---GSTAKTLKAMGEDPYQYLKNNDSYNALKKSGALLITG 414
>pdb|1AJO|B Chain B, Circularly Permuted (1-3,1-4)-Beta-D-Glucan
4-Glucanohydrolase Cpa16m-127
pdb|1AJO|A Chain A, Circularly Permuted (1-3,1-4)-Beta-D-Glucan
4-Glucanohydrolase Cpa16m-127
Length = 214
Score = 26.6 bits (57), Expect = 3.4
Identities = 11/26 (42%), Positives = 13/26 (49%)
Query: 64 SVNKGDWDKEDGINGIDEFNYQWINN 89
S N G W+K DG + FN W N
Sbjct: 100 SYNSGTWEKADGYSNGGVFNCTWRAN 125
>pdb|1GBG| Bacillus Licheniformis Beta-Glucanase
Length = 214
Score = 25.8 bits (55), Expect = 5.7
Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 66 NKGDWDKEDGINGIDEFNYQW-INNAKKALKDTGSLLISGTYHNIFSLG 113
N G W K DG + + FN W NN L ++ +N F G
Sbjct: 14 NTGLWQKADGYSNGNMFNCTWRANNVSMTSLGEMRLSLTSPSYNKFDCG 62
>pdb|1BSG| Beta-Lactamase From Streptomyces Albus G
Length = 266
Score = 25.0 bits (53), Expect = 9.8
Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 7/80 (8%)
Query: 190 EKVNGKHPTQKPLALLVRLLLMASDENSLIGDPFSGSSTTGIAANLLKREFIGIEKESEF 249
E+ +G T KP L + + E S+ +++ AANL+ RE G + F
Sbjct: 76 EQADGAPETGKPQNLANGMTVEELCEVSI-------TASDNCAANLMLRELGGPAAVTRF 128
Query: 250 IKISMDRKIELDARYKEIRS 269
++ DR LD E+ S
Sbjct: 129 VRSLGDRVTRLDRWEPELNS 148
>pdb|1J7D|A Chain A, Crystal Structure Of Hmms2-Hubc13
pdb|1J74|A Chain A, Crystal Structure Of Mms2
Length = 145
Score = 25.0 bits (53), Expect = 9.8
Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 171 INNDKQMRDVWSFPAIAPWEKVNGKHPTQKPLALLVRLLLMASDENSLIGDPFSGSS 227
INN M D S P +A W+ + + L L R LM S EN + P G +
Sbjct: 91 INNSSGMVDARSIPVLAKWQ---NSYSIKVVLQELRR--LMMSKENMKLPQPPEGQT 142
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 0.137 0.410
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,716,914
Number of Sequences: 13198
Number of extensions: 74876
Number of successful extensions: 129
Number of sequences better than 10.0: 13
Number of HSP's better than 10.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 117
Number of HSP's gapped (non-prelim): 14
length of query: 277
length of database: 2,899,336
effective HSP length: 87
effective length of query: 190
effective length of database: 1,751,110
effective search space: 332710900
effective search space used: 332710900
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)