BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
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.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 018450
(355 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4B4T|V Chain V, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 306
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 42/135 (31%), Positives = 60/135 (44%), Gaps = 12/135 (8%)
Query: 6 VKMSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVE 65
V +S L L H + E+MGL+LG+ NV + A PQS + + V+
Sbjct: 27 VYISSIALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVNVVDVF--AMPQSGTGVSVEAVD 84
Query: 66 TNPEQLAAASAQADRMTVL--TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGF 123
QA M +L TGR V+GWYHSHP S VDV TQ ++ L++
Sbjct: 85 D--------VFQAKMMDMLKQTGRDQMVVGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRA 136
Query: 124 IGLIFSCFSEDANKV 138
+ ++ KV
Sbjct: 137 VAVVVDPIQSVKGKV 151
>pdb|4F7O|A Chain A, Crystal Structure Of Csn5
pdb|4F7O|B Chain B, Crystal Structure Of Csn5
Length = 257
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 35/121 (28%), Positives = 51/121 (42%), Gaps = 7/121 (5%)
Query: 7 KMSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVET 66
K+S L + HA S E+ GL LG ++ + A P ++ R +
Sbjct: 56 KISALALLKXVXHARSGGNLEVXGLXLGKVDGETXIIXDSF---ALPVEGTETRVNAQAA 112
Query: 67 NPEQLAAASAQADRMTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGL 126
E AA A ++ GR IGWYHSHP S +DV TQ + Q F+ +
Sbjct: 113 AYEYXAAYIENAKQV----GRLENAIGWYHSHPGYGCWLSGIDVSTQXLNQQFQEPFVAV 168
Query: 127 I 127
+
Sbjct: 169 V 169
>pdb|2ZNR|A Chain A, Crystal Structure Of The Dub Domain Of Human Amsh-Lp
Length = 178
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 38/138 (27%), Positives = 57/138 (41%), Gaps = 20/138 (14%)
Query: 27 EIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRMTVLTG 86
E G+L G + H++ +T +I QS D N E+L Q D +T
Sbjct: 34 ETCGILCGKLTHNEF-TITHVI--VPKQSAGPDYCDM--ENVEELFNVQDQHDLLT---- 84
Query: 87 RTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDA-----NKVGRI 141
+GW H+HP T S VD+ T YQL+ I ++ S +D G +
Sbjct: 85 -----LGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHKDTGIFRLTNAGML 139
Query: 142 QVIAFQSSDGKQNHISKP 159
+V A + G H +P
Sbjct: 140 EVSACKKK-GFHPHTKEP 156
>pdb|2ZNV|A Chain A, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex
With Lys63-Linked Ubiquitin Dimer
pdb|2ZNV|D Chain D, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex
With Lys63-Linked Ubiquitin Dimer
Length = 178
Score = 35.8 bits (81), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 37/135 (27%), Positives = 56/135 (41%), Gaps = 20/135 (14%)
Query: 30 GLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRMTVLTGRTT 89
G+L G + H++ +T +I QS D N E+L Q D +T
Sbjct: 37 GILCGKLTHNEF-TITHVI--VPKQSAGPDYCDM--ENVEELFNVQDQHDLLT------- 84
Query: 90 RVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDA-----NKVGRIQVI 144
+GW H+HP T S VD+ T YQL+ I ++ S +D G ++V
Sbjct: 85 --LGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHKDTGIFRLTNAGMLEVS 142
Query: 145 AFQSSDGKQNHISKP 159
A + G H +P
Sbjct: 143 ACKKK-GFHPHTKEP 156
>pdb|3RZV|A Chain A, The Crystal Structure Of A E280a Mutant Of The Catalytic
Domain Of Amsh
Length = 211
Score = 32.3 bits (72), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 92 IGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFS 129
+GW H+HP T S VD+ T YQ++ + ++ S
Sbjct: 118 LGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCS 155
>pdb|2KCQ|A Chain A, Solution Structure Of Protein Sru_2040 From Salinibacter
Ruber (Strain Dsm 13855) . Northeast Structural Genomics
Consortium Target Srr106
Length = 153
Score = 32.3 bits (72), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 35/125 (28%), Positives = 48/125 (38%), Gaps = 13/125 (10%)
Query: 6 VKMSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVE 65
+K + D+ H EE G LLG + + V AL + RS++R R E
Sbjct: 1 MKTTPDILDQIRVHGADAYPEEGCGFLLGTVTDDGDNRVAALHRATN--RRSEQRTRRYE 58
Query: 66 TNPEQLAAASAQADRMTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIG 125
+ AA A A + V+G YHSHP PS D+ GF
Sbjct: 59 LTADDYRAADAAAQEQGL------DVVGVYHSHPDHPARPSATDLEEATF-----PGFTY 107
Query: 126 LIFSC 130
+I S
Sbjct: 108 VIVSV 112
>pdb|3RZU|A Chain A, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|B Chain B, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|C Chain C, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|D Chain D, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|E Chain E, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|F Chain F, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|G Chain G, The Crystal Structure Of The Catalytic Domain Of Amsh
Length = 187
Score = 32.3 bits (72), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 92 IGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFS 129
+GW H+HP T S VD+ T YQ++ + ++ S
Sbjct: 94 LGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCS 131
>pdb|1Z32|X Chain X, Structure-Function Relationships In Human Salivary Alpha-
Amylase: Role Of Aromatic Residues
Length = 496
Score = 31.2 bits (69), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 213 GRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMS 272
G +S G +F + P +G ++ G GDI+ M+ + +++ LD++
Sbjct: 110 GTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENMNDATQVRDCRLSGLLDLA 169
Query: 273 -GAEYVRKEI 281
G +YVR +I
Sbjct: 170 LGKDYVRSKI 179
>pdb|2C7G|A Chain A, Fpra From Mycobacterium Tuberculosis: His57gln Mutant
Length = 456
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 7/38 (18%)
Query: 71 LAAASAQADRMTVLTGR-------TTRVIGWYHSHPHI 101
+ A AQ+DRM + G +GWY++HPH
Sbjct: 101 IYAVGAQSDRMLNIPGEDLPGSIAAVDFVGWYNAHPHF 138
>pdb|1LQT|A Chain A, A Covalent Modification Of Nadp+ Revealed By The Atomic
Resolution Structure Of Fpra, A Mycobacterium
Tuberculosis Oxidoreductase
pdb|1LQT|B Chain B, A Covalent Modification Of Nadp+ Revealed By The Atomic
Resolution Structure Of Fpra, A Mycobacterium
Tuberculosis Oxidoreductase
pdb|1LQU|A Chain A, Mycobacterium Tuberculosis Fpra In Complex With Nadph
pdb|1LQU|B Chain B, Mycobacterium Tuberculosis Fpra In Complex With Nadph
Length = 456
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 7/38 (18%)
Query: 71 LAAASAQADRMTVLTGR-------TTRVIGWYHSHPHI 101
+ A AQ+DRM + G +GWY++HPH
Sbjct: 101 IYAVGAQSDRMLNIPGEDLPGSIAAVDFVGWYNAHPHF 138
>pdb|3BK7|A Chain A, Structure Of The Complete Abce1RNAASE-L Inhibitor Protein
From Pyrococcus Abysii
Length = 607
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 28/120 (23%), Positives = 55/120 (45%), Gaps = 17/120 (14%)
Query: 233 ARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLL 292
++ N+ +L +G ID D R+ D+SG E R I +L + +
Sbjct: 444 SKLNSNFYKTELLKPLGIIDLYD----------RNVEDLSGGELQRVAIAATLLRDADIY 493
Query: 293 KLDSPLTSFTDLQRVLYEEERAAYNQAIMQNMSNCLQFYSVMEKCIPLLTFITHQLIRLQ 352
LD P +++ D+ E+R A ++AI M + V+E + ++ +++ +LI +
Sbjct: 494 LLDEP-SAYLDV------EQRLAVSRAIRHLMEKNEKTALVVEHDVLMIDYVSDRLIVFE 546
>pdb|3J15|B Chain B, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 593
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 28/120 (23%), Positives = 55/120 (45%), Gaps = 17/120 (14%)
Query: 233 ARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLL 292
++ N+ +L +G ID D R+ D+SG E R I +L + +
Sbjct: 430 SKLNSNFYKTELLKPLGIIDLYD----------RNVEDLSGGELQRVAIAATLLRDADIY 479
Query: 293 KLDSPLTSFTDLQRVLYEEERAAYNQAIMQNMSNCLQFYSVMEKCIPLLTFITHQLIRLQ 352
LD P +++ D+ E+R A ++AI M + V+E + ++ +++ +LI +
Sbjct: 480 LLDEP-SAYLDV------EQRLAVSRAIRHLMEKNEKTALVVEHDVLMIDYVSDRLIVFE 532
>pdb|1RE6|A Chain A, Localisation Of Dynein Light Chains 1 And 2 And Their Pro-
Apoptotic Ligands
pdb|1RE6|B Chain B, Localisation Of Dynein Light Chains 1 And 2 And Their Pro-
Apoptotic Ligands
Length = 94
Score = 29.6 bits (65), Expect = 2.5, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 8/55 (14%)
Query: 242 GDLSNAIGDIDPMDMSESMQE--------AMHRSNLDMSGAEYVRKEIPLHVLPT 288
G +S+ I DMSE MQ+ AM + N++ A Y++KE PT
Sbjct: 4 GSMSDRKAVIKNADMSEDMQQDAVDCATQAMEKYNIEKDIAAYIKKEFDKKYNPT 58
>pdb|3DHP|A Chain A, Probing The Role Of Aromatic Residues At The Secondary
Saccharide Binding Sites Of Human Salivary Alpha-Amylase
In Substrate Hydrolysis And Bacterial Binding
Length = 496
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 213 GRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMS 272
G +S G +F + P +G ++ G GDI+ + + +++ LD++
Sbjct: 110 GTSSTCGSYFNPGSRDFPAVPYSGADFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLA 169
Query: 273 -GAEYVRKEI 281
G +YVR +I
Sbjct: 170 LGKDYVRSKI 179
>pdb|1JXK|A Chain A, Role Of Ethe Mobile Loop In The Mehanism Of Human Salivary
Amylase
pdb|1MFU|A Chain A, Probing The Role Of A Mobile Loop In Human Salivary
Amylase: Structural Studies On The Loop-Deleted Mutant
Length = 491
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 213 GRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMS 272
G +S G +F + P +G ++ G GDI+ + + +++ LD++
Sbjct: 110 GTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLA 169
Query: 273 -GAEYVRKEI 281
G +YVR +I
Sbjct: 170 LGKDYVRSKI 179
>pdb|1C8Q|A Chain A, Structure Solution And Refinement Of The Recombinant Human
Salivary Amylase
pdb|1MFV|A Chain A, Probing The Role Of A Mobile Loop In Human Slaivary
Amylase: Structural Studies On The Loop-Deleted Enzyme
pdb|1XV8|A Chain A, Crystal Structure Of Human Salivary Alpha-Amylase Dimer
pdb|1XV8|B Chain B, Crystal Structure Of Human Salivary Alpha-Amylase Dimer
pdb|1SMD|A Chain A, Human Salivary Amylase
Length = 496
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 213 GRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMS 272
G +S G +F + P +G ++ G GDI+ + + +++ LD++
Sbjct: 110 GTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLA 169
Query: 273 -GAEYVRKEI 281
G +YVR +I
Sbjct: 170 LGKDYVRSKI 179
>pdb|1Q4N|X Chain X, Structural Studies Of Phe256trp Of Human Salivary Alpha-
Amylase: Implications For The Role Of A Conserved Water
Molecule And Its Associated Chain In Enzyme Activity
Length = 496
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 213 GRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMS 272
G +S G +F + P +G ++ G GDI+ + + +++ LD++
Sbjct: 110 GTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLA 169
Query: 273 -GAEYVRKEI 281
G +YVR +I
Sbjct: 170 LGKDYVRSKI 179
>pdb|1JXJ|A Chain A, Role Of Mobile Loop In The Mechanism Of Human Salivary
Amylase
Length = 496
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 213 GRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMS 272
G +S G +F + P +G ++ G GDI+ + + +++ LD++
Sbjct: 110 GTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLA 169
Query: 273 -GAEYVRKEI 281
G +YVR +I
Sbjct: 170 LGKDYVRSKI 179
>pdb|1NM9|A Chain A, Crystal Structure Of Recombinant Human Salivary Amylase
Mutant W58a
Length = 496
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 213 GRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMS 272
G +S G +F + P +G ++ G GDI+ + + +++ LD++
Sbjct: 110 GTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLA 169
Query: 273 -GAEYVRKEI 281
G +YVR +I
Sbjct: 170 LGKDYVRSKI 179
>pdb|3BLK|A Chain A, Role Of Aromatic Residues In Starch Binding
Length = 496
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 213 GRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMS 272
G +S G +F + P +G ++ G GDI+ + + +++ LD++
Sbjct: 110 GTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLA 169
Query: 273 -GAEYVRKEI 281
G +YVR +I
Sbjct: 170 LGKDYVRSKI 179
>pdb|3BLP|X Chain X, Role Of Aromatic Residues In Human Salivary Alpha-Amylase
Length = 496
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 213 GRTSELGGFFANVDANHPERARTGGNYQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMS 272
G +S G +F + P +G ++ G GDI+ + + +++ LD++
Sbjct: 110 GTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLA 169
Query: 273 -GAEYVRKEI 281
G +YVR +I
Sbjct: 170 LGKDYVRSKI 179
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.131 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,804,947
Number of Sequences: 62578
Number of extensions: 382131
Number of successful extensions: 783
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 775
Number of HSP's gapped (non-prelim): 22
length of query: 355
length of database: 14,973,337
effective HSP length: 100
effective length of query: 255
effective length of database: 8,715,537
effective search space: 2222461935
effective search space used: 2222461935
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: 52 (24.6 bits)