(c) 1992-2000 Regents of the University of California, Santa Cruz
Sequence Alignment and Modeling Software System
http://www.cse.ucsc.edu/research/compbio/sam.html
Citations (SAM, SAM-T99, HMMs)
- R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
- K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting remote protein homologies, Bioinformatics 14(10):846-856, 1998.
- A. Krogh et al., Hidden Markov models in computational biology: Applications to protein modeling, JMB 235:1501-1531, Feb 1994.
Sequence numbers correspond to the following labels:
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- T0498 L1c, E coli, 56 residues
-
- gi|5542539|pdb|3GB1|A_1:56 Chain A, Structures Of B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|157831155|pdb|1GB1|A Chain A, A Novel, Highly Stable Fold Of The Immunoglobulin Binding Domain Of Streptococcal Protein G [Taxonomy]
- gi|157833473|pdb|1PGA|A Chain A, Two Crystal Structures Of The B1 Immunoglobulin-Binding Domain Of Streptococcal Protein G And Comparison With Nmr [Taxonomy]
- gi|157833474|pdb|1PGB|A Chain A, Two Crystal Structures Of The B1 Immunoglobulin-Binding Domain Of Streptoccocal Protein G And Comparison With Nmr [Taxonomy]
- gi|157835028|pdb|2GB1|A Chain A, A Novel, Highly Stable Fold Of The Immunoglobulin Binding Domain Of Streptococcal Protein G [Taxonomy]
-
- gi|14278227|pdb|1IBX|B_1:56 Chain B, Nmr Structure Of Dff40 And Dff45 N-Terminal Domain Complex
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- gi|157883859|pdb|2I2Y|A_1:56 Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc [Taxonomy]
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-
-
- gi|99032573|pdb|2GI9|A_1:56 Chain A, Backbone Conformational Constraints In A Microcrystalline U- 15n-Labeled Protein By 3d Dipolar-Shift Solid-State Nmr Spectroscopy [Taxonomy]
- gi|161760905|pdb|2JU6|X Chain X, Solid-State Protein Structure Determination With Proton- Detected Triple Resonance 3d Magic-Angle Spinning Nmr Spectroscopy [Taxonomy]
- gi|163931020|pdb|2QMT|A Chain A, Crystal Polymorphism Of Protein Gb1 Examined By Solid-State Nmr And X-Ray Diffraction [Taxonomy]
- gi|183448054|pdb|2JSV|X Chain X, Dipole Tensor-Based Refinement For Atomic-Resolution Structure Determination Of A Nanocrystalline Protein By Solid-State Nmr Spectroscopy [Taxonomy]
-
-
-
- gi|34810871|pdb|1P7E|A_1:56 Chain A, Gb3 Solution Structure Obtained By Refinement Of X-Ray Structure With Dipolar Couplings [Taxonomy]
- gi|34810872|pdb|1P7F|A Chain A, Gb3 Solution Structure Obtained By Refinement Of X-Ray Structure With Dipolar Couplings [Taxonomy]
- gi|126031555|pdb|2OED|A Chain A, Gb3 Solution Structure Obtained By Refinement Of X-Ray Structure With Dipolar Couplings [Taxonomy]
-
- gi|158428903|pdb|2J52|A_1:56 Chain A, Solution Structure Of Gb1 Domain Protein G And Low And High Pressure. [Taxonomy]
- gi|158428904|pdb|2J53|A Chain A, Solution Structure Of Gb1 Domain Protein G And Low And High Pressure [Taxonomy]
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- gi|157835189|pdb|2IGG|A_7:61 Chain A, Determination Of The Solution Structures Of Domains Ii And Iii Of Protein G From Streptococcus By 1h Nmr [Taxonomy]
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-
-
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- gi|7245924|pdb|1QKZ|A_7:61 Chain A, Fab Fragment (Mn14c11.6) In Complex With A Peptide Antigen Derived From Neisseria Meningitidis P1.7 Serosubtype Antigen And Domain Ii From Streptococcal Protein G [Taxonomy]
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- gi|71041692|pdb|1UWX|A_6:60 Chain A, P1.2 Serosubtype Antigen Derived From N. Meningitidis Pora In Complex With Fab Fragment [Taxonomy]
- gi|71041693|pdb|1UWX|B Chain B, P1.2 Serosubtype Antigen Derived From N. Meningitidis Pora In Complex With Fab Fragment [Taxonomy]
-
- gi|1065200|pdb|1FCC|C_2:56 Chain C, Crystal Structure Of The C2 Fragment Of Streptococcal Protein G In Complex With The Fc Domain Of Human Igg [Taxonomy]
- gi|157875391|pdb|1FCC|D Chain D, Crystal Structure Of The C2 Fragment Of Streptococcal Protein G In Complex With The Fc Domain Of Human Igg [Taxonomy]
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- gi|164519462|pdb|2ONQ|A_1:56 Chain A, Gbeta1 Stabilization By In Vitro Evolution And Computational Design [Taxonomy]
-
- gi|15988267|pdb|1FD6|A_3:57 Chain A, Delta0: A Computationally Designed Core Variant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
-
- gi|24987790|pdb|1MPE|A_1:56 Chain A, Ensemble Of 20 Structures Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987791|pdb|1MPE|B Chain B, Ensemble Of 20 Structures Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987792|pdb|1MPE|C Chain C, Ensemble Of 20 Structures Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987793|pdb|1MPE|D Chain D, Ensemble Of 20 Structures Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987819|pdb|1MVK|A Chain A, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987820|pdb|1MVK|B Chain B, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987821|pdb|1MVK|C Chain C, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987822|pdb|1MVK|D Chain D, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987823|pdb|1MVK|E Chain E, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987824|pdb|1MVK|F Chain F, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987825|pdb|1MVK|G Chain G, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987826|pdb|1MVK|H Chain H, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987827|pdb|1MVK|I Chain I, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987828|pdb|1MVK|J Chain J, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987829|pdb|1MVK|K Chain K, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|24987830|pdb|1MVK|L Chain L, X-Ray Structure Of The Tetrameric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
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- gi|157833481|pdb|1PGX|A_15:69 Chain A, The 1.66 Angstroms X-Ray Structure Of The B2 Immunoglobulin- Binding Domain Of Streptococcal Protein G And Comparison To The Nmr Structure Of The B1 Domain [Taxonomy]
-
-
- gi|161761023|pdb|2ON8|A_1:56 Chain A, Gbeta1 Stabilization By In Vitro Evolution And Computational Design [Taxonomy]
-
- gi|109157407|pdb|2CWB|A_8:62 Chain A, Solution Structure Of The Ubiquitin-Associated Domain Of Human Bmsc-Ubp And Its Complex With Ubiquitin
- gi|110591203|pdb|2DEN|A Chain A, Solution Structure Of The Ubiquitin-Associated Domain Of Human Bmsc-Ubp And Its Complex With Ubiquitin
-
-
- gi|157835190|pdb|2IGH|A_7:61 Chain A, Determination Of The Solution Structures Of Domains Ii And Iii Of Protein G From Streptococcus By 1h Nmr [Taxonomy]
-
- gi|38492880|pdb|1Q10|A_1:56 Chain A, Ensemble Of 40 Structures Of The Dimeric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
- gi|38492881|pdb|1Q10|B Chain B, Ensemble Of 40 Structures Of The Dimeric Mutant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
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-
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- gi|1064973|pdb|1IGC|A_7:61 Chain A, Igg1 Fab Fragment (Mopc21) Complex With Domain Iii Of Protein G From Streptococcus [Taxonomy]
- gi|157831452|pdb|1IGD|A Chain A, The Third Igg-Binding Domain From Streptococcal Protein G: An Analysis By X-Ray Crystallography Of The Structure Alone And In A Complex With Fab [Taxonomy]
- gi|157835188|pdb|2IGD|A Chain A, Anisotropic Structure Of Protein G Igg-Binding Domain Iii At 1.1 Angstrom Resolution [Taxonomy]
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-
-
- gi|119390478|pdb|2NMQ|A_2:55 Chain A, Simultaneous Determination Of Protein Structure And Dynamics Using Rdcs [Taxonomy]
-
-
- gi|157831156|pdb|1GB4|A_3:57 Chain A, Hyperthermophilic Variant Of The B1 Domain From Streptococcal Protein G, Nmr, 47 Structures [Taxonomy]
-
- gi|15988266|pdb|1FCL|A_2:56 Chain A, Delta1.5: A Computationally Designed Core Variant Of The B1 Domain Of Streptococcal Protein G [Taxonomy]
-
- gi|21465426|pdb|1EM7|A_2:56 Chain A, Helix Variant Of The B1 Domain From Streptococcal Protein G [Taxonomy]
-
- gi|149243209|pdb|2PLP|A_2:53 Chain A, Ultra High Resolution Backbone Conformation Of Protein Gb1 From Residual Dipolar Couplings Alone [Taxonomy]
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- gi|24159073|pdb|1MI0|A_11:65 Chain A, Crystal Structure Of The Redesigned Protein G Variant Nug2 [Taxonomy]
- gi|24159074|pdb|1MI0|B Chain B, Crystal Structure Of The Redesigned Protein G Variant Nug2 [Taxonomy]
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- gi|24159072|pdb|1MHX|A_11:65 Chain A, Crystal Structures Of The Redesigned Protein G Variant Nug1 [Taxonomy]
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10 20 30 40 50
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1 TTYKLILNLKQAKEEAIKELVDAGTAEKYIKLIANAKTVEGVWTLKDEIKTFTVTE
2 MTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
3 MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
4 MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
5 MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
6 MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
7 MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
8 MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYFNDNGVDGEWTYDDATKTFTVTE
9 MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTYTVTE
10 MQYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE
11 MTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDAATKTFTVTE
12 -TYKLVINGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
13 -TYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
14 -TYKLVINGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
15 -TYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
16 -TYKLVINGKTLKGETTTKAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
17 -TYKLVINGKTLKGETTTKAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
18 -TYKLVINGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
19 MQFKLIINGKTLKGEITIEAVDAAEAEKFFKQYANDNGIDGEWTYDDATKTFTVTE
20 -TFKLIINGKTLKGETTTEAVDAATAEKVFKQYANDNGIDGEWTYDDATKTFTVTE
21 MQYKVILNGKTLKGETTTEAVDAATFEKVVKQFFNDNGVDGEWTYDDATKTFTVTE
22 -TYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE
23 -TYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE
24 MQFKLIINGKTLKGEITLEAVDAAEAEKKFKQYANDNGIDGEWTYDDATKTFTVTE
25 -QYKLALNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
26 -TYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE
27 -TYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE
28 MQYKVILNGKTLKGETTTEAVDAATAEKVVKQFFNDNGVDGEWTYDDATKTFTVTE
29 -TYKLVINGKTLKGETTTKAVDAETAEKAFKQYANENGVDGVWTYDDATKTFTVTE
30 -TYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE
31 -TYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE
32 -TYKLVINGKTLKGETTTKAVDAETAEKAFKQYANENGVDGVWTYDDATKTFTVTE
33 -TYKLVINGKTLKGETTTKTVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE
34 --YKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE
35 -TYKLVINGKTLKGETTTKAVDVETAEKAFKQYANENGVDGVWTYDDATKTFTVTE
36 -TFKLIINGKTLKGEITIEAVDAAEAEKIFKQYANDNGIDGEWTYDDATKTFTVTE
37 -TFKLIINGKTLKGETTTEAVDAATAEKVLKQYINDNGIDGEWTYDDATKTWTVTE
38 -TYKLILNGKTLKGETTTEAVDAETAERVFKEYAKKNGVDGEWTYDDATKTFTVTE
39 --YKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTV--
40 -TYKLVIVLNGTTFTYTTEAVDAATAEKVFKQYANDNGVDGEWTYADATKTFTVTE
41 -TYKLFIVIGDRVVVVTTEAVDAATAEKVFKQYANDNGVDGEWTYDDAAKTFTVTE
42 -TYRLVIKGVTFSGETATKAVDAATAEQAFRQYANDNGVTGEWAYDAATKTFTVTE
43 -TYRLVIKGVTFSGETATKAVDAATAEQTFRQYANDNGITGEWAYDTATKTFTVTE
44 ------------KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
45 -SYKLVIKGATFSGETATKAVDAAVAEQTFRDYANKNGVDGVWAYDAATKTFTVTE
46 -SYKLVIKGATFSGETATKAVDAAVAEQTFRDYANKNGVDGVWAYDAATKTFTVTE
47 --YLVVNKGQNAFYETLTKAVDAETARNAFIQSLKDDGVQGVWTYDDATKTFTV--
48 -TYKLILNGKTLKGETTTEAVDAATARS----------------------------
49 -TYKLILNGKTLKGETTTEAVDAATARS----------------------------