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= 039262
(885 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KJ4|A Chain A, Structure Of Rat Nogo Receptor Bound To 1d9 Antagonist
Antibody
pdb|3KJ4|D Chain D, Structure Of Rat Nogo Receptor Bound To 1d9 Antagonist
Antibody
Length = 286
Score = 37.7 bits (86), Expect = 0.027, Method: Composition-based stats.
Identities = 41/144 (28%), Positives = 63/144 (43%), Gaps = 11/144 (7%)
Query: 502 GARLSEAPDVRKWEKVRRLSLMENQIDNLSGVPTCPYL-LTLF----LNNNKQLLIMDRG 556
G R+S P ++ R L+++ + L+G+ + LTL L++N QL ++D
Sbjct: 40 GNRISYVP-AASFQSCRNLTILWLHSNALAGIDAAAFTGLTLLEQLDLSDNAQLRVVDPT 98
Query: 557 FFQCMPRLKVLNLSGAKQLFYFPLVISKLVSLQHLDLSDTNVAVLPKE-LNALVNLKCLN 615
F+ + L L+L P + L +LQ+L L D N+ LP L NL L
Sbjct: 99 TFRGLGHLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNNLQALPDNTFRDLGNLTHLF 158
Query: 616 LENAWMLTVIPRRLISSFSSLHVL 639
L IP +F LH L
Sbjct: 159 LHG----NRIPSVPEHAFRGLHSL 178
>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
Length = 591
Score = 37.7 bits (86), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 45/185 (24%), Positives = 79/185 (42%), Gaps = 34/185 (18%)
Query: 210 VIWVVVSKD------LRLENI------QEAIGEKIGLVNDTWKNRRTEQKALDIFRNLKE 257
V WV V K ++L+N+ E+ +++ L + K+R L I K
Sbjct: 182 VHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDR------LRILMLRKH 235
Query: 258 KKFVLLLDDIWERVDLSKVGIPLPGRLNNKSKVVFTTRSEEVC-GLMEAHKKFKVEC-LS 315
+ +L+LDD+W+ L +++ +++ TTR + V +M VE L
Sbjct: 236 PRSLLILDDVWDSWVLKA--------FDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLG 287
Query: 316 HNDAWELFRQKVGGETLNCHPDILELAETVAKECGGLPLALITIGRAMSCKRMPEEWSYA 375
E+ V + D+ E A ++ KEC G PL + IG + + P W Y
Sbjct: 288 KEKGLEILSLFVNMKK----ADLPEQAHSIIKECKGSPLVVSLIGALL--RDFPNRWEYY 341
Query: 376 IQVLR 380
++ L+
Sbjct: 342 LKQLQ 346
>pdb|3G3A|A Chain A, Structure Of A Lamprey Variable Lymphocyte Receptor In
Complex With A Protein Antigen
pdb|3G3A|C Chain C, Structure Of A Lamprey Variable Lymphocyte Receptor In
Complex With A Protein Antigen
pdb|3G3A|E Chain E, Structure Of A Lamprey Variable Lymphocyte Receptor In
Complex With A Protein Antigen
pdb|3G3A|G Chain G, Structure Of A Lamprey Variable Lymphocyte Receptor In
Complex With A Protein Antigen
Length = 178
Score = 37.7 bits (86), Expect = 0.032, Method: Composition-based stats.
Identities = 36/118 (30%), Positives = 53/118 (44%), Gaps = 11/118 (9%)
Query: 531 SGVPTCPYLLTLFLNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYFPL-VISKLVSLQ 589
+G+PT +L L+ N Q+ ++ G F + +L L+L QL P V KL L
Sbjct: 34 TGIPTTTQVLYLYDN---QITKLEPGVFDRLTQLTRLDLDN-NQLTVLPAGVFDKLTQLT 89
Query: 590 HLDLSDTNVAVLPKELNALVNLKCLN----LENAWMLTVIPRRLISSFSSLHVLRMFG 643
L L+D + +P+ A NLK L L N W +S + S H +FG
Sbjct: 90 QLSLNDNQLKSIPR--GAFDNLKSLTHIWLLNNPWDCACSDILYLSRWISQHPGLVFG 145
>pdb|3G39|A Chain A, Structure Of A Lamprey Variable Lymphocyte Receptor
Length = 170
Score = 37.4 bits (85), Expect = 0.042, Method: Composition-based stats.
Identities = 36/118 (30%), Positives = 53/118 (44%), Gaps = 11/118 (9%)
Query: 531 SGVPTCPYLLTLFLNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYFPL-VISKLVSLQ 589
+G+PT +L L+ N Q+ ++ G F + +L L+L QL P V KL L
Sbjct: 26 TGIPTTTQVLYLYDN---QITKLEPGVFDRLTQLTRLDLDN-NQLTVLPAGVFDKLTQLT 81
Query: 590 HLDLSDTNVAVLPKELNALVNLKCLN----LENAWMLTVIPRRLISSFSSLHVLRMFG 643
L L+D + +P+ A NLK L L N W +S + S H +FG
Sbjct: 82 QLSLNDNQLKSIPR--GAFDNLKSLTHIWLLNNPWDCACSDILYLSRWISQHPGLVFG 137
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 37.0 bits (84), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 45/185 (24%), Positives = 79/185 (42%), Gaps = 34/185 (18%)
Query: 210 VIWVVVSKD------LRLENI------QEAIGEKIGLVNDTWKNRRTEQKALDIFRNLKE 257
V WV V K ++L+N+ E+ +++ L + K+R L I K
Sbjct: 188 VHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDR------LRILMLRKH 241
Query: 258 KKFVLLLDDIWERVDLSKVGIPLPGRLNNKSKVVFTTRSEEVC-GLMEAHKKFKVEC-LS 315
+ +L+LDD+W+ L +++ +++ TTR + V +M VE L
Sbjct: 242 PRSLLILDDVWDSWVLKA--------FDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLG 293
Query: 316 HNDAWELFRQKVGGETLNCHPDILELAETVAKECGGLPLALITIGRAMSCKRMPEEWSYA 375
E+ V + D+ E A ++ KEC G PL + IG + + P W Y
Sbjct: 294 KEKGLEILSLFVNMKK----ADLPEQAHSIIKECKGSPLVVSLIGALL--RDFPNRWEYY 347
Query: 376 IQVLR 380
++ L+
Sbjct: 348 LKQLQ 352
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 36.2 bits (82), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 43/185 (23%), Positives = 80/185 (43%), Gaps = 34/185 (18%)
Query: 210 VIWVVVSKD------LRLENI------QEAIGEKIGLVNDTWKNRRTEQKALDIFRNLKE 257
V WV + K ++L+N+ +E+ +++ L + K+R L + K
Sbjct: 182 VHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDR------LRVLMLRKH 235
Query: 258 KKFVLLLDDIWERVDLSKVGIPLPGRLNNKSKVVFTTRSEEVC-GLMEAHKKFKVEC-LS 315
+ +L+LDD+W+ L +N+ +++ TTR + V +M VE L
Sbjct: 236 PRSLLILDDVWDPWVLKA--------FDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLG 287
Query: 316 HNDAWELFRQKVGGETLNCHPDILELAETVAKECGGLPLALITIGRAMSCKRMPEEWSYA 375
E+ V + D+ A ++ KEC G PL + IG + + P W+Y
Sbjct: 288 REKGLEILSLFVNMKK----EDLPAEAHSIIKECKGSPLVVSLIGALL--RDFPNRWAYY 341
Query: 376 IQVLR 380
++ L+
Sbjct: 342 LRQLQ 346
>pdb|2WQX|A Chain A, Inlb321_4r: S199r, D200r, G206r, A227r, C242a Mutant Of
The Listeria Monocytogenes Inlb Internalin Domain
pdb|2WQX|B Chain B, Inlb321_4r: S199r, D200r, G206r, A227r, C242a Mutant Of
The Listeria Monocytogenes Inlb Internalin Domain
Length = 289
Score = 35.4 bits (80), Expect = 0.14, Method: Composition-based stats.
Identities = 30/92 (32%), Positives = 47/92 (51%), Gaps = 6/92 (6%)
Query: 525 NQIDNLSGVPTCPYLLTLFLNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYFPLVISK 584
N I +++G+ P L +L+L NNK I D + +L L+L + PL ++
Sbjct: 120 NGISDINGLVHLPQLESLYLGNNK---ITDITVLSRLTKLDTLSLEDNQIRRIVPL--AR 174
Query: 585 LVSLQHLDLSDTNVAVLPKELNALVNLKCLNL 616
L LQ+L LS +++ L + L L NL L L
Sbjct: 175 LTKLQNLYLSKNHISDL-RALRGLKNLDVLEL 205
>pdb|3G3B|A Chain A, Structure Of A Lamprey Variable Lymphocyte Receptor Mutant
In Complex With A Protein Antigen
pdb|3G3B|C Chain C, Structure Of A Lamprey Variable Lymphocyte Receptor Mutant
In Complex With A Protein Antigen
pdb|3G3B|E Chain E, Structure Of A Lamprey Variable Lymphocyte Receptor Mutant
In Complex With A Protein Antigen
pdb|3G3B|G Chain G, Structure Of A Lamprey Variable Lymphocyte Receptor Mutant
In Complex With A Protein Antigen
Length = 170
Score = 35.4 bits (80), Expect = 0.15, Method: Composition-based stats.
Identities = 35/118 (29%), Positives = 52/118 (44%), Gaps = 11/118 (9%)
Query: 531 SGVPTCPYLLTLFLNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYFPL-VISKLVSLQ 589
+G+PT +L L+ N +L + G F + +L L+L QL P V KL L
Sbjct: 26 TGIPTTTQVLYLYDNRITKL---EPGVFDRLTQLTRLDLDN-NQLTVLPAGVFDKLTQLT 81
Query: 590 HLDLSDTNVAVLPKELNALVNLKCLN----LENAWMLTVIPRRLISSFSSLHVLRMFG 643
L L+D + +P+ A NL+ L L N W +S + S H +FG
Sbjct: 82 QLSLNDNQLKSIPR--GAFDNLRSLTHIWLLNNPWDCACSDILYLSRWISQHPWLVFG 137
>pdb|1OZN|A Chain A, 1.5a Crystal Structure Of The Nogo Receptor Ligand Binding
Domain Reveals A Convergent Recognition Scaffold
Mediating Inhibition Of Myelination
Length = 285
Score = 34.3 bits (77), Expect = 0.35, Method: Composition-based stats.
Identities = 39/144 (27%), Positives = 62/144 (43%), Gaps = 11/144 (7%)
Query: 502 GARLSEAPDVRKWEKVRRLSLMENQIDNLSGVPTCPY-----LLTLFLNNNKQLLIMDRG 556
G R+S P + R L+++ + L+ + + L L L++N QL +D
Sbjct: 41 GNRISHVP-AASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRSVDPA 99
Query: 557 FFQCMPRLKVLNLSGAKQLFYFPLVISKLVSLQHLDLSDTNVAVLPKE-LNALVNLKCLN 615
F + RL L+L P + L +LQ+L L D + LP + L NL L
Sbjct: 100 TFHGLGRLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFRDLGNLTHLF 159
Query: 616 LENAWMLTVIPRRLISSFSSLHVL 639
L ++ +P R +F LH L
Sbjct: 160 LHGN-RISSVPER---AFRGLHSL 179
>pdb|1P8T|A Chain A, Crystal Structure Of Nogo-66 Receptor
Length = 285
Score = 34.3 bits (77), Expect = 0.35, Method: Composition-based stats.
Identities = 39/144 (27%), Positives = 62/144 (43%), Gaps = 11/144 (7%)
Query: 502 GARLSEAPDVRKWEKVRRLSLMENQIDNLSGVPTCPY-----LLTLFLNNNKQLLIMDRG 556
G R+S P + R L+++ + L+ + + L L L++N QL +D
Sbjct: 40 GNRISHVP-AASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRSVDPA 98
Query: 557 FFQCMPRLKVLNLSGAKQLFYFPLVISKLVSLQHLDLSDTNVAVLPKE-LNALVNLKCLN 615
F + RL L+L P + L +LQ+L L D + LP + L NL L
Sbjct: 99 TFHGLGRLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFRDLGNLTHLF 158
Query: 616 LENAWMLTVIPRRLISSFSSLHVL 639
L ++ +P R +F LH L
Sbjct: 159 LHGN-RISSVPER---AFRGLHSL 178
>pdb|2Z64|A Chain A, Crystal Structure Of Mouse Tlr4 And Mouse Md-2 Complex
Length = 599
Score = 33.9 bits (76), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 47/161 (29%), Positives = 70/161 (43%), Gaps = 17/161 (10%)
Query: 501 AGARLSEAPDVRKWEKVRRLSLMENQIDNLSGVPTC--PYLLTLFLNNNKQLLIMDRGFF 558
AG + DV K K + LS++ Q L PT P+L +L L NK + +
Sbjct: 288 AGVSIKYLEDVPKHFKWQSLSIIRCQ---LKQFPTLDLPFLKSLTLTMNKGSISFKK--- 341
Query: 559 QCMPRLKVLNLSGAKQLFYFPLVISKLV--SLQHLDLSDTNVAVLPKELNALVNLKCLNL 616
+P L L+LS F S L SL+HLDLS ++ L L+ L+
Sbjct: 342 VALPSLSYLDLSRNALSFSGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEELQHLDF 401
Query: 617 ENAWMLTVIPRRLISSFSSLHVLRMFGIGYSSS----DGII 653
+++ + V S+F SL L I Y+++ DGI
Sbjct: 402 QHSTLKRVTE---FSAFLSLEKLLYLDISYTNTKIDFDGIF 439
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 33.9 bits (76), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 42/185 (22%), Positives = 79/185 (42%), Gaps = 34/185 (18%)
Query: 210 VIWVVVSKD------LRLENI------QEAIGEKIGLVNDTWKNRRTEQKALDIFRNLKE 257
V WV + K ++L+N+ +E+ +++ L + K+R L + K
Sbjct: 189 VHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDR------LRVLMLRKH 242
Query: 258 KKFVLLLDDIWERVDLSKVGIPLPGRLNNKSKVVFTTRSEEVC-GLMEAHKKFKVEC-LS 315
+ +L+LDD+W+ L +N+ +++ TT + V +M VE L
Sbjct: 243 PRSLLILDDVWDPWVLKA--------FDNQCQILLTTSDKSVTDSVMGPKHVVPVESGLG 294
Query: 316 HNDAWELFRQKVGGETLNCHPDILELAETVAKECGGLPLALITIGRAMSCKRMPEEWSYA 375
E+ V + D+ A ++ KEC G PL + IG + + P W+Y
Sbjct: 295 REKGLEILSLFVNMKK----EDLPAEAHSIIKECKGSPLVVSLIGALL--RDFPNRWAYY 348
Query: 376 IQVLR 380
++ L+
Sbjct: 349 LRQLQ 353
>pdb|3VQ1|A Chain A, Crystal Structure Of Mouse Tlr4MD-2LIPID IVA COMPLEX
pdb|3VQ1|B Chain B, Crystal Structure Of Mouse Tlr4MD-2LIPID IVA COMPLEX
pdb|3VQ2|A Chain A, Crystal Structure Of Mouse Tlr4MD-2LPS COMPLEX
pdb|3VQ2|B Chain B, Crystal Structure Of Mouse Tlr4MD-2LPS COMPLEX
Length = 606
Score = 33.9 bits (76), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 47/161 (29%), Positives = 70/161 (43%), Gaps = 17/161 (10%)
Query: 501 AGARLSEAPDVRKWEKVRRLSLMENQIDNLSGVPTC--PYLLTLFLNNNKQLLIMDRGFF 558
AG + DV K K + LS++ Q L PT P+L +L L NK + +
Sbjct: 293 AGVSIKYLEDVPKHFKWQSLSIIRCQ---LKQFPTLDLPFLKSLTLTMNKGSISFKK--- 346
Query: 559 QCMPRLKVLNLSGAKQLFYFPLVISKLV--SLQHLDLSDTNVAVLPKELNALVNLKCLNL 616
+P L L+LS F S L SL+HLDLS ++ L L+ L+
Sbjct: 347 VALPSLSYLDLSRNALSFSGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEELQHLDF 406
Query: 617 ENAWMLTVIPRRLISSFSSLHVLRMFGIGYSSS----DGII 653
+++ + V S+F SL L I Y+++ DGI
Sbjct: 407 QHSTLKRVTE---FSAFLSLEKLLYLDISYTNTKIDFDGIF 444
>pdb|1H6U|A Chain A, Internalin H: Crystal Structure Of Fused N-Terminal
Domains
Length = 308
Score = 33.5 bits (75), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 40/135 (29%), Positives = 62/135 (45%), Gaps = 21/135 (15%)
Query: 684 LSSHRLRSCT-----QALYLKDFKSSKSLDVSALADLKHLKRL-----QIVECYELEEL- 732
LS + L++ + Q++ D S++ DV+ LA L +L+ L QI L L
Sbjct: 92 LSGNPLKNVSAIAGLQSIKTLDLTSTQITDVTPLAGLSNLQVLYLDLNQITNISPLAGLT 151
Query: 733 KMDYTGV----VQNRSQPFVFHSLRKIQIDDCNKLKDLTFLAFAPNLKSIEVNSCHGIQE 788
+ Y + V + + L ++ DD NK+ D++ LA PNL IEV H
Sbjct: 152 NLQYLSIGNAQVSDLTPLANLSKLTTLKADD-NKISDISPLASLPNL--IEV---HLKNN 205
Query: 789 IVSDVPEVMRNLNLF 803
+SDV + NLF
Sbjct: 206 QISDVSPLANTSNLF 220
>pdb|1H6T|A Chain A, Internalin B: Crystal Structure Of Fused N-Terminal
Domains
Length = 291
Score = 33.1 bits (74), Expect = 0.65, Method: Composition-based stats.
Identities = 30/92 (32%), Positives = 46/92 (50%), Gaps = 6/92 (6%)
Query: 525 NQIDNLSGVPTCPYLLTLFLNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYFPLVISK 584
N I +++G+ P L +L+L NNK I D + +L L+L + PL +
Sbjct: 122 NGISDINGLVHLPQLESLYLGNNK---ITDITVLSRLTKLDTLSLEDNQISDIVPL--AG 176
Query: 585 LVSLQHLDLSDTNVAVLPKELNALVNLKCLNL 616
L LQ+L LS +++ L + L L NL L L
Sbjct: 177 LTKLQNLYLSKNHISDL-RALAGLKNLDVLEL 207
>pdb|2UZX|A Chain A, Structure Of The Human Receptor Tyrosine Kinase Met In
Complex With The Listeria Monocytogenes Invasion Protein
Inlb: Crystal Form I
pdb|2UZX|C Chain C, Structure Of The Human Receptor Tyrosine Kinase Met In
Complex With The Listeria Monocytogenes Invasion Protein
Inlb: Crystal Form I
pdb|2UZY|A Chain A, Structure Of The Human Receptor Tyrosine Kinase Met In
Complex With The Listeria Monocytogenes Invasion Protein
Inlb: Low Resolution, Crystal Form Ii
pdb|2UZY|C Chain C, Structure Of The Human Receptor Tyrosine Kinase Met In
Complex With The Listeria Monocytogenes Invasion Protein
Inlb: Low Resolution, Crystal Form Ii
pdb|2WQU|A Chain A, Internalin Domain Of Listeria Monocytogenes Inlb:
Triclinic Crystal Form
pdb|2WQU|B Chain B, Internalin Domain Of Listeria Monocytogenes Inlb:
Triclinic Crystal Form
pdb|2WQU|C Chain C, Internalin Domain Of Listeria Monocytogenes Inlb:
Triclinic Crystal Form
pdb|2WQU|D Chain D, Internalin Domain Of Listeria Monocytogenes Inlb:
Triclinic Crystal Form
pdb|2WQU|E Chain E, Internalin Domain Of Listeria Monocytogenes Inlb:
Triclinic Crystal Form
pdb|2WQU|F Chain F, Internalin Domain Of Listeria Monocytogenes Inlb:
Triclinic Crystal Form
pdb|2WQV|A Chain A, Internalin Domain Of Listeria Monocytogenes Inlb:
Rhombohedral Crystal Form
pdb|2WQV|B Chain B, Internalin Domain Of Listeria Monocytogenes Inlb:
Rhombohedral Crystal Form
Length = 289
Score = 33.1 bits (74), Expect = 0.67, Method: Composition-based stats.
Identities = 30/92 (32%), Positives = 46/92 (50%), Gaps = 6/92 (6%)
Query: 525 NQIDNLSGVPTCPYLLTLFLNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYFPLVISK 584
N I +++G+ P L +L+L NNK I D + +L L+L + PL +
Sbjct: 120 NGISDINGLVHLPQLESLYLGNNK---ITDITVLSRLTKLDTLSLEDNQISDIVPL--AG 174
Query: 585 LVSLQHLDLSDTNVAVLPKELNALVNLKCLNL 616
L LQ+L LS +++ L + L L NL L L
Sbjct: 175 LTKLQNLYLSKNHISDL-RALAGLKNLDVLEL 205
>pdb|1M9S|A Chain A, Crystal Structure Of Internalin B (Inlb), A Listeria
Monocytogenes Virulence Protein Containing Sh3-Like
Domains
Length = 605
Score = 33.1 bits (74), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 47/93 (50%), Gaps = 9/93 (9%)
Query: 524 ENQIDNLSGVPTCPYLLTLFLNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYFPLVIS 583
N I +++G+ P L +L+L NNK I D + +L L+L + PL +
Sbjct: 118 HNGISDINGLVHLPQLESLYLGNNK---ITDITVLSRLTKLDTLSLEDNQISDIVPL--A 172
Query: 584 KLVSLQHLDLSDTNVAVLPKELNALVNLKCLNL 616
L LQ+L LS +++ +L AL LK L++
Sbjct: 173 GLTKLQNLYLSKNHIS----DLRALAGLKNLDV 201
>pdb|2R9U|A Chain A, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
pdb|2R9U|B Chain B, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
pdb|2R9U|C Chain C, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
pdb|2R9U|D Chain D, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
Length = 174
Score = 32.7 bits (73), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 531 SGVPTCPYLLTLFLNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYFPLVISKLVSLQH 590
+G+PT L L NN Q+ ++ G F + L+ L + K V KL L
Sbjct: 29 AGIPTDKQRLWL---NNNQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQ 85
Query: 591 LDLSDTNVAVLPKELNALVNLKCL 614
LDL+D ++ +P+ A NLK L
Sbjct: 86 LDLNDNHLKSIPR--GAFDNLKSL 107
>pdb|4FHO|A Chain A, Crystal Structure Of An Internalin C2 (Inlc2) From
Listeria Monocytogenes Str. 4b F2365 At 1.90 A
Resolution
pdb|4FHO|B Chain B, Crystal Structure Of An Internalin C2 (Inlc2) From
Listeria Monocytogenes Str. 4b F2365 At 1.90 A
Resolution
Length = 231
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 37/120 (30%), Positives = 54/120 (45%), Gaps = 16/120 (13%)
Query: 694 QALYLKDFKSSKSLDVSALADLKHLKRL-----QIVECYELEEL-KMDYTGVVQNRSQPF 747
Q++ D S++ DV+ LA L +L+ L QI L L + Y + N+
Sbjct: 113 QSIKTLDLTSTQITDVTPLAGLSNLQVLYLDLNQITNISPLAGLTNLQYLSIGNNQVNDL 172
Query: 748 V----FHSLRKIQIDDCNKLKDLTFLAFAPNLKSIEVNSCHGIQEIVSDVPEVMRNLNLF 803
L ++ DD NK+ D++ LA PNL IEV H +SDV + NLF
Sbjct: 173 TPLANLSKLTTLRADD-NKISDISPLASLPNL--IEV---HLKDNQISDVSPLANLSNLF 226
>pdb|3RFS|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
pdb|3RFS|B Chain B, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 272
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 45/147 (30%), Positives = 66/147 (44%), Gaps = 7/147 (4%)
Query: 497 YLVYAGARLSEAPDVRKWEKVRRLSLMENQIDNL-SGV-PTCPYLLTLFLNNNKQLLIMD 554
YL G +L + +++ + L L NQ+ +L +GV L L L N QL +
Sbjct: 67 YLALGGNKLHDISALKELTNLTYLILTGNQLQSLPNGVFDKLTNLKELVLVEN-QLQSLP 125
Query: 555 RGFFQCMPRLKVLNLSGAKQLFYFPL-VISKLVSLQHLDLSDTNVAVLPKEL-NALVNLK 612
G F + L LNL+ QL P V KL +L LDLS + LP+ + + L LK
Sbjct: 126 DGVFDKLTNLTYLNLA-HNQLQSLPKGVFDKLTNLTELDLSYNQLQSLPEGVFDKLTQLK 184
Query: 613 CLNLENAWMLTVIPRRLISSFSSLHVL 639
L L L +P + +SL +
Sbjct: 185 DLRLYQN-QLKSVPDGVFDRLTSLQYI 210
>pdb|2Y5Q|A Chain A, Listeria Monocytogenes Inlb (Internalin B) Residues 36-392
Length = 362
Score = 31.6 bits (70), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 47/92 (51%), Gaps = 9/92 (9%)
Query: 525 NQIDNLSGVPTCPYLLTLFLNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYFPLVISK 584
N I +++G+ P L +L+L NNK I D + +L L+L + PL +
Sbjct: 122 NGISDINGLVHLPQLESLYLGNNK---ITDITVLSRLTKLDTLSLEDNQISDIVPL--AG 176
Query: 585 LVSLQHLDLSDTNVAVLPKELNALVNLKCLNL 616
L LQ+L LS +++ +L AL LK L++
Sbjct: 177 LTKLQNLYLSKNHIS----DLRALAGLKNLDV 204
>pdb|4H0W|A Chain A, Bismuth Bound Human Serum Transferrin
Length = 679
Score = 31.2 bits (69), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 310 KVECLSHNDAWELFRQKVGGETLNCHPDILELAET---VAKECGGLPLALITIGRAMSCK 366
K+EC+S + + + GE D + L +A +CG +P+ ++ +C+
Sbjct: 365 KIECVSAETTEDCIAKIMNGEA-----DAMSLDGGFVYIAGKCGLVPVLAENYNKSDNCE 419
Query: 367 RMPEEWSYAIQVLRTSSSQF 386
PE +AI V++ S+S
Sbjct: 420 DTPEAGYFAIAVVKKSASDL 439
>pdb|4AY9|X Chain X, Structure Of Follicle-Stimulating Hormone In Complex With
The Entire Ectodomain Of Its Receptor
pdb|4AY9|Y Chain Y, Structure Of Follicle-Stimulating Hormone In Complex With
The Entire Ectodomain Of Its Receptor
pdb|4AY9|Z Chain Z, Structure Of Follicle-Stimulating Hormone In Complex With
The Entire Ectodomain Of Its Receptor
Length = 350
Score = 30.8 bits (68), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 544 LNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYF-PLVISKLVSLQHLDLSDTNVAVLP 602
++ N L +++ F +P+L + + A L Y P L +LQ+L +S+T + LP
Sbjct: 61 ISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQYLLISNTGIKHLP 120
>pdb|3QYT|A Chain A, Diferric Bound Human Serum Transferrin
Length = 679
Score = 30.4 bits (67), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 310 KVECLSHNDAWELFRQKVGGETLNCHPDILELAET---VAKECGGLPLALITIGRAMSCK 366
K+EC+S + + + GE D + L +A +CG +P+ ++ +C+
Sbjct: 365 KIECVSAETTEDCIAKIMNGEA-----DAMSLDGGFVYIAGKCGLVPVLAENYNKSDNCE 419
Query: 367 RMPEEWSYAIQVLRTSSSQF 386
PE +A+ V++ S+S
Sbjct: 420 DTPEAGYFAVAVVKKSASDL 439
>pdb|3V83|A Chain A, The 2.1 Angstrom Crystal Structure Of Diferric Human
Transferrin
pdb|3V83|B Chain B, The 2.1 Angstrom Crystal Structure Of Diferric Human
Transferrin
pdb|3V83|C Chain C, The 2.1 Angstrom Crystal Structure Of Diferric Human
Transferrin
pdb|3V83|D Chain D, The 2.1 Angstrom Crystal Structure Of Diferric Human
Transferrin
pdb|3V83|E Chain E, The 2.1 Angstrom Crystal Structure Of Diferric Human
Transferrin
pdb|3V83|F Chain F, The 2.1 Angstrom Crystal Structure Of Diferric Human
Transferrin
pdb|3V8X|B Chain B, The Crystal Structure Of Transferrin Binding Protein A
(Tbpa) From Neisserial Meningitidis Serogroup B In
Complex With Full Length Human Transferrin
Length = 698
Score = 30.4 bits (67), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 310 KVECLSHNDAWELFRQKVGGETLNCHPDILELAET---VAKECGGLPLALITIGRAMSCK 366
K+EC+S + + + GE D + L +A +CG +P+ ++ +C+
Sbjct: 384 KIECVSAETTEDCIAKIMNGEA-----DAMSLDGGFVYIAGKCGLVPVLAENYNKSDNCE 438
Query: 367 RMPEEWSYAIQVLRTSSSQF 386
PE +A+ V++ S+S
Sbjct: 439 DTPEAGYFAVAVVKKSASDL 458
>pdb|2HAV|A Chain A, Apo-Human Serum Transferrin (Glycosylated)
pdb|2HAV|B Chain B, Apo-Human Serum Transferrin (Glycosylated)
Length = 676
Score = 30.4 bits (67), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 310 KVECLSHNDAWELFRQKVGGETLNCHPDILELAET---VAKECGGLPLALITIGRAMSCK 366
K+EC+S + + + GE D + L +A +CG +P+ ++ +C+
Sbjct: 362 KIECVSAETTEDCIAKIMNGEA-----DAMSLDGGFVYIAGKCGLVPVLAENYNKSDNCE 416
Query: 367 RMPEEWSYAIQVLRTSSSQF 386
PE +A+ V++ S+S
Sbjct: 417 DTPEAGYFAVAVVKKSASDL 436
>pdb|3V89|B Chain B, The Crystal Structure Of Transferrin Binding Protein A
(Tbpa) From Neisseria Meningitidis Serogroup B In
Complex With The C-Lobe Of Human Transferrin
Length = 343
Score = 30.4 bits (67), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 310 KVECLSHNDAWELFRQKVGGETLNCHPDILELAET---VAKECGGLPLALITIGRAMSCK 366
K+EC+S + + + GE D + L +A +CG +P+ ++ +C+
Sbjct: 29 KIECVSAETTEDCIAKIMNGEA-----DAMSLDGGFVYIAGKCGLVPVLAENYNKSDNCE 83
Query: 367 RMPEEWSYAIQVLRTSSSQF 386
PE +A+ V++ S+S
Sbjct: 84 DTPEAGYFAVAVVKKSASDL 103
>pdb|1OTM|A Chain A, Calcium-Binding Mutant Of The Internalin B Lrr Domain
Length = 236
Score = 30.4 bits (67), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 47/93 (50%), Gaps = 9/93 (9%)
Query: 524 ENQIDNLSGVPTCPYLLTLFLNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYFPLVIS 583
N I +++G+ P L +L+L NNK I D + +L L+L + PL +
Sbjct: 139 HNGISDINGLVHLPQLESLYLGNNK---ITDITVLSRLTKLDTLSLEDNQISDIVPL--A 193
Query: 584 KLVSLQHLDLSDTNVAVLPKELNALVNLKCLNL 616
L LQ+L LS +++ +L AL LK L++
Sbjct: 194 GLTKLQNLYLSKNHIS----DLRALAGLKNLDV 222
>pdb|1OTN|A Chain A, Calcium-Binding Mutant Of The Internalin B Lrr Domain
Length = 236
Score = 30.4 bits (67), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 47/93 (50%), Gaps = 9/93 (9%)
Query: 524 ENQIDNLSGVPTCPYLLTLFLNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYFPLVIS 583
N I +++G+ P L +L+L NNK I D + +L L+L + PL +
Sbjct: 139 HNGISDINGLVHLPQLESLYLGNNK---ITDITVLSRLTKLDTLSLEDNQISDIVPL--A 193
Query: 584 KLVSLQHLDLSDTNVAVLPKELNALVNLKCLNL 616
L LQ+L LS +++ +L AL LK L++
Sbjct: 194 GLTKLQNLYLSKNHIS----DLRALAGLKNLDV 222
>pdb|1OTO|A Chain A, Calcium-Binding Mutant Of The Internalin B Lrr Domain
Length = 236
Score = 30.4 bits (67), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 47/93 (50%), Gaps = 9/93 (9%)
Query: 524 ENQIDNLSGVPTCPYLLTLFLNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYFPLVIS 583
N I +++G+ P L +L+L NNK I D + +L L+L + PL +
Sbjct: 139 HNGISDINGLVHLPQLESLYLGNNK---ITDITVLSRLTKLDTLSLEDNQISDIVPL--A 193
Query: 584 KLVSLQHLDLSDTNVAVLPKELNALVNLKCLNL 616
L LQ+L LS +++ +L AL LK L++
Sbjct: 194 GLTKLQNLYLSKNHIS----DLRALAGLKNLDV 222
>pdb|3SKP|A Chain A, The Structure Of Apo-Human Transferrin C-Lobe With Bound
Sulfate Ions
Length = 342
Score = 30.4 bits (67), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 310 KVECLSHNDAWELFRQKVGGETLNCHPDILELAET---VAKECGGLPLALITIGRAMSCK 366
K+EC+S + + + GE D + L +A +CG +P+ ++ +C+
Sbjct: 28 KIECVSAETTEDCIAKIMNGEA-----DAMSLDGGFVYIAGKCGLVPVLAENYNKSDNCE 82
Query: 367 RMPEEWSYAIQVLRTSSSQF 386
PE +A+ V++ S+S
Sbjct: 83 DTPEAGYFAVAVVKKSASDL 102
>pdb|4AW4|A Chain A, Engineered Variant Of Listeria Monocytogenes Inlb
Internalin Domain With An Additional Leucine Rich Repeat
Inserted
pdb|4AW4|B Chain B, Engineered Variant Of Listeria Monocytogenes Inlb
Internalin Domain With An Additional Leucine Rich Repeat
Inserted
pdb|4AW4|C Chain C, Engineered Variant Of Listeria Monocytogenes Inlb
Internalin Domain With An Additional Leucine Rich Repeat
Inserted
Length = 311
Score = 30.4 bits (67), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 47/92 (51%), Gaps = 9/92 (9%)
Query: 525 NQIDNLSGVPTCPYLLTLFLNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYFPLVISK 584
N I +++G+ P L +L+L NNK I D + +L L+L + PL +
Sbjct: 142 NGISDINGLVHLPQLESLYLGNNK---ITDITVLSRLTKLDTLSLEDNQISDIVPL--AG 196
Query: 585 LVSLQHLDLSDTNVAVLPKELNALVNLKCLNL 616
L LQ+L LS +++ +L AL LK L++
Sbjct: 197 LTKLQNLYLSKNHIS----DLRALAGLKNLDV 224
>pdb|1D0B|A Chain A, Internalin B Leucine Rich Repeat Domain
Length = 213
Score = 30.0 bits (66), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 47/92 (51%), Gaps = 9/92 (9%)
Query: 525 NQIDNLSGVPTCPYLLTLFLNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYFPLVISK 584
N I +++G+ P L +L+L NNK I D + +L L+L + PL +
Sbjct: 117 NGISDINGLVHLPQLESLYLGNNK---ITDITVLSRLTKLDTLSLEDNQISDIVPL--AG 171
Query: 585 LVSLQHLDLSDTNVAVLPKELNALVNLKCLNL 616
L LQ+L LS +++ +L AL LK L++
Sbjct: 172 LTKLQNLYLSKNHIS----DLRALAGLKNLDV 199
>pdb|1XWD|C Chain C, Crystal Structure Of Human Follicle Stimulating Hormone
Complexed With Its Receptor
pdb|1XWD|F Chain F, Crystal Structure Of Human Follicle Stimulating Hormone
Complexed With Its Receptor
Length = 252
Score = 30.0 bits (66), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 544 LNNNKQLLIMDRGFFQCMPRLKVLNLSGAKQLFYF-PLVISKLVSLQHLDLSDTNVAVLP 602
++ N L +++ F +P+L + + A L Y P L +LQ+L +S+T + LP
Sbjct: 61 ISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQYLLISNTGIKHLP 120
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
0.321 0.137 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,132,895
Number of Sequences: 62578
Number of extensions: 945844
Number of successful extensions: 2195
Number of sequences better than 100.0: 56
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 42
Number of HSP's that attempted gapping in prelim test: 2121
Number of HSP's gapped (non-prelim): 106
length of query: 885
length of database: 14,973,337
effective HSP length: 107
effective length of query: 778
effective length of database: 8,277,491
effective search space: 6439887998
effective search space used: 6439887998
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)