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= psy16652
(384 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3LAF|A Chain A, Structure Of Dcc, A Netrin-1 Receptor
Length = 403
Score = 88.6 bits (218), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 76/294 (25%), Positives = 121/294 (41%), Gaps = 42/294 (14%)
Query: 86 IAQTADLKCSVQYADDYPVI-WMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTY 144
+ T LKC V D P I W K + + P+P DSR + +
Sbjct: 135 MGDTVLLKCEV-IGDPMPTIHWQK--NQQDLNPIP---------GDSRVVVLP-----SG 177
Query: 145 ILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDN-----STRSVIVSEGQ 199
L I +Q D+G+Y+C + + E E+ + P + +VI EG+
Sbjct: 178 ALQISRLQPGDSGVYRCSARNPASTRTGNEAEVRILSDPGLHRQLYFLQRPSNVIAIEGK 237
Query: 200 TVYLYCYANGFPAPTISWRRDNSA--ALSTGGSIYRGNILKIPNITKTDRGTYYCVAQNG 257
L C +G+P P+ +W R S S+ G+ L I N+T D GTY CV
Sbjct: 238 DAVLECCVSGYPPPSFTWLRGEEVIQLRSKKYSLLGGSNLLISNVTDDDSGTYTCVVTY- 296
Query: 258 VGRGMKRNIAVEVEF---APVITINRPRQGQALQ-YDAILECHVEAYPPPAIVWIKDGVQ 313
NI+ E P +N P A + D EC V P P + W+K+G
Sbjct: 297 ----KNENISASAELTVLVPPWFLNHPSNLYAYESMDIEFECAVSGKPVPTVNWMKNGDV 352
Query: 314 IMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIELF 367
++ + ++ + ++LR++ + + G Y C A N+ G+AQ +L
Sbjct: 353 VIPSDYFQI--------VGGSNLRILGVVKSDEGFYQCVAENEAGNAQSSAQLI 398
Score = 73.6 bits (179), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 70/288 (24%), Positives = 114/288 (39%), Gaps = 34/288 (11%)
Query: 92 LKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYILSI--K 149
L CS + PVI K D + +L + D + QL P S I +I
Sbjct: 41 LNCSAESDRGVPVIKWKKD----------GLILALGMDDRKQQL---PNGSLLIQNILHS 87
Query: 150 EIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG 209
+ D G+Y+CE + + + + ++ P+ + T S+ G TV L C G
Sbjct: 88 RHHKPDEGLYQCEASLGDSGSIISRTAKVMVAGPLRFLSQTESITAFMGDTVLLKCEVIG 147
Query: 210 FPAPTISWRRDNSAALSTGGS----IYRGNILKIPNITKTDRGTYYCVAQNGVGRGMKRN 265
P PTI W+++ G + L+I + D G Y C A+N
Sbjct: 148 DPMPTIHWQKNQQDLNPIPGDSRVVVLPSGALQISRLQPGDSGVYRCSARNPASTRTGNE 207
Query: 266 IAVEVEFAPVIT-----INRPRQGQALQ-YDAILECHVEAYPPPAIVWIK-DGVQIMNNQ 318
V + P + + RP A++ DA+LEC V YPPP+ W++ + V + ++
Sbjct: 208 AEVRILSDPGLHRQLYFLQRPSNVIAIEGKDAVLECCVSGYPPPSFTWLRGEEVIQLRSK 267
Query: 319 HYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
YS+ ++L + + G Y C K + EL
Sbjct: 268 KYSL--------LGGSNLLISNVTDDDSGTYTCVVTYKNENISASAEL 307
>pdb|3JXA|A Chain A, Immunoglobulin Domains 1-4 Of Mouse Cntn4
pdb|3JXA|B Chain B, Immunoglobulin Domains 1-4 Of Mouse Cntn4
Length = 383
Score = 86.3 bits (212), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 60/224 (26%), Positives = 100/224 (44%), Gaps = 22/224 (9%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNNK--VSAEVELIVRRPPIISDNSTR-------SVIVS 196
L I +++++D G Y C V ++ N + LI+R ++ + + +V
Sbjct: 158 LYIAKVEKSDVGNYTCVVTNTVTNHKVLGPPTPLILRNDGVMGEYEPKIEVQFPETVPAE 217
Query: 197 EGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGN-ILKIPNITKTDRGTYYCVAQ 255
+G TV L C+A G P PTI WRR + ++ ++ N IL+IPN + D G+Y CVA+
Sbjct: 218 KGTTVKLECFALGNPVPTILWRRADGKPIARKARRHKSNGILEIPNFQQEDAGSYECVAE 277
Query: 256 NGVGRGM-KRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAIVWIKDGVQI 314
N G+ + K + + V IN A++ EC P P W+K+G +
Sbjct: 278 NSRGKNVAKGQLTFYAQPNWVQIINDIH--VAMEESVFWECKANGRPKPTYRWLKNGDPL 335
Query: 315 MNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYG 358
+ + +L + + G Y C A NK+G
Sbjct: 336 LTRDRIQIEQ---------GTLNITIVNLSDAGMYQCVAENKHG 370
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 39/122 (31%), Positives = 56/122 (45%), Gaps = 10/122 (8%)
Query: 142 STYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPP----IISDNSTRSVIVSE 197
S IL I Q+ DAG Y+C V + K A+ +L P II+D + V+
Sbjct: 255 SNGILEIPNFQQEDAGSYEC-VAENSRGKNVAKGQLTFYAQPNWVQIIND-----IHVAM 308
Query: 198 GQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQNG 257
++V+ C ANG P PT W ++ L+ L I + +D G Y CVA+N
Sbjct: 309 EESVFWECKANGRPKPTYRWLKNGDPLLTRDRIQIEQGTLNITIVNLSDAGMYQCVAENK 368
Query: 258 VG 259
G
Sbjct: 369 HG 370
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 58/228 (25%), Positives = 82/228 (35%), Gaps = 43/228 (18%)
Query: 155 DAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYC--------- 205
DAG Y+C S VS E +L + +V V GQ + L C
Sbjct: 73 DAGTYQCIATNSFGTIVSREAKLQFAYLENFKTRTRSTVSVRRGQGMVLLCGPPPHSGEL 132
Query: 206 -YA---NGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQNGVGRG 261
YA N +P S++ + G++Y I + K+D G Y CV N V
Sbjct: 133 SYAWIFNEYP----SYQDNRRFVSQETGNLY------IAKVEKSDVGNYTCVVTNTVTNH 182
Query: 262 ---------MKRNIAVEVEFAPVITINRPRQGQALQYDAI-LECHVEAYPPPAIVWIK-D 310
+ RN V E+ P I + P A + + LEC P P I+W + D
Sbjct: 183 KVLGPPTPLILRNDGVMGEYEPKIEVQFPETVPAEKGTTVKLECFALGNPVPTILWRRAD 242
Query: 311 GVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYG 358
G I S+ L + ++ G Y C A N G
Sbjct: 243 GKPIAR---------KARRHKSNGILEIPNFQQEDAGSYECVAENSRG 281
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 47/174 (27%), Positives = 68/174 (39%), Gaps = 30/174 (17%)
Query: 196 SEGQTVYLYCYANGFPAPTISWR---RDNSAALSTGGSIYRGNILKIPNITKT-DRGTYY 251
SE + V L C G P P I W+ D + S+ G++L I N KT D GTY
Sbjct: 20 SEEKKVKLSCEVKGNPKPHIRWKLNGTDVDIGMDFRYSVVDGSLL-INNPNKTQDAGTYQ 78
Query: 252 CVAQNGVGRGMKRNIAVEVEFAPVI-TINRP----RQGQALQYDAILECHVEAYPPP--- 303
C+A N G + R ++ + T R R+GQ + +L C PPP
Sbjct: 79 CIATNSFGTIVSREAKLQFAYLENFKTRTRSTVSVRRGQGM----VLLCG----PPPHSG 130
Query: 304 --AIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAAN 355
+ WI + + VS +L + +E+ G Y C N
Sbjct: 131 ELSYAWIFNEYPSYQDNRRFVSQ-------ETGNLYIAKVEKSDVGNYTCVVTN 177
>pdb|3KLD|A Chain A, Ptprg Cntn4 Complex
Length = 384
Score = 86.3 bits (212), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 60/224 (26%), Positives = 100/224 (44%), Gaps = 22/224 (9%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNNK--VSAEVELIVRRPPIISDNSTR-------SVIVS 196
L I +++++D G Y C V ++ N + LI+R ++ + + +V
Sbjct: 159 LYIAKVEKSDVGNYTCVVTNTVTNHKVLGPPTPLILRNDGVMGEYEPKIEVQFPETVPAE 218
Query: 197 EGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGN-ILKIPNITKTDRGTYYCVAQ 255
+G TV L C+A G P PTI WRR + ++ ++ N IL+IPN + D G+Y CVA+
Sbjct: 219 KGTTVKLECFALGNPVPTILWRRADGKPIARKARRHKSNGILEIPNFQQEDAGSYECVAE 278
Query: 256 NGVGRGM-KRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAIVWIKDGVQI 314
N G+ + K + + V IN A++ EC P P W+K+G +
Sbjct: 279 NSRGKNVAKGQLTFYAQPNWVQIINDIH--VAMEESVFWECKANGRPKPTYRWLKNGDPL 336
Query: 315 MNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYG 358
+ + +L + + G Y C A NK+G
Sbjct: 337 LTRDRIQIEQ---------GTLNITIVNLSDAGMYQCVAENKHG 371
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 39/122 (31%), Positives = 56/122 (45%), Gaps = 10/122 (8%)
Query: 142 STYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPP----IISDNSTRSVIVSE 197
S IL I Q+ DAG Y+C V + K A+ +L P II+D + V+
Sbjct: 256 SNGILEIPNFQQEDAGSYEC-VAENSRGKNVAKGQLTFYAQPNWVQIIND-----IHVAM 309
Query: 198 GQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQNG 257
++V+ C ANG P PT W ++ L+ L I + +D G Y CVA+N
Sbjct: 310 EESVFWECKANGRPKPTYRWLKNGDPLLTRDRIQIEQGTLNITIVNLSDAGMYQCVAENK 369
Query: 258 VG 259
G
Sbjct: 370 HG 371
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 58/228 (25%), Positives = 82/228 (35%), Gaps = 43/228 (18%)
Query: 155 DAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYC--------- 205
DAG Y+C S VS E +L + +V V GQ + L C
Sbjct: 74 DAGTYQCIATNSFGTIVSREAKLQFAYLENFKTRTRSTVSVRRGQGMVLLCGPPPHSGEL 133
Query: 206 -YA---NGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQNGVGRG 261
YA N +P S++ + G++Y I + K+D G Y CV N V
Sbjct: 134 SYAWIFNEYP----SYQDNRRFVSQETGNLY------IAKVEKSDVGNYTCVVTNTVTNH 183
Query: 262 ---------MKRNIAVEVEFAPVITINRPRQGQALQYDAI-LECHVEAYPPPAIVWIK-D 310
+ RN V E+ P I + P A + + LEC P P I+W + D
Sbjct: 184 KVLGPPTPLILRNDGVMGEYEPKIEVQFPETVPAEKGTTVKLECFALGNPVPTILWRRAD 243
Query: 311 GVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYG 358
G I S+ L + ++ G Y C A N G
Sbjct: 244 GKPIAR---------KARRHKSNGILEIPNFQQEDAGSYECVAENSRG 282
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 47/174 (27%), Positives = 68/174 (39%), Gaps = 30/174 (17%)
Query: 196 SEGQTVYLYCYANGFPAPTISWR---RDNSAALSTGGSIYRGNILKIPNITKT-DRGTYY 251
SE + V L C G P P I W+ D + S+ G++L I N KT D GTY
Sbjct: 21 SEEKKVKLSCEVKGNPKPHIRWKLNGTDVDIGMDFRYSVVDGSLL-INNPNKTQDAGTYQ 79
Query: 252 CVAQNGVGRGMKRNIAVEVEFAPVI-TINRP----RQGQALQYDAILECHVEAYPPP--- 303
C+A N G + R ++ + T R R+GQ + +L C PPP
Sbjct: 80 CIATNSFGTIVSREAKLQFAYLENFKTRTRSTVSVRRGQGM----VLLCG----PPPHSG 131
Query: 304 --AIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAAN 355
+ WI + + VS +L + +E+ G Y C N
Sbjct: 132 ELSYAWIFNEYPSYQDNRRFVSQ-------ETGNLYIAKVEKSDVGNYTCVVTN 178
>pdb|2IEP|A Chain A, Crystal Structure Of Immunoglobulin-Like Domains 1 And 2
Of The Receptor Tyrosine Kinase Musk
pdb|2IEP|B Chain B, Crystal Structure Of Immunoglobulin-Like Domains 1 And 2
Of The Receptor Tyrosine Kinase Musk
Length = 192
Score = 78.2 bits (191), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 60/202 (29%), Positives = 89/202 (44%), Gaps = 22/202 (10%)
Query: 176 ELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNS--AALSTGGSIYR 233
E + + P I + T +V E T C +P P ISW R+ T SI
Sbjct: 2 EKLPKAPVITTPLETVDALVEEVAT--FMCAVESYPQPEISWTRNKILIKLFDTRYSIRE 59
Query: 234 -GNILKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQAL--QYD 290
G +L I ++ +D G Y C A NGVG ++ A++V+ P IT RP +
Sbjct: 60 NGQLLTILSVEDSDDGIYCCTANNGVGGAVESCGALQVKMKPKIT--RPPINVKIIEGLK 117
Query: 291 AILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYA 350
A+L C P P++ WIK + N +V SLR+ +++ GQY
Sbjct: 118 AVLPCTTMGNPKPSVSWIKGDSALRENSRIAV--------LESGSLRIHNVQKEDAGQYR 169
Query: 351 CKAANKYGSA-----QKEIELF 367
C A N G+A + E+E+F
Sbjct: 170 CVAKNSLGTAYSKLVKLEVEVF 191
>pdb|1QZ1|A Chain A, Crystal Structure Of The Ig 1-2-3 Fragment Of Ncam
Length = 291
Score = 75.5 bits (184), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 69/244 (28%), Positives = 101/244 (41%), Gaps = 28/244 (11%)
Query: 137 TDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVS 196
D ++ST L+I DAGIYKC V + A V + + + ++ N+
Sbjct: 57 NDDDSST--LTIYNANIDDAGIYKCVVTAEDGTQSEATVNVKIFQK-LMFKNAPTPQEFK 113
Query: 197 EGQTVYLYCYANGFPAPTISWR---RDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCV 253
EG+ + C PTI W+ RD + N L+I I KTD GTY C
Sbjct: 114 EGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNNYLQIRGIKKTDEGTYRCE 173
Query: 254 AQNGVGRGMKRNIAVEVEFAPV-ITINRPRQGQALQ----------YDAILECHVEAYPP 302
GR + R E+ F + + +N P QA Q L C + +P
Sbjct: 174 -----GRILARG---EINFKDIQVIVNVPPTVQARQSIVNATANLGQSVTLVCDADGFPE 225
Query: 303 PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQK 362
P + W KDG I N + H SD+ S+ ++R +++ +Y C A NK G
Sbjct: 226 PTMSWTKDGEPIENEEEDDEKHI-FSDDSSELTIR--NVDKNDEAEYVCIAENKAGEQDA 282
Query: 363 EIEL 366
I L
Sbjct: 283 SIHL 286
>pdb|3B43|A Chain A, I-band Fragment I65-i70 From Titin
Length = 570
Score = 73.9 bits (180), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 77/340 (22%), Positives = 145/340 (42%), Gaps = 37/340 (10%)
Query: 31 FIHEVTGEKV----TSVILLFKMSVAGPSIIVALSFLISLASSQRTPTISYISQEQIKDI 86
FIH V ++ S + + S + P + S ++L+ + P +
Sbjct: 152 FIHNVATLQILQTDQSHVGQYNCSASNPLGTASSSAKLTLSEHEVPPFFDLKPVSVDLAL 211
Query: 87 AQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYIL 146
++ KC V + W K + +++ P +++T T+T L
Sbjct: 212 GESGTFKCHVTGTAPIKITWAKDN--REIRP------------GGNYKMTLVENTAT--L 255
Query: 147 SIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCY 206
++ ++ + DAG Y C ++ K S +L V+ PP S IV + + C
Sbjct: 256 TVLKVTKGDAGQYTC-YASNVAGKDSCSAQLGVQEPPRFIKKLEPSRIVKQDEHTRYECK 314
Query: 207 ANGFPAPTISWRRDNSAALSTGGSIYRGN------ILKIPNITKTDRGTYYCVAQNGVGR 260
G P + W +D + + S +R + +L++ N++ D G Y C A N G
Sbjct: 315 IGGSPEIKVLWYKDETEIQES--SKFRMSFVESVAVLEMYNLSVEDSGDYTCEAHNAAGS 372
Query: 261 GMKRNIAVEVEFAPVITINRPRQGQALQ-YDAILECHVEAYPPPAIVWIKDGVQIMNNQH 319
+ +++V+ PV +P + L+ D LEC ++ PP + W KD ++ + +
Sbjct: 373 -ASSSTSLKVKEPPVFR-KKPHPVETLKGADVHLECELQGTPPFQVSWHKDKRELRSGKK 430
Query: 320 YSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGS 359
Y + S+ F TS+ ++ ++ G+Y CKA+N GS
Sbjct: 431 YKI----MSENFL-TSIHILNVDSADIGEYQCKASNDVGS 465
Score = 62.8 bits (151), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 58/222 (26%), Positives = 88/222 (39%), Gaps = 16/222 (7%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRR--PPIISDNSTRSVIVSEGQTVYL 203
L I ++ +D G Y C+ S+ S+ V +I R PP + + V + G V
Sbjct: 63 LVINKVDHSDVGEYTCKAENSVGAVASSAVLVIKERKLPPSFA-RKLKDVHETLGFPVAF 121
Query: 204 YCYANGFPAPTISWRRD-----NSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQN-- 256
C NG +SW +D + A L T I+ L+I ++ G Y C A N
Sbjct: 122 ECRINGSEPLQVSWYKDGELLKDDANLQT-SFIHNVATLQILQTDQSHVGQYNCSASNPL 180
Query: 257 GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAIVWIKDGVQIMN 316
G + E E P + AL +CHV P I W KD +I
Sbjct: 181 GTASSSAKLTLSEHEVPPFFDLKPVSVDLALGESGTFKCHVTGTAPIKITWAKDNREIRP 240
Query: 317 NQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYG 358
+Y ++ + +L V+ + + GQY C A+N G
Sbjct: 241 GGNYKMTLVENT-----ATLTVLKVTKGDAGQYTCYASNVAG 277
Score = 62.0 bits (149), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 46/190 (24%), Positives = 82/190 (43%), Gaps = 15/190 (7%)
Query: 198 GQTVYLYCYANGFPAPTISWRRDNSAALSTGG--SIYRGNI--LKIPNITKTDRGTYYCV 253
G+ + L C +G P I+W ++++ S ++ N+ L I + +D G Y C
Sbjct: 20 GEPITLQCKVDGTPEIRIAWYKEHTKLRSAPAYKMQFKNNVASLVINKVDHSDVGEYTCK 79
Query: 254 AQNGVGRGMKRNIAV--EVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAIVWIKDG 311
A+N VG + V E + P + L + EC + P + W KDG
Sbjct: 80 AENSVGAVASSAVLVIKERKLPPSFARKLKDVHETLGFPVAFECRINGSEPLQVSWYKDG 139
Query: 312 VQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIELFDRET 371
+ ++ ++ TS + +L+++ ++ GQY C A+N G+A +L T
Sbjct: 140 ELLKDD-----ANLQTSFIHNVATLQILQTDQSHVGQYNCSASNPLGTASSSAKL----T 190
Query: 372 QTGDETFPIF 381
+ E P F
Sbjct: 191 LSEHEVPPFF 200
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 60/252 (23%), Positives = 100/252 (39%), Gaps = 24/252 (9%)
Query: 116 EPLPIS--MSGSLIIHDSRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNN-KVS 172
EPL +S G L+ D+ Q + +T L I + ++ G Y C L S
Sbjct: 129 EPLQVSWYKDGELLKDDANLQTSFIHNVAT--LQILQTDQSHVGQYNCSASNPLGTASSS 186
Query: 173 AEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGS-- 230
A++ L P D SV ++ G++ C+ G I+W +DN + GG+
Sbjct: 187 AKLTLSEHEVPPFFDLKPVSVDLALGESGTFKCHVTGTAPIKITWAKDNRE-IRPGGNYK 245
Query: 231 ---IYRGNILKIPNITKTDRGTYYCVAQNGVGR---GMKRNIAVEVEFAPVITINR-PRQ 283
+ L + +TK D G Y C A N G+ + + F + +R +Q
Sbjct: 246 MTLVENTATLTVLKVTKGDAGQYTCYASNVAGKDSCSAQLGVQEPPRFIKKLEPSRIVKQ 305
Query: 284 GQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER 343
+ +Y EC + P ++W KD +I + + +S S L + +
Sbjct: 306 DEHTRY----ECKIGGSPEIKVLWYKDETEIQESSKFRMSFVE-----SVAVLEMYNLSV 356
Query: 344 RQFGQYACKAAN 355
G Y C+A N
Sbjct: 357 EDSGDYTCEAHN 368
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 64/277 (23%), Positives = 108/277 (38%), Gaps = 35/277 (12%)
Query: 93 KCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYILSIKEIQ 152
+C + + + V+W K +T I S+F+++ S +L + +
Sbjct: 312 ECKIGGSPEIKVLWYKDETE--------------IQESSKFRMSF--VESVAVLEMYNLS 355
Query: 153 ETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPA 212
D+G Y CE + S+ L V+ PP+ V +G V+L C G P
Sbjct: 356 VEDSGDYTCEAH-NAAGSASSSTSLKVKEPPVFR-KKPHPVETLKGADVHLECELQGTPP 413
Query: 213 PTISWRRDNSAALSTGGS--IYRGNIL---KIPNITKTDRGTYYCVAQNGVGRGMKRNIA 267
+SW +D L +G I N L I N+ D G Y C A N VG +
Sbjct: 414 FQVSWHKDKRE-LRSGKKYKIMSENFLTSIHILNVDSADIGEYQCKASNDVGSDTCVG-S 471
Query: 268 VEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAIVWIKDGVQIM---NNQHYSVSH 324
+ ++ P + + L+ +E P ++ W KD +I+ +N S S
Sbjct: 472 ITLKAPPRFVKKLSDISTVVGEEVQLQATIEGAEPISVAWFKDKGEIVRESDNIWISYSE 531
Query: 325 FATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQ 361
+ +FS E G+Y C+ N+ G+ +
Sbjct: 532 NIATLQFSRA-------EPANAGKYTCQIKNEAGTQE 561
>pdb|2RIK|A Chain A, I-Band Fragment I67-I69 From Titin
Length = 284
Score = 73.9 bits (180), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 67/281 (23%), Positives = 125/281 (44%), Gaps = 33/281 (11%)
Query: 86 IAQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYI 145
+ ++ KC V + W K + +++ P +++T T+T
Sbjct: 19 LGESGTFKCHVTGTAPIKITWAKDN--REIRP------------GGNYKMTLVENTAT-- 62
Query: 146 LSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYC 205
L++ ++ + DAG Y C ++ K S +L V+ PP S IV + + C
Sbjct: 63 LTVLKVTKGDAGQYTC-YASNVAGKDSCSAQLGVQEPPRFIKKLEPSRIVKQDEHTRYEC 121
Query: 206 YANGFPAPTISWRRDNSAALSTGGSIYRGN------ILKIPNITKTDRGTYYCVAQNGVG 259
G P + W +D + + S +R + +L++ N++ D G Y C A N G
Sbjct: 122 KIGGSPEIKVLWYKDETEIQES--SKFRMSFVESVAVLEMYNLSVEDSGDYTCEAHNAAG 179
Query: 260 RGMKRNIAVEVEFAPVITINRPRQGQALQ-YDAILECHVEAYPPPAIVWIKDGVQIMNNQ 318
+ +++V+ PV +P + L+ D LEC ++ PP + W KD ++ + +
Sbjct: 180 S-ASSSTSLKVKEPPVFR-KKPHPVETLKGADVHLECELQGTPPFQVSWHKDKRELRSGK 237
Query: 319 HYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGS 359
Y + S+ F TS+ ++ ++ G+Y CKA+N GS
Sbjct: 238 KYKI----MSENFL-TSIHILNVDSADIGEYQCKASNDVGS 273
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 43/183 (23%), Positives = 73/183 (39%), Gaps = 20/183 (10%)
Query: 182 PPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGS-----IYRGNI 236
PP D SV ++ G++ C+ G I+W +DN + GG+ +
Sbjct: 5 PPFF-DLKPVSVDLALGESGTFKCHVTGTAPIKITWAKDNRE-IRPGGNYKMTLVENTAT 62
Query: 237 LKIPNITKTDRGTYYCVAQNGVGR---GMKRNIAVEVEFAPVITINR-PRQGQALQYDAI 292
L + +TK D G Y C A N G+ + + F + +R +Q + +Y
Sbjct: 63 LTVLKVTKGDAGQYTCYASNVAGKDSCSAQLGVQEPPRFIKKLEPSRIVKQDEHTRY--- 119
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACK 352
EC + P ++W KD +I + + +S S L + + G Y C+
Sbjct: 120 -ECKIGGSPEIKVLWYKDETEIQESSKFRMSFVE-----SVAVLEMYNLSVEDSGDYTCE 173
Query: 353 AAN 355
A N
Sbjct: 174 AHN 176
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 5/73 (6%)
Query: 286 ALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQ 345
AL +CHV P I W KD +I +Y ++ + +L V+ + +
Sbjct: 18 ALGESGTFKCHVTGTAPIKITWAKDNREIRPGGNYKMTLVENT-----ATLTVLKVTKGD 72
Query: 346 FGQYACKAANKYG 358
GQY C A+N G
Sbjct: 73 AGQYTCYASNVAG 85
>pdb|1CS6|A Chain A, N-terminal Fragment Of Axonin-1 From Chicken
Length = 382
Score = 73.6 bits (179), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 62/234 (26%), Positives = 93/234 (39%), Gaps = 28/234 (11%)
Query: 146 LSIKEIQETDAGIYKC----------EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV 195
L I + + +D G Y C + + S +++S E + P I
Sbjct: 160 LYIAKTEASDLGNYSCFATSHIDFITKSVFSKFSQLSLAAEDARQYAPSIKAKFPADTYA 219
Query: 196 SEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQ 255
GQ V L C+A G P P I WR+ + + T + +L I N+ D GTY C A+
Sbjct: 220 LTGQMVTLECFAFGNPVPQIKWRKLDGS--QTSKWLSSEPLLHIQNVDFEDEGTYECEAE 277
Query: 256 NGVGRGMKRN---IAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAIVWIKDGV 312
N GR + I + ++ VIT G L++ C P PA+ W++DG
Sbjct: 278 NIKGRDTYQGRIIIHAQPDWLDVITDTEADIGSDLRWS----CVASGKPRPAVRWLRDGQ 333
Query: 313 QIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
+ + E S LR + G Y C A NK+G+ EL
Sbjct: 334 PLASQNRI---------EVSGGELRFSKLVLEDSGMYQCVAENKHGTVYASAEL 378
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 10/123 (8%)
Query: 141 TSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPP----IISDNSTRSVIVS 196
+S +L I+ + D G Y+CE ++ + + + +I+ P +I+D T + I
Sbjct: 254 SSEPLLHIQNVDFEDEGTYECEAE-NIKGRDTYQGRIIIHAQPDWLDVITD--TEADI-- 308
Query: 197 EGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQN 256
G + C A+G P P + W RD S G L+ + D G Y CVA+N
Sbjct: 309 -GSDLRWSCVASGKPRPAVRWLRDGQPLASQNRIEVSGGELRFSKLVLEDSGMYQCVAEN 367
Query: 257 GVG 259
G
Sbjct: 368 KHG 370
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 3/80 (3%)
Query: 196 SEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYR---GNILKIPNITKTDRGTYYC 252
S + V L C A P T W+ + + S YR G+++ + D G+Y C
Sbjct: 20 SAEEKVTLTCRARANPPATYRWKMNGTELKMGPDSRYRLVAGDLVISNPVKAKDAGSYQC 79
Query: 253 VAQNGVGRGMKRNIAVEVEF 272
VA N G + R ++ F
Sbjct: 80 VATNARGTVVSREASLRFGF 99
>pdb|2RJM|A Chain A, 3ig Structure Of Titin Domains I67-I69 E-To-A Mutated
Variant
Length = 284
Score = 73.2 bits (178), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 67/281 (23%), Positives = 125/281 (44%), Gaps = 33/281 (11%)
Query: 86 IAQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYI 145
+ ++ KC V + W K + +++ P +++T T+T
Sbjct: 19 LGESGTFKCHVTGTAPIKITWAKDN--REIRP------------GGNYKMTLVENTAT-- 62
Query: 146 LSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYC 205
L++ ++ + DAG Y C ++ K S +L V+ PP S IV + + C
Sbjct: 63 LTVLKVTKGDAGQYTC-YASNVAGKDSCSAQLGVQAPPRFIKKLEPSRIVKQDEHTRYEC 121
Query: 206 YANGFPAPTISWRRDNSAALSTGGSIYRGN------ILKIPNITKTDRGTYYCVAQNGVG 259
G P + W +D + + S +R + +L++ N++ D G Y C A N G
Sbjct: 122 KIGGSPEIKVLWYKDETEIQES--SKFRMSFVESVAVLEMYNLSVEDSGDYTCEAHNAAG 179
Query: 260 RGMKRNIAVEVEFAPVITINRPRQGQALQ-YDAILECHVEAYPPPAIVWIKDGVQIMNNQ 318
+ +++V+ PV +P + L+ D LEC ++ PP + W KD ++ + +
Sbjct: 180 S-ASSSTSLKVKEPPVFR-KKPHPVETLKGADVHLECELQGTPPFQVSWHKDKRELRSGK 237
Query: 319 HYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGS 359
Y + S+ F TS+ ++ ++ G+Y CKA+N GS
Sbjct: 238 KYKI----MSENFL-TSIHILNVDSADIGEYQCKASNDVGS 273
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 44/182 (24%), Positives = 73/182 (40%), Gaps = 18/182 (9%)
Query: 182 PPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGS-----IYRGNI 236
PP D SV ++ G++ C+ G I+W +DN + GG+ +
Sbjct: 5 PPFF-DLKPVSVDLALGESGTFKCHVTGTAPIKITWAKDNRE-IRPGGNYKMTLVENTAT 62
Query: 237 LKIPNITKTDRGTYYCVAQNGVGR-GMKRNIAVEVEFAPVITINRPRQGQALQYD--AIL 293
L + +TK D G Y C A N G+ + V+ AP I + + ++ D
Sbjct: 63 LTVLKVTKGDAGQYTCYASNVAGKDSCSAQLGVQ---APPRFIKKLEPSRIVKQDEHTRY 119
Query: 294 ECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKA 353
EC + P ++W KD +I + + +S S L + + G Y C+A
Sbjct: 120 ECKIGGSPEIKVLWYKDETEIQESSKFRMSFVE-----SVAVLEMYNLSVEDSGDYTCEA 174
Query: 354 AN 355
N
Sbjct: 175 HN 176
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 5/73 (6%)
Query: 286 ALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQ 345
AL +CHV P I W KD +I +Y ++ + +L V+ + +
Sbjct: 18 ALGESGTFKCHVTGTAPIKITWAKDNREIRPGGNYKMTLVENT-----ATLTVLKVTKGD 72
Query: 346 FGQYACKAANKYG 358
GQY C A+N G
Sbjct: 73 AGQYTCYASNVAG 85
>pdb|3DMK|A Chain A, Crystal Structure Of Down Syndrome Cell Adhesion Molecule
(Dscam) Isoform 1.30.30, N-Terminal Eight Ig Domains
pdb|3DMK|B Chain B, Crystal Structure Of Down Syndrome Cell Adhesion Molecule
(Dscam) Isoform 1.30.30, N-Terminal Eight Ig Domains
pdb|3DMK|C Chain C, Crystal Structure Of Down Syndrome Cell Adhesion Molecule
(Dscam) Isoform 1.30.30, N-Terminal Eight Ig Domains
Length = 816
Score = 73.2 bits (178), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 78/307 (25%), Positives = 126/307 (41%), Gaps = 32/307 (10%)
Query: 64 ISLASSQRTPTISYISQEQIKDIAQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMS 123
+ L P I QE+ + + LKC V + P I ++D
Sbjct: 421 LKLGGRFDPPVIRQAFQEETMEPGPSVFLKC-VAGGNPTPEISWELD------------- 466
Query: 124 GSLIIHDSRFQL----TTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIV 179
G I ++ R+Q+ T + + +Y L+I + D G+YKC + S +L V
Sbjct: 467 GKKIANNDRYQVGQYVTVNGDVVSY-LNITSVHANDGGLYKC-IAKSKVGVAEHSAKLNV 524
Query: 180 RRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSA-ALSTGGSIYRGNILK 238
P I ++++ G+T+ + C G+P +I W RDN A ++ ++ L
Sbjct: 525 YGLPYIRQMEKKAIVA--GETLIVTCPVAGYPIDSIVWERDNRALPINRKQKVFPNGTLI 582
Query: 239 IPNITK-TDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQG--QALQYDAILEC 295
I N+ + +D+ TY CVA+N G + ++ V+V P I +G Q QY L C
Sbjct: 583 IENVERNSDQATYTCVAKNQEGYSARGSLEVQVMVLPRIIPFAFEEGPAQVGQY-LTLHC 641
Query: 296 HVEAYPPPA-IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAA 354
V P I W DG I + + S + L + +E G + C A
Sbjct: 642 SVPGGDLPLNIDWTLDGQAISEDLGITTSRVGR----RGSVLTIEAVEASHAGNFTCHAR 697
Query: 355 NKYGSAQ 361
N G Q
Sbjct: 698 NLAGHQQ 704
Score = 72.4 bits (176), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 61/230 (26%), Positives = 95/230 (41%), Gaps = 24/230 (10%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNNKVSAE-VELIVR-RPPIISDNSTRSVIVSEGQTVYL 203
L IK+ D+G Y C V NN V E VE ++ P+ + + V G+
Sbjct: 308 LIIKDAVVEDSGKYLCVV----NNSVGGESVETVLTVTAPLSAKIDPPTQTVDFGRPAVF 363
Query: 204 YCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQNGVGRGMK 263
C G P T+SW +D A + ++L+I ++ K D+G Y C +N +
Sbjct: 364 TCQYTGNPIKTVSWMKDGKAIG------HSESVLRIESVKKEDKGMYQCFVRND-----R 412
Query: 264 RNIAVEVEFAPVITINRPRQGQALQYDAI-------LECHVEAYPPPAIVWIKDGVQIMN 316
+ E + P QA Q + + L+C P P I W DG +I N
Sbjct: 413 ESAEASAELKLGGRFDPPVIRQAFQEETMEPGPSVFLKCVAGGNPTPEISWELDGKKIAN 472
Query: 317 NQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
N Y V + T + + L + ++ G Y C A +K G A+ +L
Sbjct: 473 NDRYQVGQYVTVNGDVVSYLNITSVHANDGGLYKCIAKSKVGVAEHSAKL 522
Score = 71.2 bits (173), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 88/352 (25%), Positives = 139/352 (39%), Gaps = 61/352 (17%)
Query: 30 FFIHEVTGEKVTSVILLFKMSVAGPSIIVALSFLISLASSQRTPTISYISQEQIKDIAQT 89
I + E + + SV G S+ L+ L++ PT Q D +
Sbjct: 308 LIIKDAVVEDSGKYLCVVNNSVGGESVETVLTVTAPLSAKIDPPT-------QTVDFGRP 360
Query: 90 ADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYILSIK 149
A C V WMK G I H S +L I+
Sbjct: 361 AVFTCQYTGNPIKTVSWMK--------------DGKAIGH------------SESVLRIE 394
Query: 150 EIQETDAGIYKCEVIISLNN-KVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYAN 208
+++ D G+Y+C V + + SAE++L R P + + + + G +V+L C A
Sbjct: 395 SVKKEDKGMYQCFVRNDRESAEASAELKLGGRFDPPVIRQAFQEETMEPGPSVFLKCVAG 454
Query: 209 GFPAPTISWRRD-----NSAALSTGGSI-YRGNILKIPNITK---TDRGTYYCVAQNGVG 259
G P P ISW D N+ G + G+++ NIT D G Y C+A++ VG
Sbjct: 455 GNPTPEISWELDGKKIANNDRYQVGQYVTVNGDVVSYLNITSVHANDGGLYKCIAKSKVG 514
Query: 260 RGMKRNIAVEVEFAPVITINRPR---QGQALQYDAILECHVEAYPPPAIVWIKDGVQIMN 316
+ + + V P I + G+ L I+ C V YP +IVW +D +
Sbjct: 515 VA-EHSAKLNVYGLPYIRQMEKKAIVAGETL----IVTCPVAGYPIDSIVWERDNRALPI 569
Query: 317 NQHYSVSHFATSDEFSDTSLRVITIERR-QFGQYACKAANKYG-SAQKEIEL 366
N+ V F + +L + +ER Y C A N+ G SA+ +E+
Sbjct: 570 NRKQKV--------FPNGTLIIENVERNSDQATYTCVAKNQEGYSARGSLEV 613
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 45/178 (25%), Positives = 66/178 (37%), Gaps = 24/178 (13%)
Query: 196 SEGQTVYLYCYANGFPAPTISW-------RRDNSAALSTGGSIYRGNILKIPNITKTDRG 248
S T+ L C A G+P P W R + L+ G ++ I + D G
Sbjct: 261 SGSSTMALLCPAQGYPVPVFRWYKFIEGTTRKQAVVLNDRVKQVSGTLI-IKDAVVEDSG 319
Query: 249 TYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAIVWI 308
Y CV N VG G + V I+ P Q A+ C P + W+
Sbjct: 320 KYLCVVNNSVG-GESVETVLTVTAPLSAKIDPPTQTVDFGRPAVFTCQYTGNPIKTVSWM 378
Query: 309 KDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
KDG I + S++ LR+ ++++ G Y C N SA+ EL
Sbjct: 379 KDGKAIGH---------------SESVLRIESVKKEDKGMYQCFVRNDRESAEASAEL 421
Score = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 43/171 (25%), Positives = 68/171 (39%), Gaps = 13/171 (7%)
Query: 198 GQTVYLYCYANGFPAP-TISWRRDNSA-----ALSTGGSIYRGNILKIPNITKTDRGTYY 251
GQ + L+C G P I W D A ++T RG++L I + + G +
Sbjct: 634 GQYLTLHCSVPGGDLPLNIDWTLDGQAISEDLGITTSRVGRRGSVLTIEAVEASHAGNFT 693
Query: 252 CVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAIVWIKDG 311
C A+N G + + V P + + A DA +EC + +P P + W K
Sbjct: 694 CHARNLAGH-QQFTTPLNVYVPPRWILEPTDKAFAQGSDAKVECKADGFPKPQVTWKK-- 750
Query: 312 VQIMNNQHYSVSHFATSDEF--SDTSLRVITIERRQFGQYACKAANKYGSA 360
+ + SD + +L V I++ G Y C+A N GS
Sbjct: 751 --AVGDTPGEYKDLKKSDNIRVEEGTLHVDNIQKTNEGYYLCEAINGIGSG 799
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 34/134 (25%), Positives = 59/134 (44%), Gaps = 9/134 (6%)
Query: 145 ILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLY 204
+L+I+ ++ + AG + C +L L V PP T ++G +
Sbjct: 678 VLTIEAVEASHAGNFTCHAR-NLAGHQQFTTPLNVYVPPRWILEPTDKAF-AQGSDAKVE 735
Query: 205 CYANGFPAPTISWRRDNSAALSTGGSIYRGN-------ILKIPNITKTDRGTYYCVAQNG 257
C A+GFP P ++W++ + + + L + NI KT+ G Y C A NG
Sbjct: 736 CKADGFPKPQVTWKKAVGDTPGEYKDLKKSDNIRVEEGTLHVDNIQKTNEGYYLCEAING 795
Query: 258 VGRGMKRNIAVEVE 271
+G G+ I + V+
Sbjct: 796 IGSGLSAVIMISVQ 809
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 28/130 (21%), Positives = 49/130 (37%), Gaps = 9/130 (6%)
Query: 180 RRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISW-RRDNSAALSTGG--SIYRGNI 236
++ P+ T + S + C A+G P P I W R D +A G I
Sbjct: 36 QKGPVFLKEPTNRIDFSNSTGAEIECKASGNPMPEIIWIRSDGTAVGDVPGLRQISSDGK 95
Query: 237 LKIPNITKTD------RGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYD 290
L P D Y C+A+N G + R++ V A + ++
Sbjct: 96 LVFPPFRAEDYRQEVHAQVYACLARNQFGSIISRDVHVRAVVAQYYEADVNKEHVIRGNS 155
Query: 291 AILECHVEAY 300
A+++C + ++
Sbjct: 156 AVIKCLIPSF 165
>pdb|2OM5|A Chain A, N-Terminal Fragment Of Human Tax1
Length = 381
Score = 67.4 bits (163), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 51/172 (29%), Positives = 76/172 (44%), Gaps = 18/172 (10%)
Query: 198 GQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQNG 257
GQ V L C+A G P P I WR+ + +LS + L+IP+++ D GTY C A+N
Sbjct: 221 GQQVTLECFAFGNPVPRIKWRKVD-GSLSPQWTTAE-PTLQIPSVSFEDEGTYECEAENS 278
Query: 258 VGRGMKRN---IAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAIVWIKDGVQI 314
GR + + + E+ VI+ G L++ C P P + W+++G +
Sbjct: 279 KGRDTVQGRIIVQAQPEWLKVISDTEADIGSNLRWG----CAAAGKPRPTVRWLRNGEPL 334
Query: 315 MNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
+ V A FS SL G Y C A NK+G+ EL
Sbjct: 335 ASQNRVEV--LAGDLRFSKLSL-------EDSGMYQCVAENKHGTIYASAEL 377
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 36/123 (29%), Positives = 53/123 (43%), Gaps = 10/123 (8%)
Query: 141 TSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPP----IISDNSTRSVIVS 196
T+ L I + D G Y+CE S + + + +IV+ P +ISD T + I
Sbjct: 253 TAEPTLQIPSVSFEDEGTYECEAENS-KGRDTVQGRIIVQAQPEWLKVISD--TEADI-- 307
Query: 197 EGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQN 256
G + C A G P PT+ W R+ S L+ ++ D G Y CVA+N
Sbjct: 308 -GSNLRWGCAAAGKPRPTVRWLRNGEPLASQNRVEVLAGDLRFSKLSLEDSGMYQCVAEN 366
Query: 257 GVG 259
G
Sbjct: 367 KHG 369
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 47/190 (24%), Positives = 75/190 (39%), Gaps = 14/190 (7%)
Query: 183 PIISDNSTRSVIVSEGQT---VYLYCYANGFPAPTISWRRDNSAALSTGGSIYR--GNIL 237
P+ D SV+ E T V L C A P T W+ + + GS ++ G L
Sbjct: 4 PVFEDQPL-SVLFPEESTEEQVLLACRARASPPATYRWKMNGTEMKLEPGSRHQLVGGNL 62
Query: 238 KIPNITKT-DRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQ-YDAILEC 295
I N TK D G Y C+A N VG + R + F + +A + + +L C
Sbjct: 63 VIMNPTKAQDAGVYQCLASNPVGTVVSREAILRFGFLQEFSKEERDPVKAHEGWGVMLPC 122
Query: 296 HVEA-YPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAA 354
+ A YP + W+ + + N HF + + +L + G Y+C A
Sbjct: 123 NPPAHYPGLSYRWLLN--EFPNFIPTDGRHFVSQ---TTGNLYIARTNASDLGNYSCLAT 177
Query: 355 NKYGSAQKEI 364
+ + K +
Sbjct: 178 SHMDFSTKSV 187
>pdb|2A38|A Chain A, Crystal Structure Of The N-Terminus Of Titin
pdb|2A38|B Chain B, Crystal Structure Of The N-Terminus Of Titin
pdb|2A38|C Chain C, Crystal Structure Of The N-Terminus Of Titin
Length = 194
Score = 67.0 bits (162), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 56/190 (29%), Positives = 81/190 (42%), Gaps = 23/190 (12%)
Query: 191 RSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGG------SIYRGNI-LKIPNIT 243
+SV+V EG T + +GFP P +SW RD +ST S G L IP +T
Sbjct: 13 QSVVVLEGSTATFEAHISGFPVPEVSWFRDGQ-VISTSTLPGVQISFSDGRAKLTIPAVT 71
Query: 244 KTDRGTYYCVAQNGVGRGMKR-NIAVEVEFAPVITINR-----PRQGQALQYDAILECHV 297
K + G Y A NG G+ + V+ E AP + R RQG ++ L+ V
Sbjct: 72 KANSGRYSLKATNGSGQATSTAELLVKAETAPPNFVQRLQSMTVRQGSQVR----LQVRV 127
Query: 298 EAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKY 357
P P + + +DG +I ++ + +S E SL + G Y+ A N
Sbjct: 128 TGIPTPVVKFYRDGAEIQSSLDFQISQ-----EGDLYSLLIAEAYPEDSGTYSVNATNSV 182
Query: 358 GSAQKEIELF 367
G A EL
Sbjct: 183 GRATSTAELL 192
>pdb|1YA5|A Chain A, Crystal Structure Of The Titin Domains Z1z2 In Complex
With Telethonin
pdb|1YA5|B Chain B, Crystal Structure Of The Titin Domains Z1z2 In Complex
With Telethonin
pdb|2F8V|A Chain A, Structure Of Full Length Telethonin In Complex With The
N-Terminus Of Titin
pdb|2F8V|B Chain B, Structure Of Full Length Telethonin In Complex With The
N-Terminus Of Titin
pdb|2F8V|C Chain C, Structure Of Full Length Telethonin In Complex With The
N-Terminus Of Titin
pdb|2F8V|D Chain D, Structure Of Full Length Telethonin In Complex With The
N-Terminus Of Titin
Length = 201
Score = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 56/190 (29%), Positives = 81/190 (42%), Gaps = 23/190 (12%)
Query: 191 RSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGG------SIYRGNI-LKIPNIT 243
+SV+V EG T + +GFP P +SW RD +ST S G L IP +T
Sbjct: 13 QSVVVLEGSTATFEAHISGFPVPEVSWFRDGQ-VISTSTLPGVQISFSDGRAKLTIPAVT 71
Query: 244 KTDRGTYYCVAQNGVGRGMKR-NIAVEVEFAPVITINR-----PRQGQALQYDAILECHV 297
K + G Y A NG G+ + V+ E AP + R RQG ++ L+ V
Sbjct: 72 KANSGRYSLKATNGSGQATSTAELLVKAETAPPNFVQRLQSMTVRQGSQVR----LQVRV 127
Query: 298 EAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKY 357
P P + + +DG +I ++ + +S E SL + G Y+ A N
Sbjct: 128 TGIPTPVVKFYRDGAEIQSSLDFQISQ-----EGDLYSLLIAEAYPEDSGTYSVNATNSV 182
Query: 358 GSAQKEIELF 367
G A EL
Sbjct: 183 GRATSTAELL 192
>pdb|2VRA|A Chain A, Drosophila Robo Ig1-2 (Monoclinic Form)
pdb|2VRA|B Chain B, Drosophila Robo Ig1-2 (Monoclinic Form)
pdb|2VRA|C Chain C, Drosophila Robo Ig1-2 (Monoclinic Form)
pdb|2VRA|D Chain D, Drosophila Robo Ig1-2 (Monoclinic Form)
Length = 208
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 44/179 (24%), Positives = 80/179 (44%), Gaps = 10/179 (5%)
Query: 193 VIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYR-----GNIL---KIPNITK 244
++V + + L C G P PTI W +D + +R G + + +
Sbjct: 19 LVVKKNEPATLNCKVEGKPEPTIEWFKDGEPVSTNEKKSHRVQFKDGALFFYRTMQGKKE 78
Query: 245 TDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYD-AILECH-VEAYPP 302
D G Y+CVA+N VG+ + R+ ++++ P+ + + + A+LEC + P
Sbjct: 79 QDGGEYWCVAKNRVGQAVSRHASLQIAVLRDDFRVEPKDTRVAKGETALLECGPPKGIPE 138
Query: 303 PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQ 361
P ++WIKDGV + + + S + +L + +E G Y C A N G+ +
Sbjct: 139 PTLIWIKDGVPLDDLKAMSFGASSRVRIVDGGNLLISNVEPIDEGNYKCIAQNLVGTRE 197
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 55/207 (26%), Positives = 85/207 (41%), Gaps = 28/207 (13%)
Query: 66 LASSQRTPTISYISQEQIKDIAQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGS 125
LA ++P I + + + A L C V+ + + W K EP+ + S
Sbjct: 3 LAGQYQSPRIIEHPTDLVVKKNEPATLNCKVEGKPEPTIEWFK-----DGEPVSTNEKKS 57
Query: 126 LIIHDSRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVEL---IVRRP 182
H +F+ + +++ +E D G Y C + VS L ++R
Sbjct: 58 ---HRVQFKDGA----LFFYRTMQGKKEQDGGEYWCVAKNRVGQAVSRHASLQIAVLRDD 110
Query: 183 PIISDNSTRSVIVSEGQTVYLYCYA-NGFPAPTISWRRD-----NSAALSTGGS----IY 232
+ TR V++G+T L C G P PT+ W +D + A+S G S I
Sbjct: 111 FRVEPKDTR---VAKGETALLECGPPKGIPEPTLIWIKDGVPLDDLKAMSFGASSRVRIV 167
Query: 233 RGNILKIPNITKTDRGTYYCVAQNGVG 259
G L I N+ D G Y C+AQN VG
Sbjct: 168 DGGNLLISNVEPIDEGNYKCIAQNLVG 194
>pdb|2VR9|A Chain A, Drosophila Robo Ig1-2 (Tetragonal Form)
pdb|2VR9|B Chain B, Drosophila Robo Ig1-2 (Tetragonal Form)
pdb|2VR9|C Chain C, Drosophila Robo Ig1-2 (Tetragonal Form)
Length = 217
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 44/179 (24%), Positives = 80/179 (44%), Gaps = 10/179 (5%)
Query: 193 VIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYR-----GNIL---KIPNITK 244
++V + + L C G P PTI W +D + +R G + + +
Sbjct: 19 LVVKKNEPATLNCKVEGKPEPTIEWFKDGEPVSTNEKKSHRVQFKDGALFFYRTMQGKKE 78
Query: 245 TDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYD-AILECH-VEAYPP 302
D G Y+CVA+N VG+ + R+ ++++ P+ + + + A+LEC + P
Sbjct: 79 QDGGEYWCVAKNRVGQAVSRHASLQIAVLRDDFRVEPKDTRVAKGETALLECGPPKGIPE 138
Query: 303 PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQ 361
P ++WIKDGV + + + S + +L + +E G Y C A N G+ +
Sbjct: 139 PTLIWIKDGVPLDDLKAMSFGASSRVRIVDGGNLLISNVEPIDEGNYKCIAQNLVGTRE 197
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 55/207 (26%), Positives = 85/207 (41%), Gaps = 28/207 (13%)
Query: 66 LASSQRTPTISYISQEQIKDIAQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGS 125
LA ++P I + + + A L C V+ + + W K EP+ + S
Sbjct: 3 LAGQYQSPRIIEHPTDLVVKKNEPATLNCKVEGKPEPTIEWFK-----DGEPVSTNEKKS 57
Query: 126 LIIHDSRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVEL---IVRRP 182
H +F+ + +++ +E D G Y C + VS L ++R
Sbjct: 58 ---HRVQFKDGA----LFFYRTMQGKKEQDGGEYWCVAKNRVGQAVSRHASLQIAVLRDD 110
Query: 183 PIISDNSTRSVIVSEGQTVYLYCYA-NGFPAPTISWRRD-----NSAALSTGGS----IY 232
+ TR V++G+T L C G P PT+ W +D + A+S G S I
Sbjct: 111 FRVEPKDTR---VAKGETALLECGPPKGIPEPTLIWIKDGVPLDDLKAMSFGASSRVRIV 167
Query: 233 RGNILKIPNITKTDRGTYYCVAQNGVG 259
G L I N+ D G Y C+AQN VG
Sbjct: 168 DGGNLLISNVEPIDEGNYKCIAQNLVG 194
>pdb|2XY1|A Chain A, Crystal Structure Of Ncam2 Ig3-4
Length = 192
Score = 62.8 bits (151), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 49/189 (25%), Positives = 74/189 (39%), Gaps = 6/189 (3%)
Query: 182 PPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGN--ILKI 239
P I + + G+ + C A+G P P ISW R+ I +G+ L +
Sbjct: 3 PAISMPQKSFNATAERGEEMTFSCRASGSPEPAISWFRNGKLIEENEKYILKGSNTELTV 62
Query: 240 PNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEA 299
NI +D G Y C A N G K+ ++V P I I + L C E
Sbjct: 63 RNIINSDGGPYVCRATNKAGEDEKQAF-LQVFVQPHI-IQLKNETTYENGQVTLVCDAEG 120
Query: 300 YPPPAIVWIK--DGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKY 357
P P I W + DG + +SL + ++ G+Y C+AA++
Sbjct: 121 EPIPEITWKRAVDGFTFTEGDKSLDGRIEVKGQHGSSSLHIKDVKLSDSGRYDCEAASRI 180
Query: 358 GSAQKEIEL 366
G QK + L
Sbjct: 181 GGHQKSMYL 189
>pdb|2WIM|A Chain A, Crystal Structure Of Ncam2 Ig1-3
pdb|2WIM|B Chain B, Crystal Structure Of Ncam2 Ig1-3
Length = 291
Score = 62.0 bits (149), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 61/223 (27%), Positives = 93/223 (41%), Gaps = 30/223 (13%)
Query: 155 DAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVI----VSEGQTVYLYCYANGF 210
DAGIY+C+ + A V L I + R V+ +G+ + C +
Sbjct: 71 DAGIYRCQATDAKGQTQEATVVL-----EIYQKLTFREVVSPQEFKQGEDAEVVCRVSSS 125
Query: 211 PAPTISWRRDNSAALSTGG---SIYRGNILKIPNITKTDRGTYYCVAQ-NGVGRGMKRNI 266
PAP +SW N + ++ N L+I NI K+D G Y C + G R+I
Sbjct: 126 PAPAVSWLYHNEEVTTISDNRFAMLANNNLQILNINKSDEGIYRCEGRVEARGEIDFRDI 185
Query: 267 AVEVEFAPVITINR------PRQGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHY 320
V V P I++ + +G+ + + C P PAI W ++G I N+ Y
Sbjct: 186 IVIVNVPPAISMPQKSFNATAERGEEMTFS----CRASGSPEPAISWFRNGKLIEENEKY 241
Query: 321 SVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKE 363
+ S+T L V I G Y C+A NK G +K+
Sbjct: 242 ILKG-------SNTELTVRNIINSDGGPYVCRATNKAGEDEKQ 277
Score = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 35/116 (30%), Positives = 55/116 (47%), Gaps = 4/116 (3%)
Query: 153 ETDAGIYKCEVIISLNNKVS-AEVELIVRRPPIIS-DNSTRSVIVSEGQTVYLYCYANGF 210
++D GIY+CE + ++ ++ +IV PP IS + + G+ + C A+G
Sbjct: 162 KSDEGIYRCEGRVEARGEIDFRDIIVIVNVPPAISMPQKSFNATAERGEEMTFSCRASGS 221
Query: 211 PAPTISWRRDNSAALSTGGSIYRGN--ILKIPNITKTDRGTYYCVAQNGVGRGMKR 264
P P ISW R+ I +G+ L + NI +D G Y C A N G K+
Sbjct: 222 PEPAISWFRNGKLIEENEKYILKGSNTELTVRNIINSDGGPYVCRATNKAGEDEKQ 277
>pdb|2V9Q|A Chain A, First And Second Ig Domains From Human Robo1
pdb|2V9R|A Chain A, First And Second Ig Domains From Human Robo1 (Form 2)
Length = 212
Score = 61.6 bits (148), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 53/203 (26%), Positives = 87/203 (42%), Gaps = 36/203 (17%)
Query: 182 PPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAA------------LSTGG 229
PP I ++ + +IVS+G+ L C A G P PTI W + L G
Sbjct: 9 PPRIVEHPS-DLIVSKGEPATLNCKAEGRPTPTIEWYKGGERVETDKDDPRSHRMLLPSG 67
Query: 230 SIYRGNILKIPNITKT--DRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQ-- 285
S++ L+I + K+ D G Y CVA+N +G + + ++EV I + RQ
Sbjct: 68 SLF---FLRIVHGRKSRPDEGVYVCVARNYLGEAVSHDASLEV----AILRDDFRQNPSD 120
Query: 286 ---ALQYDAILECH-VEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITI 341
A+ A++EC +P P I W KDG ++++ ++ L +
Sbjct: 121 VMVAVGEPAVMECQPPRGHPEPTISWKKDG-SPLDDKDERIT-------IRGGKLMITYT 172
Query: 342 ERRQFGQYACKAANKYGSAQKEI 364
+ G+Y C N G + E+
Sbjct: 173 RKSDAGKYVCVGTNMVGERESEV 195
>pdb|3P3Y|A Chain A, Crystal Structure Of Neurofascin Homophilic Adhesion
Complex In Space Group P6522
pdb|3P40|A Chain A, Crystal Structure Of Neurofascin Adhesion Complex In Space
Group P3221
Length = 404
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 78/172 (45%), Gaps = 16/172 (9%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGN-ILKIPNITKTDRGTY 250
S +V G + L C A+G P P I+W + S N L+I N+++ D G Y
Sbjct: 231 SQMVLRGMDLLLECIASGVPTPDIAWYKKGGDLPSDKAKFENFNKALRITNVSEEDSGEY 290
Query: 251 YCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQG-QALQYDAILECHVEAYPPPAIVWIK 309
+C+A N +G ++ I+V V+ AP ++ P+ A D L C P P + W+
Sbjct: 291 FCLASNKMG-SIRHTISVRVKAAPYW-LDEPKNLILAPGEDGRLVCRANGNPKPTVQWMV 348
Query: 310 DGVQIMN---NQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYG 358
+G + + N + V+ + F DT + + Y C +N++G
Sbjct: 349 NGEPLQSAPPNPNREVA--GDTIIFRDTQISSRAV-------YQCNTSNEHG 391
Score = 54.7 bits (130), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 55/226 (24%), Positives = 90/226 (39%), Gaps = 24/226 (10%)
Query: 157 GIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYAN-GFPAPTI 215
G Y+C +S + L V + P+ + V+V EG + L C G P+P I
Sbjct: 90 GEYQCFARNKFGTALSNRIRLQVSKSPLWPKENLDPVVVQEGAPLTLQCNPPPGLPSPVI 149
Query: 216 SWRRDNSAALSTGGSIYRGN--ILKIPNITKTDRGT-YYCVAQNGVGRGM--KRNIAVEV 270
W + ++ + +G+ L N+ D T Y C A+ + K ++V
Sbjct: 150 FWMSSSMEPITQDKRVSQGHNGDLYFSNVMLQDMQTDYSCNARFHFTHTIQQKNPFTLKV 209
Query: 271 EFAPVITINRPR----QGQALQ------YDAILECHVEAYPPPAIVWIKDGVQIMNNQHY 320
+ P QG A D +LEC P P I W K G + +++
Sbjct: 210 LTTRGVAERTPSFMYPQGTASSQMVLRGMDLLLECIASGVPTPDIAWYKKGGDLPSDK-- 267
Query: 321 SVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
A + F + +LR+ + G+Y C A+NK GS + I +
Sbjct: 268 -----AKFENF-NKALRITNVSEEDSGEYFCLASNKMGSIRHTISV 307
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 47/198 (23%), Positives = 77/198 (38%), Gaps = 46/198 (23%)
Query: 181 RPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIP 240
+PP I+ S + IV + + C A G PAP+ W R++ NI K P
Sbjct: 15 QPPTITKQSAKDHIVDPRDNILIECEAKGNPAPSFHWTRNSRFF----------NIAKDP 64
Query: 241 NITKTDR------------------GTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPR 282
++ R G Y C A+N G + I ++V +P+ P+
Sbjct: 65 RVSMRRRSGTLVIDFRSGGRPEEYEGEYQCFARNKFGTALSNRIRLQVSKSPLW----PK 120
Query: 283 QGQ---ALQYDA--ILECH-VEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSD-EFSDTS 335
+ +Q A L+C+ P P I W+ ++ + Q VS D FS+
Sbjct: 121 ENLDPVVVQEGAPLTLQCNPPPGLPSPVIFWMSSSMEPI-TQDKRVSQGHNGDLYFSNVM 179
Query: 336 LRVITIERRQFGQYACKA 353
L+ + + Y+C A
Sbjct: 180 LQDMQTD------YSCNA 191
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 30/123 (24%), Positives = 51/123 (41%), Gaps = 5/123 (4%)
Query: 140 ETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQ 199
E L I + E D+G Y C + + + + + V+ P D +++I++ G+
Sbjct: 271 ENFNKALRITNVSEEDSGEYFCLASNKMGS-IRHTISVRVKAAPYWLD-EPKNLILAPGE 328
Query: 200 TVYLYCYANGFPAPTISWRRDNSAALSTGGSIYR---GNILKIPNITKTDRGTYYCVAQN 256
L C ANG P PT+ W + S + R G+ + + + R Y C N
Sbjct: 329 DGRLVCRANGNPKPTVQWMVNGEPLQSAPPNPNREVAGDTIIFRDTQISSRAVYQCNTSN 388
Query: 257 GVG 259
G
Sbjct: 389 EHG 391
>pdb|2V5S|A Chain A, Structural Basis For Dscam Isoform Specificity
pdb|2V5S|B Chain B, Structural Basis For Dscam Isoform Specificity
Length = 394
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 60/237 (25%), Positives = 89/237 (37%), Gaps = 33/237 (13%)
Query: 146 LSIKEIQETDA-GIYKCEVIISLNN--KVSAEVELIVRRPPIISDNSTRSVIVSE----- 197
L I+E+ D Y+C L ++SA +V PI S +V +
Sbjct: 172 LHIREVGPEDGYKSYQCRTKHRLTGETRLSATKGRLVITEPISSSAPRTPALVQKPLELM 231
Query: 198 -GQTVYLYCYANGFPAPTISW-------RRDNSAALSTGGSIYRGNILKIPNITKTDRGT 249
T+ L C A GFPAP+ W R + L+ G ++ I + D G
Sbjct: 232 VAHTISLLCPAQGFPAPSFRWYKFIEGTTRKQAVVLNDRVKQVSGTLI-IKDAVVEDSGK 290
Query: 250 YYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAIVWIK 309
Y CV N VG G + V I+ P Q A+ C P + W+K
Sbjct: 291 YLCVVNNSVG-GESVETVLTVTAPLSAKIDPPTQTVDFGRPAVFTCQYTGNPIKTVSWMK 349
Query: 310 DGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
DG I + S++ LR+ ++++ G Y C N SA+ EL
Sbjct: 350 DGKAIGH---------------SESVLRIESVKKEDKGMYQCFVRNDRESAEASAEL 391
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 28/130 (21%), Positives = 49/130 (37%), Gaps = 9/130 (6%)
Query: 180 RRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISW-RRDNSAALSTGG--SIYRGNI 236
++ P+ T + S + C A+G P P I W R D +A G I
Sbjct: 7 QKGPVFLKEPTNRIDFSNSTGAEIECKASGNPMPEIIWIRSDGTAVGDVPGLRQISSDGK 66
Query: 237 LKIPNITKTD------RGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYD 290
L P D Y C+A+N G + R++ V A + ++
Sbjct: 67 LVFPPFRAEDYRQEVHAQVYACLARNQFGSIISRDVHVRAVVAQYYEADVNKEHVIRGNS 126
Query: 291 AILECHVEAY 300
A+++C + ++
Sbjct: 127 AVIKCLIPSF 136
>pdb|2V5M|A Chain A, Structural Basis For Dscam Isoform Specificity
Length = 388
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 60/237 (25%), Positives = 89/237 (37%), Gaps = 33/237 (13%)
Query: 146 LSIKEIQETDA-GIYKCEVIISLNN--KVSAEVELIVRRPPIISDNSTRSVIVSE----- 197
L I+E+ D Y+C L ++SA +V PI S +V +
Sbjct: 166 LHIREVGPEDGYKSYQCRTKHRLTGETRLSATKGRLVITEPISSSAPRTPALVQKPLELM 225
Query: 198 -GQTVYLYCYANGFPAPTISW-------RRDNSAALSTGGSIYRGNILKIPNITKTDRGT 249
T+ L C A GFPAP+ W R + L+ G ++ I + D G
Sbjct: 226 VAHTISLLCPAQGFPAPSFRWYKFIEGTTRKQAVVLNDRVKQVSGTLI-IKDAVVEDSGK 284
Query: 250 YYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAIVWIK 309
Y CV N VG G + V I+ P Q A+ C P + W+K
Sbjct: 285 YLCVVNNSVG-GESVETVLTVTAPLSAKIDPPTQTVDFGRPAVFTCQYTGNPIKTVSWMK 343
Query: 310 DGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
DG I + S++ LR+ ++++ G Y C N SA+ EL
Sbjct: 344 DGKAIGH---------------SESVLRIESVKKEDKGMYQCFVRNDRESAEASAEL 385
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 28/130 (21%), Positives = 49/130 (37%), Gaps = 9/130 (6%)
Query: 180 RRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISW-RRDNSAALSTGG--SIYRGNI 236
++ P+ T + S + C A+G P P I W R D +A G I
Sbjct: 1 QKGPVFLKEPTNRIDFSNSTGAEIECKASGNPMPEIIWIRSDGTAVGDVPGLRQISSDGK 60
Query: 237 LKIPNITKTD------RGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYD 290
L P D Y C+A+N G + R++ V A + ++
Sbjct: 61 LVFPPFRAEDYRQEVHAQVYACLARNQFGSIISRDVHVRAVVAQYYEADVNKEHVIRGNS 120
Query: 291 AILECHVEAY 300
A+++C + ++
Sbjct: 121 AVIKCLIPSF 130
>pdb|2JLL|A Chain A, Crystal Structure Of Ncam2 Igiv-Fn3ii
Length = 389
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 46/182 (25%), Positives = 81/182 (44%), Gaps = 23/182 (12%)
Query: 197 EGQTVYLYCYANGFPAPTISWRRD-NSAALSTGGSIYRGNI----------LKIPNITKT 245
E V L C A G P P I+W+R + + G G I L I ++ +
Sbjct: 14 ENGQVTLVCDAEGEPIPEITWKRAVDGFTFTEGDKSLDGRIEVKGQHGSSSLHIKDVKLS 73
Query: 246 DRGTYYCVAQNGVGRGMKRNIAVEVEFAPVI----TINRPRQGQALQYDAILECHVEAYP 301
D G Y C A + +G G ++++ +++E+AP TI +G + + C V++ P
Sbjct: 74 DSGRYDCEAASRIG-GHQKSMYLDIEYAPKFISNQTIYYSWEGNPIN----ISCDVKSNP 128
Query: 302 PPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQ 361
P +I W +D + + ++ ++T + L + FG+Y C A N G+
Sbjct: 129 PASIHWRRDKLVLPAKNTTNLKTYSTGRKM---ILEIAPTSDNDFGRYNCTATNHIGTRF 185
Query: 362 KE 363
+E
Sbjct: 186 QE 187
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 40/138 (28%), Positives = 62/138 (44%), Gaps = 14/138 (10%)
Query: 130 DSRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNS 189
D R ++ +S+ L IK+++ +D+G Y CE + + I P IS+
Sbjct: 51 DGRIEVKGQHGSSS--LHIKDVKLSDSGRYDCEAASRIGGHQKSMYLDIEYAPKFISN-- 106
Query: 190 TRSVIVS-EGQTVYLYCYANGFPAPTISWRRD-------NSAALSTGGSIYRGNILKIPN 241
+++ S EG + + C P +I WRRD N+ L T S R IL+I
Sbjct: 107 -QTIYYSWEGNPINISCDVKSNPPASIHWRRDKLVLPAKNTTNLKT-YSTGRKMILEIAP 164
Query: 242 ITKTDRGTYYCVAQNGVG 259
+ D G Y C A N +G
Sbjct: 165 TSDNDFGRYNCTATNHIG 182
Score = 36.2 bits (82), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 2/76 (2%)
Query: 293 LECHVEAYPPPAIVWIK--DGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYA 350
L C E P P I W + DG + +SL + ++ G+Y
Sbjct: 20 LVCDAEGEPIPEITWKRAVDGFTFTEGDKSLDGRIEVKGQHGSSSLHIKDVKLSDSGRYD 79
Query: 351 CKAANKYGSAQKEIEL 366
C+AA++ G QK + L
Sbjct: 80 CEAASRIGGHQKSMYL 95
>pdb|2XYC|A Chain A, Crystal Structure Of Ncam2 Igiv-Fn3i
Length = 291
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 46/182 (25%), Positives = 81/182 (44%), Gaps = 23/182 (12%)
Query: 197 EGQTVYLYCYANGFPAPTISWRRD-NSAALSTGGSIYRGNI----------LKIPNITKT 245
E V L C A G P P I+W+R + + G G I L I ++ +
Sbjct: 14 ENGQVTLVCDAEGEPIPEITWKRAVDGFTFTEGDKSLDGRIEVKGQHGSSSLHIKDVKLS 73
Query: 246 DRGTYYCVAQNGVGRGMKRNIAVEVEFAPVI----TINRPRQGQALQYDAILECHVEAYP 301
D G Y C A + +G G ++++ +++E+AP TI +G + + C V++ P
Sbjct: 74 DSGRYDCEAASRIG-GHQKSMYLDIEYAPKFISNQTIYYSWEGNPIN----ISCDVKSNP 128
Query: 302 PPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQ 361
P +I W +D + + ++ ++T + L + FG+Y C A N G+
Sbjct: 129 PASIHWRRDKLVLPAKNTTNLKTYSTGRKM---ILEIAPTSDNDFGRYNCTATNHIGTRF 185
Query: 362 KE 363
+E
Sbjct: 186 QE 187
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 40/138 (28%), Positives = 62/138 (44%), Gaps = 14/138 (10%)
Query: 130 DSRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNS 189
D R ++ +S+ L IK+++ +D+G Y CE + + I P IS+
Sbjct: 51 DGRIEVKGQHGSSS--LHIKDVKLSDSGRYDCEAASRIGGHQKSMYLDIEYAPKFISN-- 106
Query: 190 TRSVIVS-EGQTVYLYCYANGFPAPTISWRRD-------NSAALSTGGSIYRGNILKIPN 241
+++ S EG + + C P +I WRRD N+ L T S R IL+I
Sbjct: 107 -QTIYYSWEGNPINISCDVKSNPPASIHWRRDKLVLPAKNTTNLKT-YSTGRKMILEIAP 164
Query: 242 ITKTDRGTYYCVAQNGVG 259
+ D G Y C A N +G
Sbjct: 165 TSDNDFGRYNCTATNHIG 182
Score = 36.2 bits (82), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 2/76 (2%)
Query: 293 LECHVEAYPPPAIVWIK--DGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYA 350
L C E P P I W + DG + +SL + ++ G+Y
Sbjct: 20 LVCDAEGEPIPEITWKRAVDGFTFTEGDKSLDGRIEVKGQHGSSSLHIKDVKLSDSGRYD 79
Query: 351 CKAANKYGSAQKEIEL 366
C+AA++ G QK + L
Sbjct: 80 CEAASRIGGHQKSMYL 95
>pdb|1BIH|A Chain A, Crystal Structure Of The Insect Immune Protein Hemolin: A
New Domain Arrangement With Implications For Homophilic
Adhesion
pdb|1BIH|B Chain B, Crystal Structure Of The Insect Immune Protein Hemolin: A
New Domain Arrangement With Implications For Homophilic
Adhesion
Length = 395
Score = 59.3 bits (142), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 38/137 (27%), Positives = 58/137 (42%), Gaps = 1/137 (0%)
Query: 123 SGSLIIHDSRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRP 182
+G + + ++T TS L K D G+Y CEV + ++L V
Sbjct: 249 NGKDVNGNPEDRITRHNRTSGKRLLFKTTLPEDEGVYTCEVDNGVGKPQKHSLKLTVVSA 308
Query: 183 PIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNI 242
P + ++V +GQ V + C G PAP + W N+ LS G + + L I +
Sbjct: 309 PKYEQKPEKVIVVKQGQDVTIPCKVTGLPAPNVVWSH-NAKPLSGGRATVTDSGLVIKGV 367
Query: 243 TKTDRGTYYCVAQNGVG 259
D+G Y C A N G
Sbjct: 368 KNGDKGYYGCRATNEHG 384
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 58/257 (22%), Positives = 96/257 (37%), Gaps = 46/257 (17%)
Query: 128 IHDSRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRR-PPIIS 186
+ D ++T P+ + Y + +E + IYK V + N V EV L+ +
Sbjct: 148 VTDFDRRITAGPDGNLYFTIV--TKEDVSDIYKY-VCTAKNAAVDEEVVLVEYEIKGVTK 204
Query: 187 DNS-----------TRSVIVSEGQTVYLYCYANGFPAPTISWRRD------NSAALSTGG 229
DNS ++ ++ G +YC P ++ ++ N T
Sbjct: 205 DNSGYKGEPVPQYVSKDMMAKAGDVTMIYCMYGSNPMGYPNYFKNGKDVNGNPEDRITRH 264
Query: 230 SIYRGNILKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFAP--------VITINRP 281
+ G L D G Y C NGVG+ K ++ + V AP VI +
Sbjct: 265 NRTSGKRLLFKTTLPEDEGVYTCEVDNGVGKPQKHSLKLTVVSAPKYEQKPEKVIVV--- 321
Query: 282 RQGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITI 341
+QGQ D + C V P P +VW H + +D+ L + +
Sbjct: 322 KQGQ----DVTIPCKVTGLPAPNVVW----------SHNAKPLSGGRATVTDSGLVIKGV 367
Query: 342 ERRQFGQYACKAANKYG 358
+ G Y C+A N++G
Sbjct: 368 KNGDKGYYGCRATNEHG 384
>pdb|2YD1|A Chain A, Crystal Structure Of The N-Terminal Ig1-2 Module Of
Drosophila Receptor Protein Tyrosine Phosphatase Dlar
Length = 212
Score = 58.9 bits (141), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 54/196 (27%), Positives = 78/196 (39%), Gaps = 32/196 (16%)
Query: 182 PPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNS---------AALSTGGSIY 232
P II + V V G YC A G P P+I WR++ L G I
Sbjct: 7 PEIIRKPQNQGVRV--GGVASFYCAARGDPPPSIVWRKNGKKVSGTQSRYTVLEQPGGI- 63
Query: 233 RGNILKI-PNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFA-------PVITINRPRQG 284
+IL+I P D Y CVA+NGVG + + + + PVIT +
Sbjct: 64 --SILRIEPVRAGRDDAPYECVAENGVGDAVSADATLTIYEGDKTPAGFPVITQGPGTRV 121
Query: 285 QALQYDAILECHVEAYPPPAIVWIKDGVQI-MNNQHYSVSHFATSDEFSDTSLRVITIER 343
+ + ++ C P P I WIK+ ++ M+N YS D L++
Sbjct: 122 IEVGHTVLMTCKAIGNPTPNIYWIKNQTKVDMSNPRYS---------LKDGFLQIENSRE 172
Query: 344 RQFGQYACKAANKYGS 359
G+Y C A N G+
Sbjct: 173 EDQGKYECVAENSMGT 188
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 34/122 (27%), Positives = 51/122 (41%), Gaps = 18/122 (14%)
Query: 269 EVEFAPVITINRPR-QGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFAT 327
E P I +P+ QG + A C PPP+IVW K+G ++ Q S +
Sbjct: 1 ETGAHPPEIIRKPQNQGVRVGGVASFYCAARGDPPPSIVWRKNGKKVSGTQ----SRYTV 56
Query: 328 SDEFSDTSLRVITIER--RQFGQYACKAANKYG---SAQKEIELFDRETQTGDET---FP 379
++ S+ I R R Y C A N G SA + +++ GD+T FP
Sbjct: 57 LEQPGGISILRIEPVRAGRDDAPYECVAENGVGDAVSADATLTIYE-----GDKTPAGFP 111
Query: 380 IF 381
+
Sbjct: 112 VI 113
>pdb|3PXJ|A Chain A, Tandem Ig Repeats Of Dlar
pdb|3PXJ|B Chain B, Tandem Ig Repeats Of Dlar
pdb|3PXJ|C Chain C, Tandem Ig Repeats Of Dlar
pdb|3PXJ|D Chain D, Tandem Ig Repeats Of Dlar
Length = 210
Score = 58.9 bits (141), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 54/196 (27%), Positives = 78/196 (39%), Gaps = 32/196 (16%)
Query: 182 PPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNS---------AALSTGGSIY 232
P II + V V G YC A G P P+I WR++ L G I
Sbjct: 9 PEIIRKPQNQGVRV--GGVASFYCAARGDPPPSIVWRKNGKKVSGTQSRYTVLEQPGGI- 65
Query: 233 RGNILKI-PNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFA-------PVITINRPRQG 284
+IL+I P D Y CVA+NGVG + + + + PVIT +
Sbjct: 66 --SILRIEPVRAGRDDAPYECVAENGVGDAVSADATLTIYEGDKTPAGFPVITQGPGTRV 123
Query: 285 QALQYDAILECHVEAYPPPAIVWIKDGVQI-MNNQHYSVSHFATSDEFSDTSLRVITIER 343
+ + ++ C P P I WIK+ ++ M+N YS D L++
Sbjct: 124 IEVGHTVLMTCKAIGNPTPNIYWIKNQTKVDMSNPRYS---------LKDGFLQIENSRE 174
Query: 344 RQFGQYACKAANKYGS 359
G+Y C A N G+
Sbjct: 175 EDQGKYECVAENSMGT 190
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 33/117 (28%), Positives = 50/117 (42%), Gaps = 18/117 (15%)
Query: 274 PVITINRPR-QGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFS 332
P I +P+ QG + A C PPP+IVW K+G ++ Q S + ++
Sbjct: 8 PPEIIRKPQNQGVRVGGVASFYCAARGDPPPSIVWRKNGKKVSGTQ----SRYTVLEQPG 63
Query: 333 DTSLRVITIER--RQFGQYACKAANKYG---SAQKEIELFDRETQTGDET---FPIF 381
S+ I R R Y C A N G SA + +++ GD+T FP+
Sbjct: 64 GISILRIEPVRAGRDDAPYECVAENGVGDAVSADATLTIYE-----GDKTPAGFPVI 115
>pdb|3GRW|A Chain A, Fgfr3 In Complex With A Fab
Length = 241
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 51/191 (26%), Positives = 81/191 (42%), Gaps = 18/191 (9%)
Query: 193 VIVSEGQTVYLYCYANGFPAPTISW---RRDNSAALSTGGSIYRGN--ILKIPNITKTDR 247
+ V TV C A G P P+ISW R+ GG R L + ++ +DR
Sbjct: 25 LAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDR 84
Query: 248 GTYYCVAQNGVGRGMKRNIAVEV----EFAPVITINRP-RQGQALQYDAILECHVEAYPP 302
G Y CV +N G +++ ++V P++ P Q L D C V +
Sbjct: 85 GNYTCVVENKFG-SIRQTYTLDVLERSPHRPILQAGLPANQTAVLGSDVEFHCKVYSDAQ 143
Query: 303 PAIVWIK----DGVQIMNNQHYSVS---HFATSDEFSDTSLRVITIERRQFGQYACKAAN 355
P I W+K +G ++ + V+ + + +D LR+ + R G+Y C+A N
Sbjct: 144 PHIQWLKHVEVNGSKVGPDGTPYVTVLKSWISESVEADVRLRLANVSERDGGEYLCRATN 203
Query: 356 KYGSAQKEIEL 366
G A+K L
Sbjct: 204 FIGVAEKAFWL 214
>pdb|2V5T|A Chain A, Crystal Structure Of Ncam2 Ig2-3
Length = 189
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 49/177 (27%), Positives = 76/177 (42%), Gaps = 21/177 (11%)
Query: 197 EGQTVYLYCYANGFPAPTISWRRDNSAALSTGG---SIYRGNILKIPNITKTDRGTYYCV 253
+G+ + C + PAP +SW N + ++ N L+I NI K+D G Y C
Sbjct: 16 QGEDAEVVCRVSSSPAPAVSWLYHNEEVTTISDNRFAMLANNNLQILNINKSDEGIYRCE 75
Query: 254 AQ-NGVGRGMKRNIAVEVEFAPVITINR------PRQGQALQYDAILECHVEAYPPPAIV 306
+ G R+I V V P I++ + +G+ + + C P PAI
Sbjct: 76 GRVEARGEIDFRDIIVIVNVPPAISMPQKSFNATAERGEEMTFS----CRASGSPEPAIS 131
Query: 307 WIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKE 363
W ++G I N+ Y + S+T L V I G Y C+A NK G +K+
Sbjct: 132 WFRNGKLIEENEKYILKG-------SNTELTVRNIINSDGGPYVCRATNKAGEDEKQ 181
Score = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 35/116 (30%), Positives = 55/116 (47%), Gaps = 4/116 (3%)
Query: 153 ETDAGIYKCEVIISLNNKVS-AEVELIVRRPPIIS-DNSTRSVIVSEGQTVYLYCYANGF 210
++D GIY+CE + ++ ++ +IV PP IS + + G+ + C A+G
Sbjct: 66 KSDEGIYRCEGRVEARGEIDFRDIIVIVNVPPAISMPQKSFNATAERGEEMTFSCRASGS 125
Query: 211 PAPTISWRRDNSAALSTGGSIYRGN--ILKIPNITKTDRGTYYCVAQNGVGRGMKR 264
P P ISW R+ I +G+ L + NI +D G Y C A N G K+
Sbjct: 126 PEPAISWFRNGKLIEENEKYILKGSNTELTVRNIINSDGGPYVCRATNKAGEDEKQ 181
>pdb|1IE5|A Chain A, Nmr Structure Of The Third Immunoglobulin Domain From The
Neural Cell Adhesion Molecule
Length = 107
Score = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 47/93 (50%), Gaps = 6/93 (6%)
Query: 174 EVELIVRRPPII-SDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSI- 231
++++IV PP + + ST + + Q+V L C A+GFP PT++W +D
Sbjct: 3 DIQVIVNVPPSVRARQSTMNATANLSQSVTLACDADGFPEPTMTWTKDGEPIEQEDNEEK 62
Query: 232 ----YRGNILKIPNITKTDRGTYYCVAQNGVGR 260
Y G+ L I + K+D Y C+A+N G
Sbjct: 63 YSFNYDGSELIIKKVDKSDEAEYICIAENKAGE 95
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 10/83 (12%)
Query: 287 LQYDAILECHVEAYPPPAIVWIKDGVQIM---NNQHYSVSHFATSDEFSDTSLRVITIER 343
L L C + +P P + W KDG I N + YS + + + L + +++
Sbjct: 27 LSQSVTLACDADGFPEPTMTWTKDGEPIEQEDNEEKYSFN-------YDGSELIIKKVDK 79
Query: 344 RQFGQYACKAANKYGSAQKEIEL 366
+Y C A NK G I L
Sbjct: 80 SDEAEYICIAENKAGEQDATIHL 102
>pdb|3PXH|A Chain A, Tandem Ig Domains Of Tyrosine Phosphatase Lar
Length = 201
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 50/203 (24%), Positives = 82/203 (40%), Gaps = 27/203 (13%)
Query: 68 SSQRTPTISYISQEQIKDIAQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLI 127
S P + ++Q A C + WMK KK
Sbjct: 3 GSDSKPVFVKVPEDQTGLSGGVASFVCQATGEPKPRITWMK--KGKK------------- 47
Query: 128 IHDSRFQLTTDPETSTYILSIKEIQ-ETDAGIYKCEVIISLNN-KVSAEVELIVRRP--- 182
+ RF++ + + +L I+ ++ + D IY+C SL SA++ ++
Sbjct: 48 VSSQRFEVIEFDDGAGSVLRIQPLRVQRDEAIYECTATNSLGEINTSAKLSVLEEDQLPS 107
Query: 183 --PIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRD----NSAALSTGGSIYRGNI 236
P I D + +V +G+T + C A G P P ISW +D + AA + R
Sbjct: 108 GFPTI-DMGPQLKVVEKGRTATMLCAAGGNPDPEISWFKDFLPVDPAASNGRIKQLRSGA 166
Query: 237 LKIPNITKTDRGTYYCVAQNGVG 259
L+I + ++D+G Y CVA N G
Sbjct: 167 LQIESSEESDQGKYECVATNSAG 189
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 39/174 (22%), Positives = 63/174 (36%), Gaps = 17/174 (9%)
Query: 198 GQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYR-----GNILKI-PNITKTDRGTYY 251
G C A G P P I+W + S + G++L+I P + D Y
Sbjct: 22 GGVASFVCQATGEPKPRITWMKKGKKVSSQRFEVIEFDDGAGSVLRIQPLRVQRDEAIYE 81
Query: 252 CVAQNGVGR---GMKRNIAVEVEFA---PVITINRPRQGQALQYDAILECHVEAYPPPAI 305
C A N +G K ++ E + P I + + A + C P P I
Sbjct: 82 CTATNSLGEINTSAKLSVLEEDQLPSGFPTIDMGPQLKVVEKGRTATMLCAAGGNPDPEI 141
Query: 306 VWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGS 359
W KD + + + + +L++ + E G+Y C A N G+
Sbjct: 142 SWFKDFLPV-----DPAASNGRIKQLRSGALQIESSEESDQGKYECVATNSAGT 190
Score = 32.0 bits (71), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 46/108 (42%), Gaps = 16/108 (14%)
Query: 73 PTISYISQEQIKDIAQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSR 132
PTI Q ++ + +TA + C+ D + W K + LP+ + S + R
Sbjct: 110 PTIDMGPQLKVVEKGRTATMLCAAGGNPDPEISWFK-------DFLPVDPAAS----NGR 158
Query: 133 FQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVR 180
+ + + L I+ +E+D G Y+C S + SA L VR
Sbjct: 159 IK-----QLRSGALQIESSEESDQGKYECVATNSAGTRYSAPANLYVR 201
>pdb|2V5R|A Chain A, Structural Basis For Dscam Isoform Specificity
pdb|2V5R|B Chain B, Structural Basis For Dscam Isoform Specificity
Length = 391
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 45/193 (23%), Positives = 71/193 (36%), Gaps = 24/193 (12%)
Query: 181 RPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISW-------RRDNSAALSTGGSIYR 233
RP + + + + V + L C A +P P+ W R + L+
Sbjct: 213 RPKVNPQDKHQFIDVELASSYSLLCMAQSYPTPSFRWYKFIEGTTRKQAVVLNDRVKQVS 272
Query: 234 GNILKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAIL 293
G ++ I + D G Y CV N VG G + V I+ P Q A+
Sbjct: 273 GTLI-IKDAVVEDSGKYLCVVNNSVG-GESVETVLTVTAPLSAKIDPPTQTVDFGRPAVF 330
Query: 294 ECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKA 353
C P + W+KDG I + S++ LR+ ++++ G Y C
Sbjct: 331 TCQYTGNPIKTVSWMKDGKAIGH---------------SESVLRIESVKKEDKGMYQCFV 375
Query: 354 ANKYGSAQKEIEL 366
N SA+ EL
Sbjct: 376 RNDRESAEASAEL 388
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 33/113 (29%), Positives = 51/113 (45%), Gaps = 12/113 (10%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNNKVSAE-VELIVR-RPPIISDNSTRSVIVSEGQTVYL 203
L IK+ D+G Y C V NN V E VE ++ P+ + + V G+
Sbjct: 275 LIIKDAVVEDSGKYLCVV----NNSVGGESVETVLTVTAPLSAKIDPPTQTVDFGRPAVF 330
Query: 204 YCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQN 256
C G P T+SW +D A + ++L+I ++ K D+G Y C +N
Sbjct: 331 TCQYTGNPIKTVSWMKDGKAIG------HSESVLRIESVKKEDKGMYQCFVRN 377
Score = 28.1 bits (61), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 37/98 (37%), Gaps = 9/98 (9%)
Query: 180 RRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISW-RRDNSAALSTGG--SIYRGNI 236
++ P+ T + S + C A+G P P I W R D +A G I
Sbjct: 1 QKGPVFLKEPTNRIDFSNSTGAEIECKASGNPMPEIIWIRSDGTAVGDVPGLRQISSDGK 60
Query: 237 LKIPNITKTD------RGTYYCVAQNGVGRGMKRNIAV 268
L P D Y C+A+N G + R++ V
Sbjct: 61 LVFPPFRAEDYRQEVHAQVYACLARNQFGSIISRDVHV 98
>pdb|1E07|A Chain A, Model Of Human Carcinoembryonic Antigen By Homology
Modelling And Curve-Fitting To Experimental Solution
Scattering Data
Length = 642
Score = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 55/221 (24%), Positives = 79/221 (35%), Gaps = 34/221 (15%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVR---------RPPIISDNSTRSVIVS 196
L I I E ++G+Y C+ NN S V+ +P I S+NS V
Sbjct: 428 LFISNITEKNSGLYTCQA----NNSASGHSRTTVKTITVSAELPKPSISSNNSKP---VE 480
Query: 197 EGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGN-ILKIPNITKTDRGTYYCVAQ 255
+ V C + W S +S + GN L + N+T+ D Y C Q
Sbjct: 481 DKDAVAFTCEPEAQNTTYLWWVNGQSLPVSPRLQLSNGNRTLTLFNVTRNDARAYVCGIQ 540
Query: 256 NGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI-LECHVEAYPPPAIVWIKDGVQI 314
N V + ++V + P I P L + L CH + P P W +G+
Sbjct: 541 NSVSANRSDPVTLDVLYGPDTPIISPPDSSYLSGANLNLSCHSASNPSPQYSWRINGIP- 599
Query: 315 MNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAAN 355
QH V L + I G YAC +N
Sbjct: 600 --QQHTQV-------------LFIAKITPNNNGTYACFVSN 625
Score = 51.6 bits (122), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 74/290 (25%), Positives = 112/290 (38%), Gaps = 44/290 (15%)
Query: 73 PTISYISQEQIKDIAQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSR 132
P+IS + + ++D A C + D + W+ + LP+S R
Sbjct: 113 PSISSNNSKPVEDKDAVA-FTCEPETQDATYLWWVNNQS------LPVS---------PR 156
Query: 133 FQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRS 192
QL+ T L++ + D YKCE ++ + S V L V P S +
Sbjct: 157 LQLSNGNRT----LTLFNVTRNDTASYKCETQNPVSARRSDSVILNVLYGPDAPTISPLN 212
Query: 193 VIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYC 252
G+ + L C+A P SW + + ST L IPNIT + G+Y C
Sbjct: 213 TSYRSGENLNLSCHAASNPPAQYSWFVNGTFQQSTQE-------LFIPNITVNNSGSYTC 265
Query: 253 VAQN---GVGRGMKRNIAVEVE-FAPVITINRPRQGQALQYDAI-LECHVEAYPPPAIVW 307
A N G+ R I V E P IT N DA+ L C E + W
Sbjct: 266 QAHNSDTGLNRTTVTTITVYAEPPKPFITSN--NSNPVEDEDAVALTCEPEIQNTTYLWW 323
Query: 308 IKDGVQIMNNQHYSVS-HFATSDEFSDTSLRVITIERRQFGQYACKAANK 356
+ NNQ VS S++ + +L ++++ R G Y C N+
Sbjct: 324 V-------NNQSLPVSPRLQLSND--NRTLTLLSVTRNDVGPYECGIQNE 364
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 61/243 (25%), Positives = 88/243 (36%), Gaps = 28/243 (11%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTR 191
R QL+ D T L++ + D G Y+C + L+ S V L V P S
Sbjct: 334 RLQLSNDNRT----LTLLSVTRNDVGPYECGIQNELSVDHSDPVILNVLYGPDDPTISPS 389
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYY 251
G + L C+A P SW D + T L I NIT+ + G Y
Sbjct: 390 YTYYRPGVNLSLSCHAASNPPAQYSWLIDGNIQQHTQE-------LFISNITEKNSGLYT 442
Query: 252 CVAQN---GVGRGMKRNIAVEVEF-APVITINRPRQGQALQYDAI-LECHVEAYPPPAIV 306
C A N G R + I V E P I+ N + + DA+ C EA +
Sbjct: 443 CQANNSASGHSRTTVKTITVSAELPKPSISSNNSKPVE--DKDAVAFTCEPEAQNTTYLW 500
Query: 307 WIKDGVQIMNNQHYSVS-HFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIE 365
W+ N Q VS S+ + +L + + R Y C N + + +
Sbjct: 501 WV-------NGQSLPVSPRLQLSN--GNRTLTLFNVTRNDARAYVCGIQNSVSANRSDPV 551
Query: 366 LFD 368
D
Sbjct: 552 TLD 554
>pdb|3V2A|R Chain R, Vegfr-2VEGF-A Complex Structure
Length = 772
Score = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 54/238 (22%), Positives = 96/238 (40%), Gaps = 43/238 (18%)
Query: 156 AGIYKCEVIISLNNKVSAEVELI---VRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPA 212
+ +YKCE + NKV +I V R P I+ + +E ++V L+C A+
Sbjct: 525 SALYKCEAV----NKVGRGERVISFHVTRGPEITLQP--DMQPTEQESVSLWCTADRSTF 578
Query: 213 PTISWRRDNSAAL------------STGGSIYRGN------------ILKIPNITKTDRG 248
++W + L ++++ N I+++ N + D+G
Sbjct: 579 ENLTWYKLGPQPLPIHVGELPTPVCKNLDTLWKLNATMFSNSTNDILIMELKNASLQDQG 638
Query: 249 TYYCVAQNGVGRGMK---RNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAI 305
Y C+AQ+ + R + V AP IT N Q ++ + C PPP I
Sbjct: 639 DYVCLAQDRKTKKRHCVVRQLTVLERVAPTITGNLENQTTSIGESIEVSCTASGNPPPQI 698
Query: 306 VWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKE 363
+W KD ++ + S D + ++R + + G Y C+A + G A+ E
Sbjct: 699 MWFKDNETLVED-----SGIVLKDGNRNLTIR--RVRKEDEGLYTCQACSVLGCAKVE 749
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 43/189 (22%), Positives = 82/189 (43%), Gaps = 18/189 (9%)
Query: 126 LIIHDSRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPII 185
L+ D + Q ++ + L+I + +D G+Y C L K ++ + +P +
Sbjct: 272 LVNRDLKTQSGSEMKKFLSTLTIDGVTRSDQGLYTCAASSGLMTKKNSTFVRVHEKPFVA 331
Query: 186 SDNSTRSVI-VSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITK 244
+ S++ + G+ V + G+P P I W + N L + +I G++L I +++
Sbjct: 332 FGSGMESLVEATVGERVRIPAKYLGYPPPEIKWYK-NGIPLESNHTIKAGHVLTIMEVSE 390
Query: 245 TDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQ--------ALQYDA--ILE 294
D G Y + N + + + ++ V + P P+ G+ + QY L
Sbjct: 391 RDTGNYTVILTNPISKEKQSHVVSLVVYVP------PQIGEKSLISPVDSYQYGTTQTLT 444
Query: 295 CHVEAYPPP 303
C V A PPP
Sbjct: 445 CTVYAIPPP 453
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 47/186 (25%), Positives = 80/186 (43%), Gaps = 20/186 (10%)
Query: 88 QTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLII-----HDSRFQLT----TD 138
++ L C+ + + W K+ +PLPI + G L D+ ++L ++
Sbjct: 565 ESVSLWCTADRSTFENLTWYKLGP----QPLPIHV-GELPTPVCKNLDTLWKLNATMFSN 619
Query: 139 PETSTYILSIKEIQETDAGIYKCEVIISLNNK---VSAEVELIVRRPPIISDNSTRSVIV 195
I+ +K D G Y C K V ++ ++ R P I+ N +
Sbjct: 620 STNDILIMELKNASLQDQGDYVCLAQDRKTKKRHCVVRQLTVLERVAPTITGN-LENQTT 678
Query: 196 SEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYR-GNI-LKIPNITKTDRGTYYCV 253
S G+++ + C A+G P P I W +DN + G + + GN L I + K D G Y C
Sbjct: 679 SIGESIEVSCTASGNPPPQIMWFKDNETLVEDSGIVLKDGNRNLTIRRVRKEDEGLYTCQ 738
Query: 254 AQNGVG 259
A + +G
Sbjct: 739 ACSVLG 744
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 29/103 (28%), Positives = 44/103 (42%), Gaps = 10/103 (9%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECH 296
L I +T++D+G Y C A +G+ K + V V P + G +A +
Sbjct: 292 LTIDGVTRSDQGLYTCAASSGL-MTKKNSTFVRVHEKPFVAFG---SGMESLVEATVGER 347
Query: 297 VE------AYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSD 333
V YPPP I W K+G+ + +N H T E S+
Sbjct: 348 VRIPAKYLGYPPPEIKWYKNGIPLESNHTIKAGHVLTIMEVSE 390
>pdb|1TLK|A Chain A, X-Ray Structure Determination Of Telokin, The C-Terminal
Domain Of Myosin Light Chain Kinase, At 2.8 Angstroms
Resolution
Length = 154
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 41/85 (48%), Gaps = 8/85 (9%)
Query: 283 QGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIE 342
+G A ++D C VE YP P ++W KD + ++H+ + + DE + SL + +
Sbjct: 55 EGSAARFD----CKVEGYPDPEVMWFKDDNPVKESRHFQIDY----DEEGNCSLTISEVC 106
Query: 343 RRQFGQYACKAANKYGSAQKEIELF 367
+Y CKA N G A EL
Sbjct: 107 GDDDAKYTCKAVNSLGEATCTAELL 131
Score = 35.0 bits (79), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 29/103 (28%), Positives = 41/103 (39%), Gaps = 11/103 (10%)
Query: 169 NKVSAE---VELIVRRPPIISDNSTRSVI---VSEGQTVYLYCYANGFPAPTISW-RRDN 221
NKV E +E + P + T++++ V EG C G+P P + W + DN
Sbjct: 21 NKVENEDAFLEEVAEEKPHVKPYFTKTILDMDVVEGSAARFDCKVEGYPDPEVMWFKDDN 80
Query: 222 SAALSTGGSI---YRGNI-LKIPNITKTDRGTYYCVAQNGVGR 260
S I GN L I + D Y C A N +G
Sbjct: 81 PVKESRHFQIDYDEEGNCSLTISEVCGDDDAKYTCKAVNSLGE 123
>pdb|2NZI|A Chain A, Crystal Structure Of Domains A168-A170 From Titin
pdb|2NZI|B Chain B, Crystal Structure Of Domains A168-A170 From Titin
Length = 305
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 49/177 (27%), Positives = 74/177 (41%), Gaps = 20/177 (11%)
Query: 203 LYCYANGFPAPTISWRRDNSAALSTGGSI----YRGNI--LKIPNITKTDRGTYYCVAQN 256
L C G P P + W R ++ G ++G L I ++T D T Y V
Sbjct: 24 LVCKVTGHPKPIVKWYRQGKEIIADGLKYRIQEFKGGYHQLIIASVTDDD-ATVYQVRAT 82
Query: 257 GVGRGMKRNIAVEVEFAPVITINRPRQG----QALQYDAI-LECHVEAYPPPAIVWIKDG 311
G + ++EVE I + + +G AL+ + + ++ P P I W K
Sbjct: 83 NQGGSVSGTASLEVEVPAKIHLPKTLEGMGAVHALRGEVVSIKIPFSGKPDPVITWQKGQ 142
Query: 312 VQIMNNQHYSV--SHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
I NN HY V + TS F + +ER+ G Y A N++G QK +EL
Sbjct: 143 DLIDNNGHYQVIVTRSFTSLVFPNG------VERKDAGFYVVCAKNRFGIDQKTVEL 193
>pdb|1FHG|A Chain A, High Resolution Refinement Of Telokin
Length = 154
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 41/85 (48%), Gaps = 8/85 (9%)
Query: 283 QGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIE 342
+G A ++D C VE YP P ++W KD + ++H+ + + DE + SL + +
Sbjct: 55 EGSAARFD----CKVEGYPDPEVMWFKDDNPVKESRHFQIDY----DEEGNCSLTISEVC 106
Query: 343 RRQFGQYACKAANKYGSAQKEIELF 367
+Y CKA N G A EL
Sbjct: 107 GDDDAKYTCKAVNSLGEATCTAELL 131
Score = 35.0 bits (79), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 29/103 (28%), Positives = 41/103 (39%), Gaps = 11/103 (10%)
Query: 169 NKVSAE---VELIVRRPPIISDNSTRSVI---VSEGQTVYLYCYANGFPAPTISW-RRDN 221
NKV E +E + P + T++++ V EG C G+P P + W + DN
Sbjct: 21 NKVENEDAFLEEVAEEKPHVKPYFTKTILDMEVVEGSAARFDCKVEGYPDPEVMWFKDDN 80
Query: 222 SAALSTGGSI---YRGNI-LKIPNITKTDRGTYYCVAQNGVGR 260
S I GN L I + D Y C A N +G
Sbjct: 81 PVKESRHFQIDYDEEGNCSLTISEVCGDDDAKYTCKAVNSLGE 123
>pdb|2ILL|A Chain A, Anomalous Substructure Of Titin-A168169
Length = 195
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 49/177 (27%), Positives = 74/177 (41%), Gaps = 20/177 (11%)
Query: 203 LYCYANGFPAPTISWRRDNSAALSTGGSI----YRGNI--LKIPNITKTDRGTYYCVAQN 256
L C G P P + W R ++ G ++G L I ++T D T Y V
Sbjct: 22 LVCKVTGHPKPIVKWYRQGKEIIADGLKYRIQEFKGGYHQLIIASVTDDD-ATVYQVRAT 80
Query: 257 GVGRGMKRNIAVEVEFAPVITINRPRQG----QALQYDAI-LECHVEAYPPPAIVWIKDG 311
G + ++EVE I + + +G AL+ + + ++ P P I W K
Sbjct: 81 NQGGSVSGTASLEVEVPAKIHLPKTLEGMGAVHALRGEVVSIKIPFSGKPDPVITWQKGQ 140
Query: 312 VQIMNNQHYSV--SHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
I NN HY V + TS F + +ER+ G Y A N++G QK +EL
Sbjct: 141 DLIDNNGHYQVIVTRSFTSLVFPNG------VERKDAGFYVVCAKNRFGIDQKTVEL 191
>pdb|3V6B|R Chain R, Vegfr-2VEGF-E Complex Structure
Length = 424
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 43/189 (22%), Positives = 82/189 (43%), Gaps = 18/189 (9%)
Query: 126 LIIHDSRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPII 185
L+ D + Q ++ + L+I + +D G+Y C L K ++ + +P +
Sbjct: 142 LVNRDLKTQSGSEMKKFLSTLTIDGVTRSDQGLYTCAASSGLMTKKNSTFVRVHEKPFVA 201
Query: 186 SDNSTRSVI-VSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITK 244
+ S++ + G+ V + G+P P I W + N L + +I G++L I +++
Sbjct: 202 FGSGMESLVEATVGERVRIPAKYLGYPPPEIKWYK-NGIPLESNHTIKAGHVLTIMEVSE 260
Query: 245 TDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQ--------ALQYDA--ILE 294
D G Y + N + + + ++ V + P P+ G+ + QY L
Sbjct: 261 RDTGNYTVILTNPISKEKQSHVVSLVVYVP------PQIGEKSLISPVDSYQYGTTQTLT 314
Query: 295 CHVEAYPPP 303
C V A PPP
Sbjct: 315 CTVYAIPPP 323
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 29/103 (28%), Positives = 44/103 (42%), Gaps = 10/103 (9%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECH 296
L I +T++D+G Y C A +G+ K + V V P + G +A +
Sbjct: 162 LTIDGVTRSDQGLYTCAASSGL-MTKKNSTFVRVHEKPFVAFG---SGMESLVEATVGER 217
Query: 297 VE------AYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSD 333
V YPPP I W K+G+ + +N H T E S+
Sbjct: 218 VRIPAKYLGYPPPEIKWYKNGIPLESNHTIKAGHVLTIMEVSE 260
>pdb|1RY7|B Chain B, Crystal Structure Of The 3 Ig Form Of Fgfr3c In Complex
With Fgf1
Length = 334
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 49/184 (26%), Positives = 77/184 (41%), Gaps = 19/184 (10%)
Query: 193 VIVSEGQTVYLYCYANGFPAPTISW---RRDNSAALSTGGSIYRGN--ILKIPNITKTDR 247
+ V TV C A G P P+ISW R+ GG R L + ++ +DR
Sbjct: 133 LAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDR 192
Query: 248 GTYYCVAQNGVGRGMKRNIAVEV----EFAPVITINRP-RQGQALQYDAILECHVEAYPP 302
G Y CV +N G +++ ++V P++ P Q L D C V +
Sbjct: 193 GNYTCVVENKFG-SIRQTYTLDVLERSPHRPILQAGLPANQTAVLGSDVEFHCKVYSDAQ 251
Query: 303 PAIVWIK----DGVQIMNNQHYSVSHFATSD-EFSDTSLRVITIERRQF---GQYACKAA 354
P I W+K +G ++ + V+ T+ +D L V+++ F G+Y C A
Sbjct: 252 PHIQWLKHVEVNGSKVGPDGTPYVTVLKTAGANTTDKELEVLSLHNVTFEDAGEYTCLAG 311
Query: 355 NKYG 358
N G
Sbjct: 312 NSIG 315
Score = 31.2 bits (69), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 29/136 (21%), Positives = 53/136 (38%), Gaps = 20/136 (14%)
Query: 144 YILSIKEIQETDAGIYKCEVIISLNN-KVSAEVELIVRRP--PIISDNSTRSVIVSEGQT 200
+ L ++ + +D G Y C V + + + ++++ R P PI+ + G
Sbjct: 180 WSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDVLERSPHRPILQAGLPANQTAVLGSD 239
Query: 201 VYLYCYANGFPAPTISWRRD---NSAALSTGGSIY--------------RGNILKIPNIT 243
V +C P I W + N + + G+ Y +L + N+T
Sbjct: 240 VEFHCKVYSDAQPHIQWLKHVEVNGSKVGPDGTPYVTVLKTAGANTTDKELEVLSLHNVT 299
Query: 244 KTDRGTYYCVAQNGVG 259
D G Y C+A N +G
Sbjct: 300 FEDAGEYTCLAGNSIG 315
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 4/74 (5%)
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACK 352
C P P+I W+K+G + +H ++S V+ +R G Y C
Sbjct: 143 FRCPAAGNPTPSISWLKNGRE-FRGEHRIGGIKLRHQQWSLVMESVVPSDR---GNYTCV 198
Query: 353 AANKYGSAQKEIEL 366
NK+GS ++ L
Sbjct: 199 VENKFGSIRQTYTL 212
>pdb|2J8H|A Chain A, Structure Of The Immunoglobulin Tandem Repeat A168-A169 Of
Titin
pdb|2J8O|A Chain A, Structure Of The Immunoglobulin Tandem Repeat Of Titin
A168- A169
pdb|2J8O|B Chain B, Structure Of The Immunoglobulin Tandem Repeat Of Titin
A168- A169
Length = 197
Score = 51.2 bits (121), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 49/177 (27%), Positives = 74/177 (41%), Gaps = 20/177 (11%)
Query: 203 LYCYANGFPAPTISWRRDNSAALSTGGSI----YRGNI--LKIPNITKTDRGTYYCVAQN 256
L C G P P + W R ++ G ++G L I ++T D T Y V
Sbjct: 24 LVCKVTGHPKPIVKWYRQGKEIIADGLKYRIQEFKGGYHQLIIASVTDDD-ATVYQVRAT 82
Query: 257 GVGRGMKRNIAVEVEFAPVITINRPRQG----QALQYDAI-LECHVEAYPPPAIVWIKDG 311
G + ++EVE I + + +G AL+ + + ++ P P I W K
Sbjct: 83 NQGGSVSGTASLEVEVPAKIHLPKTLEGMGAVHALRGEVVSIKIPFSGKPDPVITWQKGQ 142
Query: 312 VQIMNNQHYSV--SHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
I NN HY V + TS F + +ER+ G Y A N++G QK +EL
Sbjct: 143 DLIDNNGHYQVIVTRSFTSLVFPNG------VERKDAGFYVVCAKNRFGIDQKTVEL 193
>pdb|2YD5|A Chain A, Crystal Structure Of The N-Terminal Ig1-2 Module Of Human
Receptor Protein Tyrosine Phosphatase Lar
pdb|2YD8|A Chain A, Crystal Structure Of The N-Terminal Ig1-2 Module Of Human
Receptor Protein Tyrosine Phosphatase Lar In Complex
With Sucrose Octasulphate
Length = 214
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 40/142 (28%), Positives = 66/142 (46%), Gaps = 10/142 (7%)
Query: 128 IHDSRFQLTTDPETSTYILSIKEIQ-ETDAGIYKCEVIISLNN-KVSAEVELIVRR--PP 183
+ RF++ + + +L I+ ++ + D IY+C SL SA++ ++ PP
Sbjct: 47 VSSQRFEVIEFDDGAGSVLRIQPLRVQRDEAIYECTATNSLGEINTSAKLSVLEEEQLPP 106
Query: 184 IIS--DNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRD---NSAALSTGG-SIYRGNIL 237
D + +V + +T + C A G P P ISW +D A S G R L
Sbjct: 107 GFPSIDMGPQLKVVEKARTATMLCAAGGNPDPEISWFKDFLPVDPATSNGRIKQLRSGAL 166
Query: 238 KIPNITKTDRGTYYCVAQNGVG 259
+I + ++D+G Y CVA N G
Sbjct: 167 QIESSEESDQGKYECVATNSAG 188
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 43/178 (24%), Positives = 70/178 (39%), Gaps = 25/178 (14%)
Query: 198 GQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYR-----GNILKI-PNITKTDRGTYY 251
G C A G P P I+W + S + G++L+I P + D Y
Sbjct: 21 GGVASFVCQATGEPKPRITWMKKGKKVSSQRFEVIEFDDGAGSVLRIQPLRVQRDEAIYE 80
Query: 252 CVAQNGVGR---GMKRNIAVEVEFAPVI-TINRPRQGQALQ--YDAILECHVEAYPPPAI 305
C A N +G K ++ E + P +I+ Q + ++ A + C P P I
Sbjct: 81 CTATNSLGEINTSAKLSVLEEEQLPPGFPSIDMGPQLKVVEKARTATMLCAAGGNPDPEI 140
Query: 306 VWIKDGVQIMNNQHYSVSHFATSD----EFSDTSLRVITIERRQFGQYACKAANKYGS 359
W KD + + ATS+ + +L++ + E G+Y C A N G+
Sbjct: 141 SWFKDFLPV---------DPATSNGRIKQLRSGALQIESSEESDQGKYECVATNSAGT 189
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 5/86 (5%)
Query: 295 CHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIE-RRQFGQYACKA 353
C P P I W+K G ++ ++Q + V F D+ + + LR+ + +R Y C A
Sbjct: 28 CQATGEPKPRITWMKKGKKV-SSQRFEVIEF---DDGAGSVLRIQPLRVQRDEAIYECTA 83
Query: 354 ANKYGSAQKEIELFDRETQTGDETFP 379
N G +L E + FP
Sbjct: 84 TNSLGEINTSAKLSVLEEEQLPPGFP 109
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 47/108 (43%), Gaps = 16/108 (14%)
Query: 73 PTISYISQEQIKDIAQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSR 132
P+I Q ++ + A+TA + C+ D + W K + LP+ + S + R
Sbjct: 109 PSIDMGPQLKVVEKARTATMLCAAGGNPDPEISWFK-------DFLPVDPATS----NGR 157
Query: 133 FQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVR 180
+ + + L I+ +E+D G Y+C S + SA L VR
Sbjct: 158 IK-----QLRSGALQIESSEESDQGKYECVATNSAGTRYSAPANLYVR 200
>pdb|2YD4|A Chain A, Crystal Structure Of The N-Terminal Ig1-2 Module Of
Chicken Receptor Protein Tyrosine Phosphatase Sigma
Length = 210
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 41/143 (28%), Positives = 69/143 (48%), Gaps = 12/143 (8%)
Query: 128 IHDSRFQLTTDPETSTYILSIKEIQ-ETDAGIYKCEVIISLNNKVSAEVELIVRR----P 182
++ RF+ E++ +L I+ ++ D IY+C V + + +V+ +L V R P
Sbjct: 47 VNSQRFETIEFDESAGAVLRIQPLRTPRDENIYEC-VAQNPHGEVTVHAKLTVLREDQLP 105
Query: 183 PIIS--DNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRD--NSAALSTGGSI--YRGNI 236
P D + +V +T + C A+G P P I+W +D ++ G I R
Sbjct: 106 PGFPNIDMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDPSTSNGRIKQLRSGG 165
Query: 237 LKIPNITKTDRGTYYCVAQNGVG 259
L+I + +TD+G Y CVA N G
Sbjct: 166 LQIESSEETDQGKYECVASNSAG 188
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 49/193 (25%), Positives = 75/193 (38%), Gaps = 26/193 (13%)
Query: 182 PPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRD----NSAALST------GGSI 231
PP+ + VS G ++ C A G P P ++W + NS T G++
Sbjct: 6 PPVFIKKPVDQIGVSGGVASFV-CQATGDPKPRVTWNKKGKKVNSQRFETIEFDESAGAV 64
Query: 232 YRGNILKIPNITKTDRGTYYCVAQNGVGR---GMKRNIAVEVEFAPVI-TINRPRQGQAL 287
R L+ P D Y CVAQN G K + E + P I+ Q + +
Sbjct: 65 LRIQPLRTPR----DENIYECVAQNPHGEVTVHAKLTVLREDQLPPGFPNIDMGPQLKVV 120
Query: 288 Q--YDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQ 345
+ A + C P P I W KD + + S S+ + L++ + E
Sbjct: 121 ERTRTATMLCAASGNPDPEITWFKDFLPV----DPSTSN-GRIKQLRSGGLQIESSEETD 175
Query: 346 FGQYACKAANKYG 358
G+Y C A+N G
Sbjct: 176 QGKYECVASNSAG 188
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 45/108 (41%), Gaps = 16/108 (14%)
Query: 73 PTISYISQEQIKDIAQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSR 132
P I Q ++ + +TA + C+ D + W K + LP+ S S + R
Sbjct: 109 PNIDMGPQLKVVERTRTATMLCAASGNPDPEITWFK-------DFLPVDPSTS----NGR 157
Query: 133 FQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVR 180
+ + + L I+ +ETD G Y+C S + S+ L VR
Sbjct: 158 IK-----QLRSGGLQIESSEETDQGKYECVASNSAGVRYSSPANLYVR 200
>pdb|3S97|C Chain C, Ptprz Cntn1 Complex
pdb|3S97|D Chain D, Ptprz Cntn1 Complex
Length = 201
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 38/123 (30%), Positives = 54/123 (43%), Gaps = 8/123 (6%)
Query: 146 LSIKEIQETDAGIYKCEVI-ISLNNKVSAEVELIVRRPPIISDNSTRSVIVS-------E 197
L I ++ +D G Y C V S+ V ++ ++ P + ++V
Sbjct: 68 LYIANVEASDKGNYSCFVSSPSITKSVFSKFIPLIPIPERTTKPYPADIVVQFKDVYALM 127
Query: 198 GQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQNG 257
GQ V L C+A G P P I WR+ ST G +LKI NI D G Y C A+N
Sbjct: 128 GQNVTLECFALGNPVPDIRWRKVLEPMPSTAEISTSGAVLKIFNIQLEDEGIYECEAENI 187
Query: 258 VGR 260
G+
Sbjct: 188 RGK 190
>pdb|2WV3|A Chain A, Neuroplastin-55 Binds To And Signals Through The
Fibroblast Growth Factor Receptor
Length = 190
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 33/116 (28%), Positives = 52/116 (44%), Gaps = 3/116 (2%)
Query: 246 DRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAI 305
D G Y+CV K N +EV+ AP IT ++ + + DA++ C YP P
Sbjct: 67 DSGEYHCVYH--FVSAPKANATIEVKAAPDITGHKRSENKNEGQDAMMYCKSVGYPHPEW 124
Query: 306 VWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIE-RRQFGQYACKAANKYGSA 360
+W K + S F ++ + T L ++ ++ G+Y C A N GSA
Sbjct: 125 MWRKKENGVFEEISNSSGRFFIINKENYTELNIVNLQITEDPGEYECNATNSIGSA 180
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 35/115 (30%), Positives = 52/115 (45%), Gaps = 13/115 (11%)
Query: 155 DAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT 214
D+G Y C K +A +E V+ P I+ + RS +EGQ +YC + G+P P
Sbjct: 67 DSGEYHCVYHFVSAPKANATIE--VKAAPDITGHK-RSENKNEGQDAMMYCKSVGYPHPE 123
Query: 215 ISWRRDNSAAL----STGGSIYRGNI-----LKIPNITKT-DRGTYYCVAQNGVG 259
WR+ + ++ G + N L I N+ T D G Y C A N +G
Sbjct: 124 WMWRKKENGVFEEISNSSGRFFIINKENYTELNIVNLQITEDPGEYECNATNSIG 178
>pdb|1NBQ|A Chain A, Crystal Structure Of Human Junctional Adhesion Molecule
Type 1
pdb|1NBQ|B Chain B, Crystal Structure Of Human Junctional Adhesion Molecule
Type 1
Length = 209
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 45/184 (24%), Positives = 80/184 (43%), Gaps = 18/184 (9%)
Query: 193 VIVSEGQTVYLYCYANGFPAPTISWR---RDNSAALSTGGSI---YRGNILKIP------ 240
V + E V L C +GF +P + W+ D + + I Y + +P
Sbjct: 14 VRIPENNPVKLSCAYSGFSSPRVEWKFDQGDTTRLVCYNNKITASYEDRVTFLPTGITFK 73
Query: 241 NITKTDRGTYYC-VAQNGVGRGMKRNIAVEVEFAPVI-TINRPRQGQALQYDAILEC-HV 297
++T+ D GTY C V++ G + + + V P T+N P + A+L C
Sbjct: 74 SVTREDTGTYTCMVSEEGGNSYGEVKVKLIVLVPPSKPTVNIPSSA-TIGNRAVLTCSEQ 132
Query: 298 EAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVI--TIERRQFGQYACKAAN 355
+ PP W KDG+ + N + + +S + T+ ++ + G+Y+C+A N
Sbjct: 133 DGSPPSEYTWFKDGIVMPTNPKSTRAFSNSSYVLNPTTGELVFDPLSASDTGEYSCEARN 192
Query: 356 KYGS 359
YG+
Sbjct: 193 GYGT 196
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 36/139 (25%), Positives = 56/139 (40%), Gaps = 15/139 (10%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNNKVS-AEVELIVRRPPIISDNSTRSVIVSEGQTVYLY 204
++ K + D G Y C V N +V+LIV PP + S + V
Sbjct: 70 ITFKSVTREDTGTYTCMVSEEGGNSYGEVKVKLIVLVPPSKPTVNIPSSATIGNRAVLTC 129
Query: 205 CYANGFPAPTISWRRD---------NSAALSTGGSIYR---GNILKIPNITKTDRGTYYC 252
+G P +W +D ++ A S + G ++ P ++ +D G Y C
Sbjct: 130 SEQDGSPPSEYTWFKDGIVMPTNPKSTRAFSNSSYVLNPTTGELVFDP-LSASDTGEYSC 188
Query: 253 VAQNGVGRGMKRNIAVEVE 271
A+NG G M N AV +E
Sbjct: 189 EARNGYGTPMTSN-AVRME 206
>pdb|1U2H|A Chain A, X-Ray Structure Of The N-Terminally Truncated Human Apep-1
Length = 99
Score = 49.3 bits (116), Expect = 4e-06, Method: Composition-based stats.
Identities = 28/85 (32%), Positives = 41/85 (48%), Gaps = 8/85 (9%)
Query: 282 RQGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITI 341
R+GQ D I+ V+ P P + W+++ + +Q FA E LR++
Sbjct: 18 REGQ----DVIMSIRVQGEPKPVVSWLRNRQPVRPDQR----RFAEEAEGGLCRLRILAA 69
Query: 342 ERRQFGQYACKAANKYGSAQKEIEL 366
ER G Y CKA N+YG+ Q E L
Sbjct: 70 ERGDAGFYTCKAVNEYGARQCEARL 94
Score = 31.2 bits (69), Expect = 0.99, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 29/73 (39%), Gaps = 11/73 (15%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDNSA--------ALSTGGSIYRGNILKIPNITKTD 246
V EGQ V + G P P +SW R+ A G + R L+I + D
Sbjct: 17 VREGQDVIMSIRVQGEPKPVVSWLRNRQPVRPDQRRFAEEAEGGLCR---LRILAAERGD 73
Query: 247 RGTYYCVAQNGVG 259
G Y C A N G
Sbjct: 74 AGFYTCKAVNEYG 86
>pdb|2ID5|A Chain A, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|B Chain B, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|C Chain C, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|D Chain D, Crystal Structure Of The Lingo-1 Ectodomain
Length = 477
Score = 48.1 bits (113), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 38/79 (48%), Gaps = 4/79 (5%)
Query: 185 ISDNSTRSVIVSEGQTVYLYCYANGFPAPTISW---RRDNSAALSTGG-SIYRGNILKIP 240
I D + V V EG TV C A+G P P I W R+ +A S G +++ L++
Sbjct: 387 IRDRKAQQVFVDEGHTVQFVCRADGDPPPAILWLSPRKHLVSAKSNGRLTVFPDGTLEVR 446
Query: 241 NITKTDRGTYYCVAQNGVG 259
D GTY C+A N G
Sbjct: 447 YAQVQDNGTYLCIAANAGG 465
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 15/80 (18%)
Query: 283 QGQALQYDAILECHVEAYPPPAIVWI---KDGVQIMNNQHYSVSHFATSDEFSDTSLRVI 339
+G +Q+ C + PPPAI+W+ K V +N +V F D +L V
Sbjct: 399 EGHTVQF----VCRADGDPPPAILWLSPRKHLVSAKSNGRLTV--------FPDGTLEVR 446
Query: 340 TIERRQFGQYACKAANKYGS 359
+ + G Y C AAN G+
Sbjct: 447 YAQVQDNGTYLCIAANAGGN 466
>pdb|1RHF|A Chain A, Crystal Structure Of Human Tyro3-D1d2
pdb|1RHF|B Chain B, Crystal Structure Of Human Tyro3-D1d2
Length = 182
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 43/186 (23%), Positives = 75/186 (40%), Gaps = 21/186 (11%)
Query: 87 AQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYIL 146
Q L CSV+ ++ + W+K G+++ + + + + L
Sbjct: 17 GQPVKLNCSVEGXEEPDIQWVK--------------DGAVVQNLDQLYIPVSEQHWIGFL 62
Query: 147 SIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCY 206
S+K ++ +DAG Y C+V ++S V L V P + + + V L C
Sbjct: 63 SLKSVERSDAGRYWCQVEDGGETEISQPVWLTVEGVPFFTVEP-KDLAVPPNAPFQLSCE 121
Query: 207 ANGFPAP-TISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQNGVGRGMKRN 265
A G P P TI W R + GG ++L + +T++ + C A N G R
Sbjct: 122 AVGPPEPVTIVWWRGTT---KIGGPAPSPSVLNVTGVTQST--XFSCEAHNLKGLASSRT 176
Query: 266 IAVEVE 271
V ++
Sbjct: 177 ATVHLQ 182
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 35/132 (26%), Positives = 59/132 (44%), Gaps = 13/132 (9%)
Query: 193 VIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRG-------NILKIPNITKT 245
+ VS+GQ V L C G P I W +D A + +Y L + ++ ++
Sbjct: 12 LTVSQGQPVKLNCSVEGXEEPDIQWVKDG-AVVQNLDQLYIPVSEQHWIGFLSLKSVERS 70
Query: 246 DRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPP-- 303
D G Y+C ++G + + + + VE P T+ P+ A+ +A + EA PP
Sbjct: 71 DAGRYWCQVEDGGETEISQPVWLTVEGVPFFTV-EPKD-LAVPPNAPFQLSCEAVGPPEP 128
Query: 304 -AIVWIKDGVQI 314
IVW + +I
Sbjct: 129 VTIVWWRGTTKI 140
Score = 36.2 bits (82), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 9/74 (12%)
Query: 283 QGQALQYDAILECHVEAYPPPAIVWIKDGVQIMN-NQHYSVSHFATSDEFSDTSLRVITI 341
QGQ ++ L C VE P I W+KDG + N +Q Y S++ L + ++
Sbjct: 16 QGQPVK----LNCSVEGXEEPDIQWVKDGAVVQNLDQLY----IPVSEQHWIGFLSLKSV 67
Query: 342 ERRQFGQYACKAAN 355
ER G+Y C+ +
Sbjct: 68 ERSDAGRYWCQVED 81
>pdb|2YD3|A Chain A, Crystal Structure Of The N-Terminal Ig1-2 Module Of Human
Receptor Protein Tyrosine Phosphatase Sigma
Length = 202
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 66/144 (45%), Gaps = 14/144 (9%)
Query: 128 IHDSRFQLTTDPETSTYILSIKEIQE-TDAGIYKC-------EVIISLNNKVSAEVELIV 179
++ RF+ E++ +L I+ ++ D +Y+C E+ + V E +L
Sbjct: 47 VNSQRFETIEFDESAGAVLRIQPLRTPRDENVYECVAQNSVGEITVHAKLTVLREDQLPS 106
Query: 180 RRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRD----NSAALSTGGSIYRGN 235
P I D + +V +T + C A+G P P I+W +D + +A + R
Sbjct: 107 GFPNI--DMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDPSASNGRIKQLRSG 164
Query: 236 ILKIPNITKTDRGTYYCVAQNGVG 259
L+I + +TD+G Y CVA N G
Sbjct: 165 ALQIESSEETDQGKYECVATNSAG 188
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 47/186 (25%), Positives = 67/186 (36%), Gaps = 43/186 (23%)
Query: 198 GQTVYLYCYANGFPAPTISWRRD----NSAALST------GGSIYRGNILKIPNITKTDR 247
G C A G P P ++W + NS T G++ R L+ P D
Sbjct: 21 GGVASFVCQATGDPKPRVTWNKKGKKVNSQRFETIEFDESAGAVLRIQPLRTPR----DE 76
Query: 248 GTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQ----------GQALQ-----YDAI 292
Y CVAQN VG E+ +T+ R Q G L+ A
Sbjct: 77 NVYECVAQNSVG---------EITVHAKLTVLREDQLPSGFPNIDMGPQLKVVERTRTAT 127
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACK 352
+ C P P I W KD + + S S+ + +L++ + E G+Y C
Sbjct: 128 MLCAASGNPDPEITWFKDFLPV----DPSASN-GRIKQLRSGALQIESSEETDQGKYECV 182
Query: 353 AANKYG 358
A N G
Sbjct: 183 ATNSAG 188
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 45/108 (41%), Gaps = 16/108 (14%)
Query: 73 PTISYISQEQIKDIAQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSR 132
P I Q ++ + +TA + C+ D + W K + LP+ S S + R
Sbjct: 109 PNIDMGPQLKVVERTRTATMLCAASGNPDPEITWFK-------DFLPVDPSAS----NGR 157
Query: 133 FQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVR 180
+ + + L I+ +ETD G Y+C S + S+ L VR
Sbjct: 158 IK-----QLRSGALQIESSEETDQGKYECVATNSAGVRYSSPANLYVR 200
>pdb|2YD2|A Chain A, Crystal Structure Of The N-Terminal Ig1-2 Module Of Human
Receptor Protein Tyrosine Phosphatase Sigma
Length = 214
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 66/144 (45%), Gaps = 14/144 (9%)
Query: 128 IHDSRFQLTTDPETSTYILSIKEIQE-TDAGIYKC-------EVIISLNNKVSAEVELIV 179
++ RF+ E++ +L I+ ++ D +Y+C E+ + V E +L
Sbjct: 47 VNSQRFETIEFDESAGAVLRIQPLRTPRDENVYECVAQNSVGEITVHAKLTVLREDQLPS 106
Query: 180 RRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRD----NSAALSTGGSIYRGN 235
P I D + +V +T + C A+G P P I+W +D + +A + R
Sbjct: 107 GFPNI--DMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDPSASNGRIKQLRSG 164
Query: 236 ILKIPNITKTDRGTYYCVAQNGVG 259
L+I + +TD+G Y CVA N G
Sbjct: 165 ALQIESSEETDQGKYECVATNSAG 188
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 47/186 (25%), Positives = 67/186 (36%), Gaps = 43/186 (23%)
Query: 198 GQTVYLYCYANGFPAPTISWRRD----NSAALST------GGSIYRGNILKIPNITKTDR 247
G C A G P P ++W + NS T G++ R L+ P D
Sbjct: 21 GGVASFVCQATGDPKPRVTWNKKGKKVNSQRFETIEFDESAGAVLRIQPLRTPR----DE 76
Query: 248 GTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQ----------GQALQ-----YDAI 292
Y CVAQN VG E+ +T+ R Q G L+ A
Sbjct: 77 NVYECVAQNSVG---------EITVHAKLTVLREDQLPSGFPNIDMGPQLKVVERTRTAT 127
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACK 352
+ C P P I W KD + + S S+ + +L++ + E G+Y C
Sbjct: 128 MLCAASGNPDPEITWFKDFLPV----DPSASN-GRIKQLRSGALQIESSEETDQGKYECV 182
Query: 353 AANKYG 358
A N G
Sbjct: 183 ATNSAG 188
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 45/108 (41%), Gaps = 16/108 (14%)
Query: 73 PTISYISQEQIKDIAQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSR 132
P I Q ++ + +TA + C+ D + W K + LP+ S S + R
Sbjct: 109 PNIDMGPQLKVVERTRTATMLCAASGNPDPEITWFK-------DFLPVDPSAS----NGR 157
Query: 133 FQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVR 180
+ + + L I+ +ETD G Y+C S + S+ L VR
Sbjct: 158 IK-----QLRSGALQIESSEETDQGKYECVATNSAGVRYSSPANLYVR 200
>pdb|2YD9|A Chain A, Crystal Structure Of The N-Terminal Ig1-3 Module Of Human
Receptor Protein Tyrosine Phosphatase Sigma
Length = 304
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 66/144 (45%), Gaps = 14/144 (9%)
Query: 128 IHDSRFQLTTDPETSTYILSIKEIQE-TDAGIYKC-------EVIISLNNKVSAEVELIV 179
++ RF+ E++ +L I+ ++ D +Y+C E+ + V E +L
Sbjct: 47 VNSQRFETIEFDESAGAVLRIQPLRTPRDENVYECVAQNSVGEITVHAKLTVLREDQLPS 106
Query: 180 RRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRD----NSAALSTGGSIYRGN 235
P I D + +V +T + C A+G P P I+W +D + +A + R
Sbjct: 107 GFPNI--DMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDPSASNGRIKQLRSG 164
Query: 236 ILKIPNITKTDRGTYYCVAQNGVG 259
L+I + +TD+G Y CVA N G
Sbjct: 165 ALQIESSEETDQGKYECVATNSAG 188
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 47/186 (25%), Positives = 67/186 (36%), Gaps = 43/186 (23%)
Query: 198 GQTVYLYCYANGFPAPTISWRRD----NSAALST------GGSIYRGNILKIPNITKTDR 247
G C A G P P ++W + NS T G++ R L+ P D
Sbjct: 21 GGVASFVCQATGDPKPRVTWNKKGKKVNSQRFETIEFDESAGAVLRIQPLRTPR----DE 76
Query: 248 GTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQ----------GQALQY-----DAI 292
Y CVAQN VG E+ +T+ R Q G L+ A
Sbjct: 77 NVYECVAQNSVG---------EITVHAKLTVLREDQLPSGFPNIDMGPQLKVVERTRTAT 127
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACK 352
+ C P P I W KD + + S S+ + +L++ + E G+Y C
Sbjct: 128 MLCAASGNPDPEITWFKDFLPV----DPSASN-GRIKQLRSGALQIESSEETDQGKYECV 182
Query: 353 AANKYG 358
A N G
Sbjct: 183 ATNSAG 188
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 45/193 (23%), Positives = 77/193 (39%), Gaps = 28/193 (14%)
Query: 73 PTISYISQEQIKDIAQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSR 132
P I Q ++ + +TA + C+ D + W K + LP+ S S + R
Sbjct: 109 PNIDMGPQLKVVERTRTATMLCAASGNPDPEITWFK-------DFLPVDPSAS----NGR 157
Query: 133 FQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRS 192
+ + + L I+ +ETD G Y+C S + S+ L VR + + + R
Sbjct: 158 IK-----QLRSGALQIESSEETDQGKYECVATNSAGVRYSSPANLYVR----VQNVAPRF 208
Query: 193 VI------VSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTD 246
I + G V + C A G P P + W + N+L++ ++ D
Sbjct: 209 SILPMSHEIMPGGNVNITCVAVGSPMPYVKWMQGAEDLTPEDDMPVGRNVLELTDV--KD 266
Query: 247 RGTYYCVAQNGVG 259
Y CVA + +G
Sbjct: 267 SANYTCVAMSSLG 279
>pdb|1F97|A Chain A, Soluble Part Of The Junction Adhesion Molecule From Mouse
Length = 212
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 46/188 (24%), Positives = 79/188 (42%), Gaps = 19/188 (10%)
Query: 193 VIVSEGQTVYLYCYANGFPAPTISWR--RDNSAALSTGGS----------IYRGNILKIP 240
V V E +++ L C +GF +P + W+ + ++ AL S + + +
Sbjct: 11 VQVPENESIKLTCTYSGFSSPRVEWKFVQGSTTALVCYNSQITAPYADRVTFSSSGITFS 70
Query: 241 NITKTDRGTYYC-VAQNGVGRGMKRNIAVEVEFAPVI-TINRPRQGQALQYDAILEC-HV 297
++T+ D G Y C V++ G + +I + V P TI+ P + A+L C
Sbjct: 71 SVTRKDNGEYTCMVSEEGGQNYGEVSIHLTVLVPPSKPTISVPSS-VTIGNRAVLTCSEH 129
Query: 298 EAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSD---TSLRVITIERRQFGQYACKAA 354
+ PP W KDG+ ++ F S D L + G+Y C+A
Sbjct: 130 DGSPPSEYSWFKDGISMLTADAKKTRAFMNSSFTIDPKSGDLIFDPVTAFDSGEYYCQAQ 189
Query: 355 NKYGSAQK 362
N YG+A +
Sbjct: 190 NGYGTAMR 197
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 35/136 (25%), Positives = 50/136 (36%), Gaps = 15/136 (11%)
Query: 146 LSIKEIQETDAGIYKCEVII-SLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLY 204
++ + D G Y C V N + L V PP S S + + V
Sbjct: 67 ITFSSVTRKDNGEYTCMVSEEGGQNYGEVSIHLTVLVPPSKPTISVPSSVTIGNRAVLTC 126
Query: 205 CYANGFPAPTISWRRDNSAALSTGGSIYR-------------GNILKIPNITKTDRGTYY 251
+G P SW +D + L+ R G+++ P +T D G YY
Sbjct: 127 SEHDGSPPSEYSWFKDGISMLTADAKKTRAFMNSSFTIDPKSGDLIFDP-VTAFDSGEYY 185
Query: 252 CVAQNGVGRGMKRNIA 267
C AQNG G M+ A
Sbjct: 186 CQAQNGYGTAMRSEAA 201
>pdb|1CR9|L Chain L, Crystal Structure Of The Anti-Prion Fab 3f4
pdb|1CU4|L Chain L, Crystal Structure Of The Anti-Prion Fab 3f4 In Complex
With Its Peptide Epitope
Length = 219
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 50/195 (25%), Positives = 82/195 (42%), Gaps = 14/195 (7%)
Query: 175 VELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT-----ISWRRDNSAALSTGG 229
+ + + +P IS S++S++ S+G+T ++ + +P +S R TG
Sbjct: 11 LSVTIGQPASISCKSSQSLLDSDGKTYLIWVFQRPGQSPKRLIFLVSKRDSGVPDRFTGS 70
Query: 230 SIYRGNILKIPNITKTDRGTYYCVAQ----NGVGRGMKRNIAVEVEFAPVITINRPRQGQ 285
LKI + D G YYC + VG G K IA + AP ++I P Q
Sbjct: 71 GSGTDFTLKISRVEAEDVGVYYCWQGTHFPHTVGGGTKLEIA-RADAAPTVSIFPPSSEQ 129
Query: 286 ALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI- 341
A + C + + P I W DG + N S + + D +S +S +T
Sbjct: 130 LTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKD 189
Query: 342 ERRQFGQYACKAANK 356
E + Y C+A +K
Sbjct: 190 EYERHNSYTCEATHK 204
>pdb|2YD6|A Chain A, Crystal Structure Of The N-Terminal Ig1-2 Module Of Human
Receptor Protein Tyrosine Phosphatase Delta
pdb|2YD7|A Chain A, Crystal Structure Of The N-Terminal Ig1-2 Module Of Human
Receptor Protein Tyrosine Phosphatase Delta
pdb|2YD7|B Chain B, Crystal Structure Of The N-Terminal Ig1-2 Module Of Human
Receptor Protein Tyrosine Phosphatase Delta
Length = 212
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 49/200 (24%), Positives = 75/200 (37%), Gaps = 35/200 (17%)
Query: 182 PPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYR-----GNI 236
PP + VS G ++ C A G P P I W + + + G++
Sbjct: 6 PPRFTRTPVDQTGVSGGVASFI-CQATGDPRPKIVWNKKGKKVSNQRFEVIEFDDGSGSV 64
Query: 237 LKI-PNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQ----------GQ 285
L+I P T D Y CVA N VG E+ + +T+ R Q G
Sbjct: 65 LRIQPLRTPRDEAIYECVASNNVG---------EISVSTRLTVLREDQIPRGFPTIDMGP 115
Query: 286 ALQ-----YDAILECHVEAYPPPAIVWIKDGVQI-MNNQHYSVSHFATSDEFSDTSLRVI 339
L+ A + C P P I W KD + + +N + + + S +L++
Sbjct: 116 QLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSE---SIGALQIE 172
Query: 340 TIERRQFGQYACKAANKYGS 359
E G+Y C A N G+
Sbjct: 173 QSEESDQGKYECVATNSAGT 192
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 41/151 (27%), Positives = 66/151 (43%), Gaps = 25/151 (16%)
Query: 128 IHDSRFQLTTDPETSTYILSIKEIQE-TDAGIYKCEVIISLNN--KVSAEVELIVRRPPI 184
+ + RF++ + S +L I+ ++ D IY+C ++ NN ++S L V R
Sbjct: 47 VSNQRFEVIEFDDGSGSVLRIQPLRTPRDEAIYEC---VASNNVGEISVSTRLTVLREDQ 103
Query: 185 IS------DNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNI-- 236
I D + +V +T + C A+G P P I+W +D L S G I
Sbjct: 104 IPRGFPTIDMGPQLKVVERTRTATMLCAASGNPDPEITWFKD---FLPVDTSNNNGRIKQ 160
Query: 237 --------LKIPNITKTDRGTYYCVAQNGVG 259
L+I ++D+G Y CVA N G
Sbjct: 161 LRSESIGALQIEQSEESDQGKYECVATNSAG 191
Score = 35.4 bits (80), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 30/109 (27%), Positives = 49/109 (44%), Gaps = 15/109 (13%)
Query: 73 PTISYISQEQIKDIAQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSR 132
PTI Q ++ + +TA + C+ D + W K + LP+ S ++ R
Sbjct: 109 PTIDMGPQLKVVERTRTATMLCAASGNPDPEITWFK-------DFLPVDTSN----NNGR 157
Query: 133 F-QLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVR 180
QL ++ S L I++ +E+D G Y+C S + SA L VR
Sbjct: 158 IKQLRSE---SIGALQIEQSEESDQGKYECVATNSAGTRYSAPANLYVR 203
>pdb|1CVS|C Chain C, Crystal Structure Of A Dimeric Fgf2-Fgfr1 Complex
pdb|1CVS|D Chain D, Crystal Structure Of A Dimeric Fgf2-Fgfr1 Complex
pdb|1FQ9|C Chain C, Crystal Structure Of A Ternary Fgf2-Fgfr1-Heparin Complex
pdb|1FQ9|D Chain D, Crystal Structure Of A Ternary Fgf2-Fgfr1-Heparin Complex
Length = 225
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 43/181 (23%), Positives = 73/181 (40%), Gaps = 17/181 (9%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDNSA---ALSTGGSIYRGNILKI--PNITKTDRGT 249
V +TV C ++G P PT+ W ++ GG R I ++ +D+G
Sbjct: 28 VPAAKTVKFKCPSSGTPQPTLRWLKNGKEFKPDHRIGGYKVRYATWSIIMDSVVPSDKGN 87
Query: 250 YYCVAQNGVG---RGMKRNIAVEVEFAPVITINRP-RQGQALQYDAILECHVEAYPPPAI 305
Y C+ +N G + ++ P++ P + AL + C V + P P I
Sbjct: 88 YTCIVENEYGSINHTYQLDVVERSPHRPILQAGLPANKTVALGSNVEFMCKVYSDPQPHI 147
Query: 306 VWIK----DGVQIMNNQHYSVSHFATSD-EFSDTSLRVITIERRQF---GQYACKAANKY 357
W+K +G +I + V T+ +D + V+ + F G+Y C A N
Sbjct: 148 QWLKHIEVNGSKIGPDNLPYVQILKTAGVNTTDKEMEVLHLRNVSFEDAGEYTCLAGNSI 207
Query: 358 G 358
G
Sbjct: 208 G 208
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 59/140 (42%), Gaps = 24/140 (17%)
Query: 142 STYILSIKEIQETDAGIYKCEV---IISLNNKVSAEVELIVRRP--PIISDNSTRSVIVS 196
+T+ + + + +D G Y C V S+N+ + +++++ R P PI+ + V+
Sbjct: 71 ATWSIIMDSVVPSDKGNYTCIVENEYGSINH--TYQLDVVERSPHRPILQAGLPANKTVA 128
Query: 197 EGQTVYLYCYANGFPAPTISWRR-----------DN---SAALSTGG---SIYRGNILKI 239
G V C P P I W + DN L T G + +L +
Sbjct: 129 LGSNVEFMCKVYSDPQPHIQWLKHIEVNGSKIGPDNLPYVQILKTAGVNTTDKEMEVLHL 188
Query: 240 PNITKTDRGTYYCVAQNGVG 259
N++ D G Y C+A N +G
Sbjct: 189 RNVSFEDAGEYTCLAGNSIG 208
>pdb|3OJV|C Chain C, Crystal Structure Of Fgf1 Complexed With The Ectodomain Of
Fgfr1c Exhibiting An Ordered Ligand
Specificity-Determining Betac'-Betae Loop
pdb|3OJV|D Chain D, Crystal Structure Of Fgf1 Complexed With The Ectodomain Of
Fgfr1c Exhibiting An Ordered Ligand
Specificity-Determining Betac'-Betae Loop
Length = 226
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 43/181 (23%), Positives = 73/181 (40%), Gaps = 17/181 (9%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDNSA---ALSTGGSIYRGNILKI--PNITKTDRGT 249
V +TV C ++G P PT+ W ++ GG R I ++ +D+G
Sbjct: 29 VPAAKTVKFKCPSSGTPQPTLRWLKNGKEFKPDHRIGGYKVRYATWSIIMDSVVPSDKGN 88
Query: 250 YYCVAQNGVG---RGMKRNIAVEVEFAPVITINRP-RQGQALQYDAILECHVEAYPPPAI 305
Y C+ +N G + ++ P++ P + AL + C V + P P I
Sbjct: 89 YTCIVENEYGSINHTYQLDVVERSPHRPILQAGLPANKTVALGSNVEFMCKVYSDPQPHI 148
Query: 306 VWIK----DGVQIMNNQHYSVSHFATSD-EFSDTSLRVITIERRQF---GQYACKAANKY 357
W+K +G +I + V T+ +D + V+ + F G+Y C A N
Sbjct: 149 QWLKHIEVNGSKIGPDNLPYVQILKTAGVNTTDKEMEVLHLRNVSFEDAGEYTCLAGNSI 208
Query: 358 G 358
G
Sbjct: 209 G 209
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 59/140 (42%), Gaps = 24/140 (17%)
Query: 142 STYILSIKEIQETDAGIYKCEV---IISLNNKVSAEVELIVRRP--PIISDNSTRSVIVS 196
+T+ + + + +D G Y C V S+N+ + +++++ R P PI+ + V+
Sbjct: 72 ATWSIIMDSVVPSDKGNYTCIVENEYGSINH--TYQLDVVERSPHRPILQAGLPANKTVA 129
Query: 197 EGQTVYLYCYANGFPAPTISWRR-----------DN---SAALSTGG---SIYRGNILKI 239
G V C P P I W + DN L T G + +L +
Sbjct: 130 LGSNVEFMCKVYSDPQPHIQWLKHIEVNGSKIGPDNLPYVQILKTAGVNTTDKEMEVLHL 189
Query: 240 PNITKTDRGTYYCVAQNGVG 259
N++ D G Y C+A N +G
Sbjct: 190 RNVSFEDAGEYTCLAGNSIG 209
>pdb|1EVT|C Chain C, Crystal Structure Of Fgf1 In Complex With The
Extracellular Ligand Binding Domain Of Fgf Receptor 1
(Fgfr1)
pdb|1EVT|D Chain D, Crystal Structure Of Fgf1 In Complex With The
Extracellular Ligand Binding Domain Of Fgf Receptor 1
(Fgfr1)
Length = 225
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 43/181 (23%), Positives = 73/181 (40%), Gaps = 17/181 (9%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDNSA---ALSTGGSIYRGNILKI--PNITKTDRGT 249
V +TV C ++G P PT+ W ++ GG R I ++ +D+G
Sbjct: 28 VPAAKTVKFKCPSSGTPNPTLRWLKNGKEFKPDHRIGGYKVRYATWSIIMDSVVPSDKGN 87
Query: 250 YYCVAQNGVG---RGMKRNIAVEVEFAPVITINRP-RQGQALQYDAILECHVEAYPPPAI 305
Y C+ +N G + ++ P++ P + AL + C V + P P I
Sbjct: 88 YTCIVENEYGSINHTYQLDVVERSPHRPILQAGLPANKTVALGSNVEFMCKVYSDPQPHI 147
Query: 306 VWIK----DGVQIMNNQHYSVSHFATSD-EFSDTSLRVITIERRQF---GQYACKAANKY 357
W+K +G +I + V T+ +D + V+ + F G+Y C A N
Sbjct: 148 QWLKHIEVNGSKIGPDNLPYVQILKTAGVNTTDKEMEVLHLRNVSFEDAGEYTCLAGNSI 207
Query: 358 G 358
G
Sbjct: 208 G 208
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 59/140 (42%), Gaps = 24/140 (17%)
Query: 142 STYILSIKEIQETDAGIYKCEV---IISLNNKVSAEVELIVRRP--PIISDNSTRSVIVS 196
+T+ + + + +D G Y C V S+N+ + +++++ R P PI+ + V+
Sbjct: 71 ATWSIIMDSVVPSDKGNYTCIVENEYGSINH--TYQLDVVERSPHRPILQAGLPANKTVA 128
Query: 197 EGQTVYLYCYANGFPAPTISWRR-----------DN---SAALSTGG---SIYRGNILKI 239
G V C P P I W + DN L T G + +L +
Sbjct: 129 LGSNVEFMCKVYSDPQPHIQWLKHIEVNGSKIGPDNLPYVQILKTAGVNTTDKEMEVLHL 188
Query: 240 PNITKTDRGTYYCVAQNGVG 259
N++ D G Y C+A N +G
Sbjct: 189 RNVSFEDAGEYTCLAGNSIG 208
>pdb|2V9T|A Chain A, Complex Between The Second Lrr Domain Of Slit2 And The
First Ig Domain From Robo1
Length = 117
Score = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 32/103 (31%), Positives = 50/103 (48%), Gaps = 18/103 (17%)
Query: 182 PPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAA------------LSTGG 229
PP I ++ + +IVS+G+ L C A G P PTI W + L G
Sbjct: 9 PPRIVEHPS-DLIVSKGEPATLNCKAEGRPTPTIEWYKGGERVETDKDDPRSHRMLLPSG 67
Query: 230 SIYRGNILKIPNITKT--DRGTYYCVAQNGVGRGMKRNIAVEV 270
S++ L+I + K+ D G Y CVA+N +G + + ++EV
Sbjct: 68 SLF---FLRIVHGRKSRPDEGVYVCVARNYLGEAVSHDASLEV 107
Score = 33.1 bits (74), Expect = 0.28, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 29/72 (40%), Gaps = 2/72 (2%)
Query: 291 AILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVI--TIERRQFGQ 348
A L C E P P I W K G ++ ++ SH S LR++ R G
Sbjct: 27 ATLNCKAEGRPTPTIEWYKGGERVETDKDDPRSHRMLLPSGSLFFLRIVHGRKSRPDEGV 86
Query: 349 YACKAANKYGSA 360
Y C A N G A
Sbjct: 87 YVCVARNYLGEA 98
>pdb|4FRW|A Chain A, Crystal Structure Of Human Nectin-4 Extracellular Fragment
D1-D2
pdb|4FRW|B Chain B, Crystal Structure Of Human Nectin-4 Extracellular Fragment
D1-D2
pdb|4FRW|C Chain C, Crystal Structure Of Human Nectin-4 Extracellular Fragment
D1-D2
pdb|4FRW|D Chain D, Crystal Structure Of Human Nectin-4 Extracellular Fragment
D1-D2
pdb|4FRW|E Chain E, Crystal Structure Of Human Nectin-4 Extracellular Fragment
D1-D2
pdb|4FRW|F Chain F, Crystal Structure Of Human Nectin-4 Extracellular Fragment
D1-D2
Length = 218
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 34/70 (48%)
Query: 148 IKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYA 207
++ + D G Y+C V A + L V PP+ S N ++ +G T+ C A
Sbjct: 83 LRNAVQADEGEYECRVSTFPAGSFQARLRLRVLVPPLPSLNPGPALEEGQGLTLAASCTA 142
Query: 208 NGFPAPTISW 217
G PAP+++W
Sbjct: 143 EGSPAPSVTW 152
>pdb|2EDJ|A Chain A, Solution Structure Of The Fifth Ig-Like Domain From Human
Roundabout Homolog 2
Length = 100
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 36/81 (44%), Gaps = 3/81 (3%)
Query: 182 PPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSA--ALSTGGSIYRGNILKI 239
PPII + +G T L C A G P P ISW ++ +I L+I
Sbjct: 8 PPIILQGPANQTLAVDG-TALLKCKATGDPLPVISWLKEGFTFPGRDPRATIQEQGTLQI 66
Query: 240 PNITKTDRGTYYCVAQNGVGR 260
N+ +D GTY CVA + G
Sbjct: 67 KNLRISDTGTYTCVATSSSGE 87
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 33/85 (38%), Gaps = 7/85 (8%)
Query: 274 PVITINRPRQGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSD 333
P+I Q A+ A+L+C P P I W+K+G AT E
Sbjct: 9 PIILQGPANQTLAVDGTALLKCKATGDPLPVISWLKEGFTFPGRDPR-----ATIQE--Q 61
Query: 334 TSLRVITIERRQFGQYACKAANKYG 358
+L++ + G Y C A + G
Sbjct: 62 GTLQIKNLRISDTGTYTCVATSSSG 86
>pdb|1EPF|A Chain A, Crystal Structure Of The Two N-Terminal Immunoglobulin
Domains Of The Neural Cell Adhesion Molecule (Ncam)
pdb|1EPF|B Chain B, Crystal Structure Of The Two N-Terminal Immunoglobulin
Domains Of The Neural Cell Adhesion Molecule (Ncam)
pdb|1EPF|C Chain C, Crystal Structure Of The Two N-Terminal Immunoglobulin
Domains Of The Neural Cell Adhesion Molecule (Ncam)
pdb|1EPF|D Chain D, Crystal Structure Of The Two N-Terminal Immunoglobulin
Domains Of The Neural Cell Adhesion Molecule (Ncam)
Length = 191
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 36/119 (30%), Positives = 50/119 (42%), Gaps = 6/119 (5%)
Query: 137 TDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVS 196
D ++ST L+I DAGIYKC V + A V + + + + + T
Sbjct: 57 NDDDSST--LTIYNANIDDAGIYKCVVTAEDGTQSEATVNVKIFQKLMFKNAPTPQEF-K 113
Query: 197 EGQTVYLYCYANGFPAPTISWR---RDNSAALSTGGSIYRGNILKIPNITKTDRGTYYC 252
EG+ + C PTI W+ RD + N L+I I KTD GTY C
Sbjct: 114 EGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNNYLQIRGIKKTDEGTYRC 172
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 35/145 (24%), Positives = 63/145 (43%), Gaps = 28/145 (19%)
Query: 214 TISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFA 273
++ W D+S+ L+ IY NI D G Y CV G + + V++ F
Sbjct: 53 SVVWNDDDSSTLT----IYNANI--------DDAGIYKCVVTAEDGTQSEATVNVKI-FQ 99
Query: 274 PVITINRP-----RQGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATS 328
++ N P ++G+ DA++ C V + PP I+W G ++ + V S
Sbjct: 100 KLMFKNAPTPQEFKEGE----DAVIVCDVVSSLPPTIIWKHKGRDVILKK--DVRFIVLS 153
Query: 329 DEFSDTSLRVITIERRQFGQYACKA 353
+ + L++ I++ G Y C+
Sbjct: 154 NNY----LQIRGIKKTDEGTYRCEG 174
>pdb|3KVQ|A Chain A, Crystal Structure Of Vegfr2 Extracellular Domain D7
Length = 108
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 27/88 (30%), Positives = 45/88 (51%), Gaps = 3/88 (3%)
Query: 174 EVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYR 233
++ ++ R P I+ N + S G+++ + C A+G P P I W +DN + G + +
Sbjct: 2 QLTVLERVAPTITGN-LENQTTSIGESIEVSCTASGNPPPQIMWFKDNETLVEDSGIVLK 60
Query: 234 -GNI-LKIPNITKTDRGTYYCVAQNGVG 259
GN L I + K D G Y C A + +G
Sbjct: 61 DGNRNLTIRRVRKEDEGLYTCQACSVLG 88
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 26/100 (26%), Positives = 42/100 (42%), Gaps = 7/100 (7%)
Query: 264 RNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVS 323
R + V AP IT N Q ++ + C PPP I+W KD ++ + S
Sbjct: 1 RQLTVLERVAPTITGNLENQTTSIGESIEVSCTASGNPPPQIMWFKDNETLVED-----S 55
Query: 324 HFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKE 363
D + +L + + + G Y C+A + G A+ E
Sbjct: 56 GIVLKD--GNRNLTIRRVRKEDEGLYTCQACSVLGCAKVE 93
>pdb|2OCW|A Chain A, Solution Structure Of Human Secretory Component
pdb|3CHN|S Chain S, Solution Structure Of Human Secretory Iga1
pdb|3CM9|S Chain S, Solution Structure Of Human Siga2
Length = 585
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 44/77 (57%), Gaps = 2/77 (2%)
Query: 129 HDSRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDN 188
+ R LT PE T++++I ++ + D+G YKC + I+ + +S +V L V + P + N
Sbjct: 60 YAGRANLTNFPENGTFVVNIAQLSQDDSGRYKCGLGIN-SRGLSFDVSLEVSQGPGLL-N 117
Query: 189 STRSVIVSEGQTVYLYC 205
T+ V G+TV + C
Sbjct: 118 DTKVYTVDLGRTVTINC 134
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 41/189 (21%), Positives = 73/189 (38%), Gaps = 27/189 (14%)
Query: 102 YPVIWMKMDTAKKMEPLPISMSGSLII-HDSRFQLTTDPETSTYILSIKEIQETDAGIYK 160
Y +W + PL + G + ++ R L +P T+ + + ++ DAG Y
Sbjct: 365 YWCLWEGAQNGRC--PLLVDSEGWVKAQYEGRLSLLEEPGNGTFTVILNQLTSRDAGFYW 422
Query: 161 CEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTIS---- 216
C + + E+++I P + + +V+ G+T+ + C+ FP S
Sbjct: 423 CLTNGDTLWRTTVEIKIIEGEPNLKVPGNVTAVL---GETLKVPCH---FPCKFSSYEKY 476
Query: 217 ---WRRDNSAALST---GGSIYRGNI--------LKIPNITKTDRGTYYCVAQNGVGRGM 262
W AL + G S N L + +T+ D G Y+C + G G
Sbjct: 477 WCKWNNTGCQALPSQDEGPSKAFVNCDENSRLVSLTLNLVTRADEGWYWCGVKQGHFYGE 536
Query: 263 KRNIAVEVE 271
+ V VE
Sbjct: 537 TAAVYVAVE 545
>pdb|3LCY|A Chain A, Titin Ig Tandem Domains A164-A165
pdb|3LCY|B Chain B, Titin Ig Tandem Domains A164-A165
pdb|3LCY|C Chain C, Titin Ig Tandem Domains A164-A165
pdb|3LCY|D Chain D, Titin Ig Tandem Domains A164-A165
Length = 197
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 47/202 (23%), Positives = 76/202 (37%), Gaps = 42/202 (20%)
Query: 191 RSVIVSEGQTVYLYCYANGFPAPTISWRR-------DNSAALSTGGSIYRGNILKIPNIT 243
+ V G+ L C G P P I W R +S+ G R + L +
Sbjct: 15 KDVTTKLGEAAQLSCQIVGRPLPDIKWYRFGKELIQSRKYKMSSDG---RTHTLTVMTEE 71
Query: 244 KTDRGTYYCVAQNGVGR---GMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVE-- 298
+ D G Y C+A N VG K + +F P + G + L HV
Sbjct: 72 QEDEGVYTCIATNEVGEVETSSKLLLQATPQFHPGYPLKEKYYGAV---GSTLRLHVMYI 128
Query: 299 AYPPPAIVWIK--------DGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERR-QFGQY 349
P PA+ W + + I N +HY T L + ++R+ G+Y
Sbjct: 129 GRPVPAMTWFHGQKLLQNSENITIENTEHY-------------THLVMKNVQRKTHAGKY 175
Query: 350 ACKAANKYGS--AQKEIELFDR 369
+ +N +G+ A ++E+ D+
Sbjct: 176 KVQLSNVFGTVDAILDVEIQDK 197
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 43/90 (47%), Gaps = 5/90 (5%)
Query: 291 AILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYA 350
A L C + P P I W + G +++ ++ Y +S SD + T L V+T E+ G Y
Sbjct: 25 AQLSCQIVGRPLPDIKWYRFGKELIQSRKYKMS----SDGRTHT-LTVMTEEQEDEGVYT 79
Query: 351 CKAANKYGSAQKEIELFDRETQTGDETFPI 380
C A N+ G + +L + T +P+
Sbjct: 80 CIATNEVGEVETSSKLLLQATPQFHPGYPL 109
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/98 (22%), Positives = 45/98 (45%), Gaps = 9/98 (9%)
Query: 124 GSLIIHDSRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLN--NKVSAEVELIVRR 181
G +I ++++++D T T L++ ++ D G+Y C I+ N +V +L+++
Sbjct: 45 GKELIQSRKYKMSSDGRTHT--LTVMTEEQEDEGVYTC---IATNEVGEVETSSKLLLQA 99
Query: 182 PPIISDNS--TRSVIVSEGQTVYLYCYANGFPAPTISW 217
P + G T+ L+ G P P ++W
Sbjct: 100 TPQFHPGYPLKEKYYGAVGSTLRLHVMYIGRPVPAMTW 137
>pdb|3FMG|L Chain L, Structure Of Rotavirus Outer Capsid Protein Vp7 Trimer In
Co A Neutralizing Fab
Length = 211
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 37/128 (28%), Positives = 55/128 (42%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI ++ D GTYYC NG G G K + + AP ++I P Q A
Sbjct: 73 LKISSVQPEDFGTYYCQHHNGPPLTFGAGTKLELK-RADAAPTVSIFPPSSKQLTSGGAS 131
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 132 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 191
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 192 YTCEATHK 199
>pdb|1TNM|A Chain A, Tertiary Structure Of An Immunoglobulin-Like Domain From
The Muscle Protein Titin: A New Member Of The I Set
pdb|1TNN|A Chain A, Tertiary Structure Of An Immunoglobulin-Like Domain From
The Muscle Protein Titin: A New Member Of The I Set
Length = 100
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 191 RSVIVSEGQTVYLYCYANGFPAPTISWRRDN-----SAALSTGGSIYRGNILKIPNITKT 245
RS+ V EG++ C +G P PT++W R SA + Y+ + +I ++ +
Sbjct: 16 RSMTVYEGESARFSCDTDGEPVPTVTWLRKGQVLSTSARHQVTTTKYK-STFEISSVQAS 74
Query: 246 DRGTYYCVAQNGVGR 260
D G Y V +N G+
Sbjct: 75 DEGNYSVVVENSEGK 89
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/90 (21%), Positives = 39/90 (43%), Gaps = 6/90 (6%)
Query: 278 INRPRQGQALQYD-AILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSL 336
+ +PR + + A C + P P + W++ G Q+++ S H T+ ++ T
Sbjct: 12 LTKPRSMTVYEGESARFSCDTDGEPVPTVTWLRKG-QVLST---SARHQVTTTKYKST-F 66
Query: 337 RVITIERRQFGQYACKAANKYGSAQKEIEL 366
+ +++ G Y+ N G + E L
Sbjct: 67 EISSVQASDEGNYSVVVENSEGKQEAEFTL 96
>pdb|1NCT|A Chain A, Titin Module M5, N-Terminally Extended, Nmr
pdb|1NCU|A Chain A, Titin Module M5, N-Terminally Extended, Nmr
Length = 106
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 191 RSVIVSEGQTVYLYCYANGFPAPTISWRRDN-----SAALSTGGSIYRGNILKIPNITKT 245
RS+ V EG++ C +G P PT++W R SA + Y+ + +I ++ +
Sbjct: 22 RSMTVYEGESARFSCDTDGEPVPTVTWLRKGQVLSTSARHQVTTTKYK-STFEISSVQAS 80
Query: 246 DRGTYYCVAQNGVGR 260
D G Y V +N G+
Sbjct: 81 DEGNYSVVVENSEGK 95
Score = 31.2 bits (69), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 19/90 (21%), Positives = 39/90 (43%), Gaps = 6/90 (6%)
Query: 278 INRPRQGQALQYD-AILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSL 336
+ +PR + + A C + P P + W++ G Q+++ S H T+ ++ T
Sbjct: 18 LTKPRSMTVYEGESARFSCDTDGEPVPTVTWLRKG-QVLST---SARHQVTTTKYKST-F 72
Query: 337 RVITIERRQFGQYACKAANKYGSAQKEIEL 366
+ +++ G Y+ N G + E L
Sbjct: 73 EISSVQASDEGNYSVVVENSEGKQEAEFTL 102
>pdb|4FP8|H Chain H, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin, Ha1 Subunit
pdb|4FP8|I Chain I, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin, Ha1 Subunit
pdb|4FP8|J Chain J, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin, Ha1 Subunit
pdb|4FP8|K Chain K, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin, Ha1 Subunit
pdb|4FQR|AA Chain a, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|CC Chain c, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|EE Chain e, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|GG Chain g, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|II Chain i, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|KK Chain k, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|MM Chain m, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|OO Chain o, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|QQ Chain q, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|SS Chain s, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|UU Chain u, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|WW Chain w, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
Length = 241
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 43/158 (27%), Positives = 63/158 (39%), Gaps = 38/158 (24%)
Query: 102 YPVIWMKMDTAKKMEPLPISMSGSLIIH-----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y V W++ K +E L I +G I + RF ++ D T L + ++ D
Sbjct: 37 YAVSWVRQAPGKGLEWLSIINAGGGDIDYADSVEGRFTISRDNSKETLYLQMTNLRVEDT 96
Query: 157 GIYKCEVIISLNNKVSAEVELIVRRPPIISD---------------NSTRSVIV------ 195
G+Y C +S+ VSA E R ++ D ST+ V
Sbjct: 97 GVYYCAKHMSMQQVVSAGWE----RADLVGDAFDVWGQGTMVTVSSASTKGPSVFPLAPS 152
Query: 196 ---SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ G T L C FP P T+SW NS AL++G
Sbjct: 153 SKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 187
>pdb|4FNL|H Chain H, Crystal Structure Of Broadly Neutralizing Antibody C05
pdb|4FNL|I Chain I, Crystal Structure Of Broadly Neutralizing Antibody C05
Length = 247
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 43/158 (27%), Positives = 63/158 (39%), Gaps = 38/158 (24%)
Query: 102 YPVIWMKMDTAKKMEPLPISMSGSLIIH-----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y V W++ K +E L I +G I + RF ++ D T L + ++ D
Sbjct: 37 YAVSWVRQAPGKGLEWLSIINAGGGDIDYADSVEGRFTISRDNSKETLYLQMTNLRVEDT 96
Query: 157 GIYKCEVIISLNNKVSAEVELIVRRPPIISD---------------NSTRSVIV------ 195
G+Y C +S+ VSA E R ++ D ST+ V
Sbjct: 97 GVYYCAKHMSMQQVVSAGWE----RADLVGDAFDVWGQGTMVTVSSASTKGPSVFPLAPS 152
Query: 196 ---SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ G T L C FP P T+SW NS AL++G
Sbjct: 153 SKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 187
>pdb|3OJM|B Chain B, Crystal Structure Of Fgf1 Complexed With The Ectodomain Of
Fgfr2b Harboring P253r Apert Mutation
Length = 231
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 44/196 (22%), Positives = 70/196 (35%), Gaps = 25/196 (12%)
Query: 191 RSVIVSEGQTVYLYCYANGFPAPTISWRRDNSA---ALSTGGSIYRGN--ILKIPNITKT 245
R V TV C A G P PT+ W ++ GG R L + ++ +
Sbjct: 27 RLHAVPAANTVKFRCPAGGNPMPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPS 86
Query: 246 DRGTYYCVAQNGVG---RGMKRNIAVEVEFAPVITINRPRQGQA-LQYDAILECHVEAYP 301
D+G Y CV +N G ++ P++ P + D C V +
Sbjct: 87 DKGNYTCVVENEYGSINHTYHLDVVERSRHRPILQAGLPANASTVVGGDVEFVCKVYSDA 146
Query: 302 PPAIVWIK-----------DGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYA 350
P I WIK DG+ + + H + ++ L + + G+Y
Sbjct: 147 QPHIQWIKHVEKNGSKYGPDGLPYLK----VLKHSGINSSNAEV-LALFNVTEADAGEYI 201
Query: 351 CKAANKYGSAQKEIEL 366
CK +N G A + L
Sbjct: 202 CKVSNYIGQANQSAWL 217
Score = 28.1 bits (61), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 30/135 (22%), Positives = 48/135 (35%), Gaps = 18/135 (13%)
Query: 144 YILSIKEIQETDAGIYKCEV---IISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQT 200
+ L ++ + +D G Y C V S+N+ +V R PI+ + G
Sbjct: 76 WSLIMESVVPSDKGNYTCVVENEYGSINHTYHLDVVERSRHRPILQAGLPANASTVVGGD 135
Query: 201 VYLYCYANGFPAPTISWRRD---NSAALSTGGSIY------------RGNILKIPNITKT 245
V C P I W + N + G Y +L + N+T+
Sbjct: 136 VEFVCKVYSDAQPHIQWIKHVEKNGSKYGPDGLPYLKVLKHSGINSSNAEVLALFNVTEA 195
Query: 246 DRGTYYCVAQNGVGR 260
D G Y C N +G+
Sbjct: 196 DAGEYICKVSNYIGQ 210
>pdb|3MTR|A Chain A, Crystal Structure Of The Ig5-Fn1 Tandem Of Human Ncam
pdb|3MTR|B Chain B, Crystal Structure Of The Ig5-Fn1 Tandem Of Human Ncam
Length = 215
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 3/79 (3%)
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACK 352
+ C V AYP I W +DG Q++ + +Y S+ + S + L V FG Y C
Sbjct: 38 ITCEVFAYPSATISWFRDG-QLLPSSNY--SNIKIYNTPSASYLEVTPDSENDFGNYNCT 94
Query: 353 AANKYGSAQKEIELFDRET 371
A N+ G E L +T
Sbjct: 95 AVNRIGQESLEFILVQADT 113
Score = 35.4 bits (80), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 6/86 (6%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGS---IYR---GNILKIPNITKT 245
+V EG V + C +P+ TISW RD S+ S IY + L++ ++
Sbjct: 27 AVYTWEGNQVNITCEVFAYPSATISWFRDGQLLPSSNYSNIKIYNTPSASYLEVTPDSEN 86
Query: 246 DRGTYYCVAQNGVGRGMKRNIAVEVE 271
D G Y C A N +G+ I V+ +
Sbjct: 87 DFGNYNCTAVNRIGQESLEFILVQAD 112
>pdb|2Y25|A Chain A, Crystal Structure Of The Myomesin Domains My11-My13
pdb|2Y25|B Chain B, Crystal Structure Of The Myomesin Domains My11-My13
pdb|2Y25|C Chain C, Crystal Structure Of The Myomesin Domains My11-My13
pdb|2Y25|D Chain D, Crystal Structure Of The Myomesin Domains My11-My13
Length = 317
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 61/257 (23%), Positives = 101/257 (39%), Gaps = 58/257 (22%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNN-------KVSAEV--ELIVRRPPIISDNSTRSVIVS 196
L I E + DAGIY EVI+ + K+ E EL++ I+ ++T I S
Sbjct: 63 LLITEFSKKDAGIY--EVILKDDRGKDKSRLKLVDEAFKELMMEVCKKIALSATDLKIQS 120
Query: 197 EGQTVYLYCYANGFPAP-TISWRRDNSA--------ALSTGGSIYRGNILKIPNITKTDR 247
+ + LY + + ++W + SA TG I+ L+I T D+
Sbjct: 121 TAEGIQLYSFVTYYVEDLKVNWSHNGSAIRYSDRVKTGVTGEQIW----LQINEPTPNDK 176
Query: 248 GTYYCVAQNGVGRGMKRNIAVE--------VEF-----APVITINRPR------------ 282
G Y +G G ++ + + EF A + NR R
Sbjct: 177 GKYVMELFDG-KTGHQKTVDLSGQAYDEAYAEFQRLKQAAIAEKNRARVLGGLPDVVTIQ 235
Query: 283 QGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIE 342
+G+AL L C+V PPP + W+K+ + ++ H ++ A + + +
Sbjct: 236 EGKALN----LTCNVWGDPPPEVSWLKNEKALASDDHCNLKFEAGRTAY----FTINGVS 287
Query: 343 RRQFGQYACKAANKYGS 359
G+Y NKYGS
Sbjct: 288 TADSGKYGLVVKNKYGS 304
>pdb|2FDB|P Chain P, Crystal Structure Of Fibroblast Growth Factor (Fgf)8b In
Complex With Fgf Receptor (Fgfr) 2c
pdb|2FDB|R Chain R, Crystal Structure Of Fibroblast Growth Factor (Fgf)8b In
Complex With Fgf Receptor (Fgfr) 2c
Length = 220
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 44/183 (24%), Positives = 64/183 (34%), Gaps = 21/183 (11%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDNSA---ALSTGGSIYRGNI--LKIPNITKTDRGT 249
V TV C A G P PT+ W ++ GG R L + ++ +D+G
Sbjct: 21 VPAANTVKFRCPAGGNPMPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPSDKGN 80
Query: 250 YYCVAQNGVG---RGMKRNIAVEVEFAPVITINRPRQGQA-LQYDAILECHVEAYPPPAI 305
Y CV +N G ++ P++ P + D C V + P I
Sbjct: 81 YTCVVENEYGSINHTYHLDVVERSRHRPILQAGLPANASTVVGGDVEFVCKVYSDAQPHI 140
Query: 306 VWIKDGVQIMNNQHYSVSHF-------ATSDEFSDTSLRVITIERRQF---GQYACKAAN 355
WIK + N Y A +D + V+ I F G+Y C A N
Sbjct: 141 QWIKHVEK--NGSKYGPDGLPYLKVLKAAGVNTTDKEIEVLYIRNVTFEDAGEYTCLAGN 198
Query: 356 KYG 358
G
Sbjct: 199 SIG 201
Score = 28.5 bits (62), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 4/74 (5%)
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACK 352
C P P + W+K+G + Q + + + ++ SL + ++ G Y C
Sbjct: 29 FRCPAGGNPMPTMRWLKNGKEF--KQEHRIGGYKVRNQH--WSLIMESVVPSDKGNYTCV 84
Query: 353 AANKYGSAQKEIEL 366
N+YGS L
Sbjct: 85 VENEYGSINHTYHL 98
Score = 28.5 bits (62), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 32/136 (23%), Positives = 48/136 (35%), Gaps = 20/136 (14%)
Query: 144 YILSIKEIQETDAGIYKCEV---IISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQT 200
+ L ++ + +D G Y C V S+N+ +V R PI+ + G
Sbjct: 66 WSLIMESVVPSDKGNYTCVVENEYGSINHTYHLDVVERSRHRPILQAGLPANASTVVGGD 125
Query: 201 VYLYCYANGFPAPTISWRRD---NSAALSTGGSIYRG--------------NILKIPNIT 243
V C P I W + N + G Y +L I N+T
Sbjct: 126 VEFVCKVYSDAQPHIQWIKHVEKNGSKYGPDGLPYLKVLKAAGVNTTDKEIEVLYIRNVT 185
Query: 244 KTDRGTYYCVAQNGVG 259
D G Y C+A N +G
Sbjct: 186 FEDAGEYTCLAGNSIG 201
>pdb|1IIL|E Chain E, Crystal Structure Of Pro253arg Apert Mutant Fgf Receptor 2
(Fgfr2) In Complex With Fgf2
pdb|1IIL|F Chain F, Crystal Structure Of Pro253arg Apert Mutant Fgf Receptor 2
(Fgfr2) In Complex With Fgf2
pdb|1IIL|G Chain G, Crystal Structure Of Pro253arg Apert Mutant Fgf Receptor 2
(Fgfr2) In Complex With Fgf2
pdb|1IIL|H Chain H, Crystal Structure Of Pro253arg Apert Mutant Fgf Receptor 2
(Fgfr2) In Complex With Fgf2
Length = 220
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 44/183 (24%), Positives = 64/183 (34%), Gaps = 21/183 (11%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDNSA---ALSTGGSIYRGN--ILKIPNITKTDRGT 249
V TV C A G P PT+ W ++ GG R L + ++ +D+G
Sbjct: 23 VPAANTVKFRCPAGGNPMPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPSDKGN 82
Query: 250 YYCVAQNGVG---RGMKRNIAVEVEFAPVITINRPRQGQA-LQYDAILECHVEAYPPPAI 305
Y CV +N G ++ P++ P + D C V + P I
Sbjct: 83 YTCVVENEYGSINHTYHLDVVERSRHRPILQAGLPANASTVVGGDVEFVCKVYSDAQPHI 142
Query: 306 VWIKDGVQIMNNQHYSVSHF-------ATSDEFSDTSLRVITIERRQF---GQYACKAAN 355
WIK + N Y A +D + V+ I F G+Y C A N
Sbjct: 143 QWIKHVEK--NGSKYGPDGLPYLKVLKAAGVNTTDKEIEVLYIRNVTFEDAGEYTCLAGN 200
Query: 356 KYG 358
G
Sbjct: 201 SIG 203
Score = 28.5 bits (62), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 4/74 (5%)
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACK 352
C P P + W+K+G + Q + + + ++ SL + ++ G Y C
Sbjct: 31 FRCPAGGNPMPTMRWLKNGKEF--KQEHRIGGYKVRNQH--WSLIMESVVPSDKGNYTCV 86
Query: 353 AANKYGSAQKEIEL 366
N+YGS L
Sbjct: 87 VENEYGSINHTYHL 100
Score = 28.1 bits (61), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 32/136 (23%), Positives = 48/136 (35%), Gaps = 20/136 (14%)
Query: 144 YILSIKEIQETDAGIYKCEV---IISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQT 200
+ L ++ + +D G Y C V S+N+ +V R PI+ + G
Sbjct: 68 WSLIMESVVPSDKGNYTCVVENEYGSINHTYHLDVVERSRHRPILQAGLPANASTVVGGD 127
Query: 201 VYLYCYANGFPAPTISWRRD---NSAALSTGGSIYRG--------------NILKIPNIT 243
V C P I W + N + G Y +L I N+T
Sbjct: 128 VEFVCKVYSDAQPHIQWIKHVEKNGSKYGPDGLPYLKVLKAAGVNTTDKEIEVLYIRNVT 187
Query: 244 KTDRGTYYCVAQNGVG 259
D G Y C+A N +G
Sbjct: 188 FEDAGEYTCLAGNSIG 203
>pdb|3OJ2|C Chain C, Crystal Structure Of Fgf1 Complexed With The Ectodomain Of
Fgfr2b Harboring The A172f Pfeiffer Syndrome Mutation
pdb|3OJ2|D Chain D, Crystal Structure Of Fgf1 Complexed With The Ectodomain Of
Fgfr2b Harboring The A172f Pfeiffer Syndrome Mutation
Length = 231
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 42/187 (22%), Positives = 68/187 (36%), Gaps = 25/187 (13%)
Query: 200 TVYLYCYANGFPAPTISWRRDNSA---ALSTGGSIYRGN--ILKIPNITKTDRGTYYCVA 254
TV C A G P PT+ W ++ GG R L + ++ +D+G Y CV
Sbjct: 36 TVKFRCPAGGNPMPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPSDKGNYTCVV 95
Query: 255 QNGVG---RGMKRNIAVEVEFAPVITINRPRQGQA-LQYDAILECHVEAYPPPAIVWIK- 309
+N G ++ P++ P + D C V + P I WIK
Sbjct: 96 ENEYGSINHTYHLDVVERSPHRPILQAGLPANASTVVGGDVEFVCKVYSDAQPHIQWIKH 155
Query: 310 ----------DGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGS 359
DG+ + + H + ++ L + + G+Y CK +N G
Sbjct: 156 VEKNGSKYGPDGLPYLK----VLKHSGINSSNAEV-LALFNVTEADAGEYICKVSNYIGQ 210
Query: 360 AQKEIEL 366
A + L
Sbjct: 211 ANQSAWL 217
>pdb|2EO9|A Chain A, Solution Structure Of The Fifth Ig-Like Domain From Human
Roundabout Homo1
Length = 118
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 34/80 (42%), Gaps = 3/80 (3%)
Query: 182 PPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYR--GNILKI 239
PP+I + +G T L C A G P PTI WR+D + I + +L+I
Sbjct: 8 PPVIRQGPVNQTVAVDG-TFVLSCVATGSPVPTILWRKDGVLVSTQDSRIKQLENGVLQI 66
Query: 240 PNITKTDRGTYYCVAQNGVG 259
D G Y C+A G
Sbjct: 67 RYAKLGDTGRYTCIASTPSG 86
Score = 31.6 bits (70), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 29/110 (26%), Positives = 45/110 (40%), Gaps = 11/110 (10%)
Query: 274 PVITINRPRQGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSD 333
PVI Q A+ +L C P P I+W KDGV +++ Q + + +
Sbjct: 9 PVIRQGPVNQTVAVDGTFVLSCVATGSPVPTILWRKDGV-LVSTQDSRI------KQLEN 61
Query: 334 TSLRVITIERRQFGQYACKAANKYG----SAQKEIELFDRETQTGDETFP 379
L++ + G+Y C A+ G SA E++ F Q T P
Sbjct: 62 GVLQIRYAKLGDTGRYTCIASTPSGEATWSAYIEVQEFGVPVQPPRPTDP 111
>pdb|2YR3|A Chain A, Solution Structure Of The Fourth Ig-Like Domain From
Myosin Light Chain Kinase, Smooth Muscle
Length = 99
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 3/68 (4%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNI--LKIPNITKTDRGTYYC 252
V EGQ L C G P P I+W N + S + L I + D GTY C
Sbjct: 23 VIEGQDFVLQCSVRGTPVPRITWLL-NGQPIQYARSTCEAGVAELHIQDALPEDHGTYTC 81
Query: 253 VAQNGVGR 260
+A+N +G+
Sbjct: 82 LAENALGQ 89
Score = 28.5 bits (62), Expect = 7.1, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 25/67 (37%), Gaps = 3/67 (4%)
Query: 290 DAILECHVEAYPPPAIVWIKDGVQIM---NNQHYSVSHFATSDEFSDTSLRVITIERRQF 346
D +L+C V P P I W+ +G I + V+ D + +
Sbjct: 28 DFVLQCSVRGTPVPRITWLLNGQPIQYARSTCEAGVAELHIQDALPEDHGTYTCLAENAL 87
Query: 347 GQYACKA 353
GQ +C A
Sbjct: 88 GQVSCSA 94
>pdb|2XY2|A Chain A, Crystal Structure Of Ncam2 Ig1-2
Length = 189
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 34/129 (26%), Positives = 57/129 (44%), Gaps = 14/129 (10%)
Query: 189 STRSVIVSEGQTVYLYCYANGFPAPTISWRR-DNSAALSTGGSIYRG----NILKIPNIT 243
S V +S G++ + C A G P +I W +ST + + + L I N
Sbjct: 8 SLSKVELSVGESKFFTCTAIGEP-ESIDWYNPQGEKIISTQRVVVQKEGVRSRLTIYNAN 66
Query: 244 KTDRGTYYCVAQNGVGRGMKRNIAVEV----EFAPVITINRPRQGQALQYDAILECHVEA 299
D G Y C A + G+ + + +E+ F V++ +QG+ DA + C V +
Sbjct: 67 IEDAGIYRCQATDAKGQTQEATVVLEIYQKLTFREVVSPQEFKQGE----DAEVVCRVSS 122
Query: 300 YPPPAIVWI 308
P PA+ W+
Sbjct: 123 SPAPAVSWL 131
Score = 32.3 bits (72), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 37/131 (28%), Positives = 55/131 (41%), Gaps = 20/131 (15%)
Query: 155 DAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVI----VSEGQTVYLYCYANGF 210
DAGIY+C+ + A V L I + R V+ +G+ + C +
Sbjct: 69 DAGIYRCQATDAKGQTQEATVVL-----EIYQKLTFREVVSPQEFKQGEDAEVVCRVSSS 123
Query: 211 PAPTISWRRDNSAALSTGG---SIYRGNILKIPNITKTDRGTYYCVAQNGVGRGMKRNIA 267
PAP +SW N + ++ N L+I NI K+D G Y C GR R
Sbjct: 124 PAPAVSWLYHNEEVTTISDNRFAMLANNNLQILNINKSDEGIYRC-----EGRVEARG-- 176
Query: 268 VEVEFAPVITI 278
E++F +I I
Sbjct: 177 -EIDFRDIIVI 186
>pdb|1E0O|B Chain B, Crystal Structure Of A Ternary Fgf1-Fgfr2-Heparin Complex
pdb|1E0O|D Chain D, Crystal Structure Of A Ternary Fgf1-Fgfr2-Heparin Complex
Length = 219
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 44/183 (24%), Positives = 64/183 (34%), Gaps = 21/183 (11%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDNSA---ALSTGGSIYRGN--ILKIPNITKTDRGT 249
V TV C A G P PT+ W ++ GG R L + ++ +D+G
Sbjct: 22 VPAANTVKFRCPAGGNPMPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPSDKGN 81
Query: 250 YYCVAQNGVG---RGMKRNIAVEVEFAPVITINRPRQGQA-LQYDAILECHVEAYPPPAI 305
Y CV +N G ++ P++ P + D C V + P I
Sbjct: 82 YTCVVENEYGSINHTYHLDVVERSPHRPILQAGLPANASTVVGGDVEFVCKVYSDAQPHI 141
Query: 306 VWIKDGVQIMNNQHYSVSHF-------ATSDEFSDTSLRVITIERRQF---GQYACKAAN 355
WIK + N Y A +D + V+ I F G+Y C A N
Sbjct: 142 QWIKHVEK--NGSKYGPDGLPYLKVLKAAGVNTTDKEIEVLYIRNVTFEDAGEYTCLAGN 199
Query: 356 KYG 358
G
Sbjct: 200 SIG 202
Score = 28.5 bits (62), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 4/74 (5%)
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACK 352
C P P + W+K+G + Q + + + ++ SL + ++ G Y C
Sbjct: 30 FRCPAGGNPMPTMRWLKNGKEF--KQEHRIGGYKVRNQH--WSLIMESVVPSDKGNYTCV 85
Query: 353 AANKYGSAQKEIEL 366
N+YGS L
Sbjct: 86 VENEYGSINHTYHL 99
>pdb|1YED|L Chain L, Structure Of A Catalytic Antibody Igg2a Fab Fragment
(D2.4)
pdb|1YED|A Chain A, Structure Of A Catalytic Antibody Igg2a Fab Fragment
(D2.4)
Length = 219
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 48/195 (24%), Positives = 77/195 (39%), Gaps = 14/195 (7%)
Query: 175 VELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT-----ISWRRDNSAALSTGG 229
+ + + +P IS S++S++ S G+T + +P +S TG
Sbjct: 11 LSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIYLVSKLESGVPDRFTGS 70
Query: 230 SIYRGNILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQ 285
LKI + D G YYCV G G K I + + AP ++I P Q
Sbjct: 71 GSGTDFTLKISRVEAADLGVYYCVQGTHFPYTFGGGTKLEI-LRADAAPTVSIFPPSSEQ 129
Query: 286 ALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI- 341
A + C + + P I W DG + N S + + D +S +S +T
Sbjct: 130 LTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKD 189
Query: 342 ERRQFGQYACKAANK 356
E + Y C+A +K
Sbjct: 190 EYERHNSYTCEATHK 204
>pdb|1ADQ|L Chain L, Crystal Structure Of A Human Igm Rheumatoid Factor Fab In
Complex With Its Autoantigen Igg Fc
Length = 213
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 37/200 (18%), Positives = 75/200 (37%), Gaps = 27/200 (13%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALS------------------TGGSIYR 233
SV V+ GQT + C N + ++ W + +G +
Sbjct: 8 SVSVAPGQTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPPGIPERFSGSNSGN 67
Query: 234 GNILKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQGQAL 287
L I + D YYC + G G K + + + AP +T+ P +
Sbjct: 68 TATLTISRVEAGDEADYYCQVWDSSSDHAVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQ 127
Query: 288 QYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-R 344
A L C + + P A + W DG + + ++++++ +S +T E+ +
Sbjct: 128 ANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWK 187
Query: 345 QFGQYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 188 SHKSYSCQVTHEGSTVEKTV 207
>pdb|3MLV|L Chain L, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With An Nof V3 Peptide
pdb|3MLV|M Chain M, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With An Nof V3 Peptide
Length = 219
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 43/208 (20%), Positives = 78/208 (37%), Gaps = 35/208 (16%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISW---RRDNSAALS---------------TGGSIYR 233
SV VS GQT + C + +SW R S L +G +
Sbjct: 9 SVSVSPGQTASISCSGDKLDDKYVSWYYQRPGQSPVLLMYQDFKRPSGIPERLSGSKSGK 68
Query: 234 GNILKIPNITKTDRGTYYCVAQN---GV-----------GRGMKRNIAVEVEFAPVITIN 279
L I D G YYC A + GV G G + + + + AP +T+
Sbjct: 69 TATLTISGTQSLDEGDYYCQAWDASTGVSGGGTKLTVLFGEGTRLTVLAQPKAAPSVTLF 128
Query: 280 RPRQGQALQYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLR 337
P + A L C + + P A + W D + + ++++++ +S
Sbjct: 129 PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL 188
Query: 338 VITIER-RQFGQYACKAANKYGSAQKEI 364
+T E+ + Y+C+ ++ + +K +
Sbjct: 189 SLTPEQWKSHKSYSCQVTHEGSTVEKTV 216
>pdb|1EV2|E Chain E, Crystal Structure Of Fgf2 In Complex With The
Extracellular Ligand Binding Domain Of Fgf Receptor 2
(Fgfr2)
pdb|1EV2|F Chain F, Crystal Structure Of Fgf2 In Complex With The
Extracellular Ligand Binding Domain Of Fgf Receptor 2
(Fgfr2)
pdb|1EV2|G Chain G, Crystal Structure Of Fgf2 In Complex With The
Extracellular Ligand Binding Domain Of Fgf Receptor 2
(Fgfr2)
pdb|1EV2|H Chain H, Crystal Structure Of Fgf2 In Complex With The
Extracellular Ligand Binding Domain Of Fgf Receptor 2
(Fgfr2)
Length = 220
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 44/183 (24%), Positives = 64/183 (34%), Gaps = 21/183 (11%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDNSA---ALSTGGSIYRGN--ILKIPNITKTDRGT 249
V TV C A G P PT+ W ++ GG R L + ++ +D+G
Sbjct: 23 VPAANTVKFRCPAGGNPMPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPSDKGN 82
Query: 250 YYCVAQNGVG---RGMKRNIAVEVEFAPVITINRPRQGQA-LQYDAILECHVEAYPPPAI 305
Y CV +N G ++ P++ P + D C V + P I
Sbjct: 83 YTCVVENEYGSINHTYHLDVVERSPHRPILQAGLPANASTVVGGDVEFVCKVYSDAQPHI 142
Query: 306 VWIKDGVQIMNNQHYSVSHF-------ATSDEFSDTSLRVITIERRQF---GQYACKAAN 355
WIK + N Y A +D + V+ I F G+Y C A N
Sbjct: 143 QWIKHVEK--NGSKYGPDGLPYLKVLKAAGVNTTDKEIEVLYIRNVTFEDAGEYTCLAGN 200
Query: 356 KYG 358
G
Sbjct: 201 SIG 203
Score = 28.5 bits (62), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 4/74 (5%)
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACK 352
C P P + W+K+G + Q + + + ++ SL + ++ G Y C
Sbjct: 31 FRCPAGGNPMPTMRWLKNGKEF--KQEHRIGGYKVRNQH--WSLIMESVVPSDKGNYTCV 86
Query: 353 AANKYGSAQKEIEL 366
N+YGS L
Sbjct: 87 VENEYGSINHTYHL 100
>pdb|3MLU|L Chain L, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With A Zam18 V3 Peptide
Length = 218
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 43/208 (20%), Positives = 78/208 (37%), Gaps = 35/208 (16%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISW---RRDNSAALS---------------TGGSIYR 233
SV VS GQT + C + +SW R S L +G +
Sbjct: 8 SVSVSPGQTASISCSGDKLDDKYVSWYYQRPGQSPVLLMYQDFKRPSGIPERLSGSKSGK 67
Query: 234 GNILKIPNITKTDRGTYYCVAQN---GV-----------GRGMKRNIAVEVEFAPVITIN 279
L I D G YYC A + GV G G + + + + AP +T+
Sbjct: 68 TATLTISGTQSLDEGDYYCQAWDASTGVSGGGTKLTVLFGEGTRLTVLAQPKAAPSVTLF 127
Query: 280 RPRQGQALQYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLR 337
P + A L C + + P A + W D + + ++++++ +S
Sbjct: 128 PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL 187
Query: 338 VITIER-RQFGQYACKAANKYGSAQKEI 364
+T E+ + Y+C+ ++ + +K +
Sbjct: 188 SLTPEQWKSHKSYSCQVTHEGSTVEKTV 215
>pdb|3BIK|B Chain B, Crystal Structure Of The Pd-1PD-L1 Complex
pdb|3BIK|C Chain C, Crystal Structure Of The Pd-1PD-L1 Complex
Length = 134
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 48/96 (50%), Gaps = 7/96 (7%)
Query: 90 ADLKCSV-QYADDYPVIWMKMDTAKKMEPLPISMSG-SLIIHDSRFQLTTDPETSTYILS 147
A CS+ +++D + W ++ + + E +G S + D+RFQ+ P + ++
Sbjct: 27 ATFTCSLSNWSEDLMLNWNRLSPSNQTEKQAAFSNGLSQPVQDARFQIIQLPNRHDFHMN 86
Query: 148 IKEIQETDAGIYKCEVIISLNNKVSAE----VELIV 179
I + + D+GIY C ISL+ K E EL+V
Sbjct: 87 ILDTRRNDSGIYLCGA-ISLHPKAKIEESPGAELVV 121
>pdb|3BP6|A Chain A, Crystal Structure Of The Mouse Pd-1 Mutant And Pd-L2
Complex
pdb|3RNK|A Chain A, Crystal Structure Of The Complex Between Mouse Pd-1 Mutant
And Pd-L2 Igv Domain
pdb|3SBW|A Chain A, Crystal Structure Of The Complex Between The Extracellular
Domains Of Mouse Pd-1 Mutant And Human Pd-L1
pdb|3SBW|B Chain B, Crystal Structure Of The Complex Between The Extracellular
Domains Of Mouse Pd-1 Mutant And Human Pd-L1
Length = 117
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 27/97 (27%), Positives = 49/97 (50%), Gaps = 7/97 (7%)
Query: 89 TADLKCSV-QYADDYPVIWMKMDTAKKMEPLPISMSG-SLIIHDSRFQLTTDPETSTYIL 146
A CS+ +++D + W ++ + + E +G S + D+RFQ+ P + +
Sbjct: 16 NATFTCSLSNWSEDLMLNWNRLSPSNQTEKQAAFSNGLSQPVQDARFQIIQLPNRHDFHM 75
Query: 147 SIKEIQETDAGIYKCEVIISLNNKVSAE----VELIV 179
+I + + D+GIY C ISL+ K+ E EL+V
Sbjct: 76 NILDTRRNDSGIYLCGA-ISLHPKLKIEESPGAELVV 111
>pdb|1YEE|L Chain L, Structure Of A Catalytic Antibody, Igg2a Fab Fragment
(D2.5)
Length = 219
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 48/195 (24%), Positives = 77/195 (39%), Gaps = 14/195 (7%)
Query: 175 VELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT-----ISWRRDNSAALSTGG 229
+ + + +P IS S++S++ S G+T + +P +S TG
Sbjct: 11 LSVTIGQPASISCKSSQSLLYSNGKTYLSWLLQRPGQSPKRLIYLVSKLDSGVPDRFTGS 70
Query: 230 SIYRGNILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQ 285
LKI + D G YYCV G G K I + + AP ++I P Q
Sbjct: 71 GSGTDFTLKISRVEAADLGLYYCVQGTHFPYTFGGGTKLEI-LRADAAPTVSIFPPSSEQ 129
Query: 286 ALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI- 341
A + C + + P I W DG + N S + + D +S +S +T
Sbjct: 130 LTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKD 189
Query: 342 ERRQFGQYACKAANK 356
E + Y C+A +K
Sbjct: 190 EYERHNSYTCEATHK 204
>pdb|2RCJ|C Chain C, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|D Chain D, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|G Chain G, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|H Chain H, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|K Chain K, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|L Chain L, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|O Chain O, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|P Chain P, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|S Chain S, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|T Chain T, Solution Structure Of Human Immunoglobulin M
Length = 523
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 31/154 (20%), Positives = 63/154 (40%), Gaps = 10/154 (6%)
Query: 237 LKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQGQALQYD 290
L I + D YYC + N G G K + + + P +T+ P +
Sbjct: 72 LAISGLEAEDESDYYCASWNSSDNSYVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANK 131
Query: 291 AILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQFG 347
A L C + + P A + W DG + + ++++++ +S +T E+ +
Sbjct: 132 ATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHR 191
Query: 348 QYACKAANKYGSAQKEIELFDRETQT-GDETFPI 380
Y+C+ ++ + +K + + T G FP+
Sbjct: 192 SYSCQVTHEGSTVEKTVAPTECSASTKGPSVFPL 225
>pdb|1II4|E Chain E, Crystal Structure Of Ser252trp Apert Mutant Fgf Receptor 2
(Fgfr2) In Complex With Fgf2
pdb|1II4|F Chain F, Crystal Structure Of Ser252trp Apert Mutant Fgf Receptor 2
(Fgfr2) In Complex With Fgf2
pdb|1II4|G Chain G, Crystal Structure Of Ser252trp Apert Mutant Fgf Receptor 2
(Fgfr2) In Complex With Fgf2
pdb|1II4|H Chain H, Crystal Structure Of Ser252trp Apert Mutant Fgf Receptor 2
(Fgfr2) In Complex With Fgf2
Length = 220
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 45/187 (24%), Positives = 65/187 (34%), Gaps = 21/187 (11%)
Query: 191 RSVIVSEGQTVYLYCYANGFPAPTISWRRDNSA---ALSTGGSIYRGNI--LKIPNITKT 245
R V TV C A G P PT+ W ++ GG R L + ++ +
Sbjct: 19 RLHAVPAANTVKFRCPAGGNPMPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPS 78
Query: 246 DRGTYYCVAQNGVG---RGMKRNIAVEVEFAPVITINRPRQGQA-LQYDAILECHVEAYP 301
D+G Y CV +N G ++ P++ P + D C V +
Sbjct: 79 DKGNYTCVVENEYGSINHTYHLDVVERWPHRPILQAGLPANASTVVGGDVEFVCKVYSDA 138
Query: 302 PPAIVWIKDGVQIMNNQHYSVSHF-------ATSDEFSDTSLRVITIERRQF---GQYAC 351
P I WIK + N Y A +D + V+ I F G+Y C
Sbjct: 139 QPHIQWIKHVEK--NGSKYGPDGLPYLKVLKAAGVNTTDKEIEVLYIRNVTFEDAGEYTC 196
Query: 352 KAANKYG 358
A N G
Sbjct: 197 LAGNSIG 203
Score = 28.5 bits (62), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 4/74 (5%)
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACK 352
C P P + W+K+G + Q + + + ++ SL + ++ G Y C
Sbjct: 31 FRCPAGGNPMPTMRWLKNGKEF--KQEHRIGGYKVRNQH--WSLIMESVVPSDKGNYTCV 86
Query: 353 AANKYGSAQKEIEL 366
N+YGS L
Sbjct: 87 VENEYGSINHTYHL 100
>pdb|1NPU|A Chain A, Crystal Structure Of The Extracellular Domain Of Murine
Pd-1
pdb|3BP5|A Chain A, Crystal Structure Of The Mouse Pd-1 And Pd-L2 Complex
Length = 117
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 27/97 (27%), Positives = 48/97 (49%), Gaps = 7/97 (7%)
Query: 89 TADLKCSV-QYADDYPVIWMKMDTAKKMEPLPISMSG-SLIIHDSRFQLTTDPETSTYIL 146
A CS+ +++D + W ++ + + E +G S + D+RFQ+ P + +
Sbjct: 16 NATFTCSLSNWSEDLMLNWNRLSPSNQTEKQAAFSNGLSQPVQDARFQIIQLPNRHDFHM 75
Query: 147 SIKEIQETDAGIYKCEVIISLNNKVSAE----VELIV 179
+I + + D+GIY C ISL+ K E EL+V
Sbjct: 76 NILDTRRNDSGIYLCGA-ISLHPKAKIEESPGAELVV 111
>pdb|1GL4|B Chain B, Nidogen-1 G2PERLECAN IG3 COMPLEX
Length = 98
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 2/77 (2%)
Query: 181 RPPIISDNSTRSVIVSEGQTVYLYCYANG-FPAPTISWRRDNSAALSTGGSIYRGNILKI 239
+P +++ RS V G V C A PA T+ W R ++ L + + G IL I
Sbjct: 8 KPIMVTVEEQRSQSVRPGADVTFICTAKSKSPAYTLVWTRLHNGKLPSRAMDFNG-ILTI 66
Query: 240 PNITKTDRGTYYCVAQN 256
N+ +D GTY C N
Sbjct: 67 RNVQPSDAGTYVCTGSN 83
>pdb|2B0S|L Chain L, Crystal Structure Analysis Of Anti-Hiv-1 V3 Fab 2219 In
Complex With Mn Peptide
pdb|2B1A|L Chain L, Crystal Structure Analysis Of Anti-Hiv-1 V3 Fab 2219 In
Complex With Ug1033 Peptide
pdb|2B1H|L Chain L, Crystal Structure Analysis Of Anti-Hiv-1 V3 Fab 2219 In
Complex With Ug29 Peptide
Length = 215
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 28/139 (20%), Positives = 58/139 (41%), Gaps = 11/139 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG--------VGRGMKRNIAVEVEFAPVITINRPRQGQALQ 288
L I + D G YYC A + G G K + + + AP +T+ P +
Sbjct: 74 LAISGLRPEDEGDYYCAAWDDSRGGPDWVFGGGTKLTVLAQPKAAPSVTLFPPSSEELQA 133
Query: 289 YDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQ 345
A L C + + P A + W D + + ++++++ +S +T E+ +
Sbjct: 134 NKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKS 193
Query: 346 FGQYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 194 HKSYSCQVTHEGSTVEKTV 212
>pdb|1C5D|H Chain H, The Crystal Structure Of The Fab Fragment Of A Rat
Monoclonal Antibody Against The Main Immunogenic Region
Of The Human Muscle Acetylcholine Receptor
pdb|1C5D|B Chain B, The Crystal Structure Of The Fab Fragment Of A Rat
Monoclonal Antibody Against The Main Immunogenic Region
Of The Human Muscle Acetylcholine Receptor
Length = 215
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 39/152 (25%), Positives = 56/152 (36%), Gaps = 33/152 (21%)
Query: 194 IVSEGQTVYLYCYANGFPAPT--ISWRRDNS-------AALSTGGSIYRGN--------- 235
+V QT+ L C +GFP T +SW R AA+S+GGS Y +
Sbjct: 11 LVQPSQTLSLTCTVSGFPLTTNGVSWVRQPPGKGLEWIAAISSGGSPYYNSALKSRLSIN 70
Query: 236 --------ILKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRP 281
LK+ ++ D Y+C ++G G G ++ AP + P
Sbjct: 71 RDTSKSQVFLKMNSLQTEDTAIYFCTREDGWNYFDYWGPGTMVTVSSAQTTAPSVYPLAP 130
Query: 282 RQGQALQYDAILECHVEAY-PPPAIVWIKDGV 312
G L C V+ Y P P V G
Sbjct: 131 GCGDTTSSTVTLGCLVKGYFPEPVTVTWNSGA 162
>pdb|1YEI|L Chain L, Catalytic Antibody D2.3 Complex
pdb|1YEJ|L Chain L, Catalytic Antibody Complex
pdb|1YEK|L Chain L, Catalytic Antibody D2.3 Complex
pdb|1KN2|L Chain L, Catalytic Antibody D2.3 Complex
pdb|1KN4|L Chain L, Catalytic Antibody D2.3 Complex
Length = 219
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 48/195 (24%), Positives = 77/195 (39%), Gaps = 14/195 (7%)
Query: 175 VELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT-----ISWRRDNSAALSTGG 229
+ + + +P IS S++S++ S G+T + +P +S TG
Sbjct: 11 LSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIHLVSKLDSGVPDRITGS 70
Query: 230 SIYRGNILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQ 285
LKI + D G YYCV G G K I + + AP ++I P Q
Sbjct: 71 GSGTDFTLKISRVEAADLGVYYCVQGTHFPYTFGGGTKLEI-LRADAAPTVSIFPPSSEQ 129
Query: 286 ALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI- 341
A + C + + P I W DG + N S + + D +S +S +T
Sbjct: 130 LTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKD 189
Query: 342 ERRQFGQYACKAANK 356
E + Y C+A +K
Sbjct: 190 EYERHNSYTCEATHK 204
>pdb|3CFB|L Chain L, High-Resolution Structure Of Blue Fluorescent Antibody
Ep2-19g2 In Complex With Stilbene Hapten At 100k
pdb|3CFB|A Chain A, High-Resolution Structure Of Blue Fluorescent Antibody
Ep2-19g2 In Complex With Stilbene Hapten At 100k
pdb|3CFC|L Chain L, High-Resolution Structure Of Blue Fluorescent Antibody
Ep2-19g2
Length = 219
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 56/190 (29%), Positives = 81/190 (42%), Gaps = 24/190 (12%)
Query: 185 ISDNSTRSVIVSEGQTVYLYCYAN--GFPAPTISWRRDNSAA-----LSTGGSIYRGN-- 235
IS ST+S++ S G T YLY Y G + ++ N A+ S+ GS G
Sbjct: 21 ISCRSTKSLLHSNGIT-YLYWYLQKPGQSPQLLIYQMSNLASGVPDRFSSSGS---GTDF 76
Query: 236 ILKIPNITKTDRGTYYCVAQN-----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYD 290
L+I + D G YYC AQN G G K I + AP ++I P Q
Sbjct: 77 TLRISRVEAEDVGVYYC-AQNLELPPTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGG 134
Query: 291 AILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQF 346
A + C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 135 ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERH 194
Query: 347 GQYACKAANK 356
Y C+A +K
Sbjct: 195 NSYTCEATHK 204
>pdb|3G6D|L Chain L, Crystal Structure Of The Complex Between Cnto607 Fab And
Il-13
pdb|3G6A|L Chain L, Crystal Structure Of Anti-Il-13 Antibody Cnto607
pdb|3G6A|A Chain A, Crystal Structure Of Anti-Il-13 Antibody Cnto607
Length = 213
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 40/199 (20%), Positives = 75/199 (37%), Gaps = 26/199 (13%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRR-------------DNSAALS-----TGGSIYR 233
SV V+ GQT + C + +SW + DN +G +
Sbjct: 9 SVSVAPGQTARISCSGDNIGGTFVSWYQQKPGQAPVLVIYDDNDRPSGIPERFSGSNSGN 68
Query: 234 GNILKIPNITKTDRGTYYC-----VAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQ 288
L I D YYC V N G G K + + + AP +T+ P +
Sbjct: 69 TATLTISGTQAEDEADYYCGTWDMVTNNVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQA 128
Query: 289 YDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQ 345
A L C + + P A + W D + + ++++++ +S +T E+ +
Sbjct: 129 NKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKS 188
Query: 346 FGQYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 189 HRSYSCQVTHEGSTVEKTV 207
>pdb|1MEX|H Chain H, Antibody Catalysis Of A Bimolecular Cycloaddition Reaction
Length = 215
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 35/137 (25%), Positives = 61/137 (44%), Gaps = 12/137 (8%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
D+ + W+K + +E + IS I ++ +F+ LT D +ST + + + D
Sbjct: 31 DHAIHWVKQKPEQGLEWIGYISPGNGDIKYNEKFKGKATLTADKSSSTAYMQLNSLTSED 90
Query: 156 AGIYKC--EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FPA 212
+ +Y C E + + V PP + + S + +V L C G FP
Sbjct: 91 SAVYFCKMEYLDYWGQGTTLTVSSGGTTPPSVYPLAPGSAAQAATNSVTLGCLVKGYFPE 150
Query: 213 P-TISWRRDNSAALSTG 228
P T++W NS +LS+G
Sbjct: 151 PVTVTW---NSGSLSSG 164
>pdb|3G5Z|A Chain A, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
Length = 213
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 54/200 (27%), Positives = 77/200 (38%), Gaps = 29/200 (14%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGN-------- 235
I+ S S+ VS G TV + C+A+ I W + S G IY G
Sbjct: 2 ILMTQSPSSMSVSLGDTVSITCHASQDIISNIGWLQQKPGK-SFAGLIYHGTNLSDGVPS 60
Query: 236 -----------ILKIPNITKTDRGTYYCV--AQN--GVGRGMKRNIAVEVEFAPVITINR 280
L I ++ D YYCV AQ G G K IA + AP ++I
Sbjct: 61 RFSGSGSGADYSLTISSLESEDFADYYCVQYAQFPWTFGGGTKLEIA-RADAAPTVSIFP 119
Query: 281 PRQGQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLR 337
P Q A + C + + P I W DG + N S + + D +S +S
Sbjct: 120 PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTL 179
Query: 338 VITI-ERRQFGQYACKAANK 356
+T E + Y C+A +K
Sbjct: 180 TLTKDEYERHNSYTCEATHK 199
>pdb|2DM3|A Chain A, Solution Structure Of The Second Ig Domain Of Human
Palladin
Length = 110
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 193 VIVSEGQTVYLYCYANGFPAPTISWRRDNSAAL--STGGSIYRGN---ILKIPNITKTDR 247
+ V EG+ + C +G P P +SW+ D S + R N L I +T D
Sbjct: 19 LTVQEGKLCRMDCKVSGLPTPDLSWQLDGKPVRPDSAHKMLVRENGVHSLIIEPVTSRDA 78
Query: 248 GTYYCVAQNGVGR 260
G Y C+A N G+
Sbjct: 79 GIYTCIATNRAGQ 91
Score = 32.3 bits (72), Expect = 0.48, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 33/82 (40%), Gaps = 4/82 (4%)
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACK 352
++C V P P + W DG + + +H E SL + + R G Y C
Sbjct: 29 MDCKVSGLPTPDLSWQLDGKPVRPDS----AHKMLVRENGVHSLIIEPVTSRDAGIYTCI 84
Query: 353 AANKYGSAQKEIELFDRETQTG 374
A N+ G +EL ++G
Sbjct: 85 ATNRAGQNSFSLELVVAAKESG 106
>pdb|1KEM|L Chain L, Catalytic Antibody 28b4 Fab Fragment
pdb|1KEL|L Chain L, Catalytic Antibody 28b4 Fab Fragment Complexed With Hapten
(1-[n-4'-Nitrobenzyl-N-4'-Carboxybutylamino]
Methylphosphonic Acid)
Length = 217
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 34/127 (26%), Positives = 53/127 (41%), Gaps = 7/127 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEV---EFAPVITINRPRQGQALQYDAIL 293
LKI + D G YYC + V R +E+ + AP ++I P Q A +
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASV 137
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 138 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 197
Query: 350 ACKAANK 356
C+A +K
Sbjct: 198 TCEATHK 204
>pdb|1UB5|L Chain L, Crystal Structure Of Antibody 19g2 With Hapten At 100k
pdb|1UB5|B Chain B, Crystal Structure Of Antibody 19g2 With Hapten At 100k
Length = 214
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 56/190 (29%), Positives = 81/190 (42%), Gaps = 24/190 (12%)
Query: 185 ISDNSTRSVIVSEGQTVYLYCYAN--GFPAPTISWRRDNSAA-----LSTGGSIYRGN-- 235
IS ST+S++ S G T YLY Y G + ++ N A+ S+ GS G
Sbjct: 21 ISCRSTKSLLHSNGIT-YLYWYLQKPGQSPQLLIYQMSNLASGVPNRFSSSGS---GTDF 76
Query: 236 ILKIPNITKTDRGTYYCVAQN-----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYD 290
L+I + D G YYC AQN G G K I + AP ++I P Q
Sbjct: 77 TLRISRVEAEDVGVYYC-AQNLELPPTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGG 134
Query: 291 AILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQF 346
A + C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 135 ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERH 194
Query: 347 GQYACKAANK 356
Y C+A +K
Sbjct: 195 NGYTCEATHK 204
>pdb|3Q6G|L Chain L, Crystal Structure Of Fab Of Rhesus Mab 2.5b Specific For
Quaternary Neutralizing Epitope Of Hiv-1 Gp120
pdb|3Q6G|M Chain M, Crystal Structure Of Fab Of Rhesus Mab 2.5b Specific For
Quaternary Neutralizing Epitope Of Hiv-1 Gp120
Length = 209
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 37/201 (18%), Positives = 80/201 (39%), Gaps = 27/201 (13%)
Query: 191 RSVIVSEGQTVYLYCYANGFPAPTISWRR---------------DNSAALS---TGGSIY 232
RSV VS GQT + C + + ++ W + + S+ + +G +
Sbjct: 7 RSVSVSPGQTARVTCGGDNIGSKSVQWYQQKPPQAPVLVMSADDERSSGIPERFSGSNSG 66
Query: 233 RGNILKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQGQA 286
L I + D YYC + G G + + + + AP +T+ P +
Sbjct: 67 NTATLTISGVEAGDEADYYCQVWDSSSHHMLFGGGTRLTVLGQPKAAPSVTLFPPSSEEL 126
Query: 287 LQYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTS-LRVITIER 343
A L C + + P A + W DG + + ++++++ +S L + + +
Sbjct: 127 QANKATLVCLISDFYPGAVEVAWKADGSAVNAGVETTKPSKQSNNKYAASSYLSLTSDQW 186
Query: 344 RQFGQYACKAANKYGSAQKEI 364
+ Y+C+ ++ + +K +
Sbjct: 187 KSHKSYSCQVTHEGSTVEKTV 207
>pdb|2KKQ|A Chain A, Solution Nmr Structure Of The Ig-Like C2-Type 2 Domain Of
Human Myotilin. Northeast Structural Genomics Target
Hr3158
Length = 116
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 26/104 (25%), Positives = 50/104 (48%), Gaps = 7/104 (6%)
Query: 273 APVITINRPRQGQALQYDAI-LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEF 331
AP+ I +P+ + L+ D++ LEC + A PPP + W ++ + N +S + D
Sbjct: 15 APMF-IYKPQSKKVLEGDSVKLECQISAIPPPKLFWKRNNEMVQFNTD-RISLY--QDNT 70
Query: 332 SDTSLRVITIERRQFGQYACKAANKYG--SAQKEIELFDRETQT 373
+L + + ++ G Y A N+ G + +++ R QT
Sbjct: 71 GRVTLLIKDVNKKDAGWYTVSAVNEAGVTTCNTRLDVTARPNQT 114
Score = 35.8 bits (81), Expect = 0.041, Method: Composition-based stats.
Identities = 26/86 (30%), Positives = 38/86 (44%), Gaps = 8/86 (9%)
Query: 180 RRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGG--SIYRGN-- 235
R P I ++ V+ EG +V L C + P P + W+R+N S+Y+ N
Sbjct: 14 RAPMFIYKPQSKKVL--EGDSVKLECQISAIPPPKLFWKRNNEMVQFNTDRISLYQDNTG 71
Query: 236 --ILKIPNITKTDRGTYYCVAQNGVG 259
L I ++ K D G Y A N G
Sbjct: 72 RVTLLIKDVNKKDAGWYTVSAVNEAG 97
>pdb|3IF1|A Chain A, Crystal Structure Of 237mab In Complex With A Galnac
pdb|3IF1|C Chain C, Crystal Structure Of 237mab In Complex With A Galnac
Length = 215
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 39/141 (27%), Positives = 60/141 (42%), Gaps = 9/141 (6%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV---GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAIL 293
LKI ++ D G Y+C V G G K I + AP ++I P Q A +
Sbjct: 77 LKISSVEAEDLGVYFCSQSTHVPTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGASV 135
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 136 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 195
Query: 350 ACKAANKYGSAQKEIELFDRE 370
C+A +K S ++ F+RE
Sbjct: 196 TCEATHKT-STSPIVKSFNRE 215
>pdb|2C1P|A Chain A, Fab-Fragment Of Enantioselective Antibody Complexed With
Finrozole
pdb|2C1P|L Chain L, Fab-Fragment Of Enantioselective Antibody Complexed With
Finrozole
Length = 218
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 47/195 (24%), Positives = 77/195 (39%), Gaps = 14/195 (7%)
Query: 175 VELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT-----ISWRRDNSAALSTGG 229
+ + + +P IS S++S++ S G+T + +P +S TG
Sbjct: 11 LSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIYLVSKLDSGDPDRFTGS 70
Query: 230 SIYRGNILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQ 285
LKI + D G YYCV + G G K + + AP ++I P Q
Sbjct: 71 GSGTDFTLKISRVEAEDLGIYYCVQGSHFPPTFGAGTKLELK-RADAAPTVSIFPPSSEQ 129
Query: 286 ALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI- 341
A + C + + P I W DG + N S + + D +S +S +T
Sbjct: 130 LTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKD 189
Query: 342 ERRQFGQYACKAANK 356
E + Y C+A +K
Sbjct: 190 EYERHNSYTCEATHK 204
>pdb|3VG9|B Chain B, Crystal Structure Of Human Adenosine A2a Receptor With An
Allosteric Inverse-Agonist Antibody At 2.7 A Resolution
pdb|3VGA|B Chain B, Crystal Structure Of Human Adenosine A2a Receptor With An
Allosteric Inverse-Agonist Antibody At 3.1 A Resolution
Length = 214
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 51/200 (25%), Positives = 77/200 (38%), Gaps = 29/200 (14%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAA------------------- 224
I+ S S+ S G TV + C A+ F +++W +
Sbjct: 2 IVMTQSPASLSASVGDTVTITCRASEFIYSSLTWYQQKQGGSPQLLVYAATNLADAVPSR 61
Query: 225 LSTGGSIYRGNILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINR 280
S GS + + LKI + D GTYYC G G G K I + AP ++I
Sbjct: 62 FSGSGSGTQFS-LKINRLQPEDFGTYYCQHFYGSTWAFGGGTKLEIK-RADAAPTVSIFP 119
Query: 281 PRQGQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLR 337
P Q A + C + + P I W DG + N S + + D +S +S
Sbjct: 120 PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTL 179
Query: 338 VITI-ERRQFGQYACKAANK 356
+T E + Y C+A +K
Sbjct: 180 TLTKDEYERHNSYTCEATHK 199
>pdb|3IET|A Chain A, Crystal Structure Of 237mab With Antigen
pdb|3IET|C Chain C, Crystal Structure Of 237mab With Antigen
Length = 217
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 39/141 (27%), Positives = 60/141 (42%), Gaps = 9/141 (6%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV---GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAIL 293
LKI ++ D G Y+C V G G K I + AP ++I P Q A +
Sbjct: 78 LKISSVEAEDLGVYFCSQSTHVPTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGASV 136
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 137 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 196
Query: 350 ACKAANKYGSAQKEIELFDRE 370
C+A +K S ++ F+RE
Sbjct: 197 TCEATHKT-STSPIVKSFNRE 216
>pdb|1NUN|B Chain B, Crystal Structure Analysis Of The Fgf10-fgfr2b Complex
Length = 230
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 43/196 (21%), Positives = 68/196 (34%), Gaps = 25/196 (12%)
Query: 191 RSVIVSEGQTVYLYCYANGFPAPTISWRRDNSA---ALSTGGSIYRGNILKI--PNITKT 245
R V TV C A G P PT W ++ GG R + ++ +
Sbjct: 26 RLHAVPAANTVKFRCPAGGNPXPTXRWLKNGKEFKQEHRIGGYKVRNQHWSLIXESVVPS 85
Query: 246 DRGTYYCVAQNGVG---RGMKRNIAVEVEFAPVITINRPRQGQA-LQYDAILECHVEAYP 301
D+G Y CV +N G ++ P++ P + D C V +
Sbjct: 86 DKGNYTCVVENEYGSINHTYHLDVVERSPHRPILQAGLPANASTVVGGDVEFVCKVYSDA 145
Query: 302 PPAIVWIK-----------DGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYA 350
P I WIK DG+ + + H + ++ L + + G+Y
Sbjct: 146 QPHIQWIKHVEKNGSKYGPDGLPYLK----VLKHSGINSSNAEV-LALFNVTEADAGEYI 200
Query: 351 CKAANKYGSAQKEIEL 366
CK +N G A + L
Sbjct: 201 CKVSNYIGQANQSAWL 216
>pdb|3UJI|L Chain L, Crystal Structure Of Anti-Hiv-1 V3 Fab 2558 In Complex
With Mn Peptide
Length = 209
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 41/199 (20%), Positives = 75/199 (37%), Gaps = 26/199 (13%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALS------------------TGGSIYR 233
SV VS GQT + C + +SW + S +G
Sbjct: 9 SVSVSPGQTASITCSGDILGDKYVSWYQQKSGQSPLLVIYEDTKRPSGIPDRFSGSKSGN 68
Query: 234 GNILKIPNITKTDRGTYYCVAQN---GV--GRGMKRNIAVEVEFAPVITINRPRQGQALQ 288
L I D YYC A + GV G G K + + + AP +T+ P +
Sbjct: 69 TATLTISGTQAMDEADYYCQAWDSTLGVVFGGGTKVTVLGQPKAAPSVTLFPPSSEELQA 128
Query: 289 YDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQ 345
A L C + + P A + W D + + ++++++ +S +T E+ +
Sbjct: 129 NKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKS 188
Query: 346 FGQYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 189 HKSYSCQVTHEGSTVEKTV 207
>pdb|1UZ8|A Chain A, Anti-Lewis X Fab Fragment In Complex With Lewis X
pdb|1UZ8|L Chain L, Anti-Lewis X Fab Fragment In Complex With Lewis X
Length = 218
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 55/190 (28%), Positives = 81/190 (42%), Gaps = 24/190 (12%)
Query: 185 ISDNSTRSVIVSEGQTVYLYCYAN--GFPAPTISWRRDNSAA-----LSTGGSIYRGN-- 235
IS S++S++ S G T YLY Y G + ++ N A+ S+ GS G
Sbjct: 21 ISCRSSKSLLYSNGIT-YLYWYLQKPGQSPQLLIYQMSNLASGVPDRFSSSGS---GTDF 76
Query: 236 ILKIPNITKTDRGTYYCVAQN-----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYD 290
L+I + D G YYC AQN G G K I + AP ++I P Q
Sbjct: 77 TLRISRVEAEDVGVYYC-AQNLEVPWTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGG 134
Query: 291 AILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQF 346
A + C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 135 ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERH 194
Query: 347 GQYACKAANK 356
Y C+A +K
Sbjct: 195 NSYTCEATHK 204
>pdb|3VI3|H Chain H, Crystal Structure Of Alpha5beta1 Integrin Headpiece
(Ligand-Free Form)
pdb|3VI3|F Chain F, Crystal Structure Of Alpha5beta1 Integrin Headpiece
(Ligand-Free Form)
pdb|3VI4|H Chain H, Crystal Structure Of Alpha5beta1 Integrin Headpiece In
Complex With Rgd Peptide
pdb|3VI4|F Chain F, Crystal Structure Of Alpha5beta1 Integrin Headpiece In
Complex With Rgd Peptide
Length = 218
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 37/141 (26%), Positives = 60/141 (42%), Gaps = 17/141 (12%)
Query: 101 DYPVIWMKMDTAKKMEPLPISMSGSLIIH-DSRFQ----LTTDPETSTYILSIKEIQETD 155
Y + W+K +E L + GS IH + +F+ TTD ++T + + + D
Sbjct: 31 SYWIEWVKQRPGHGLEWLGEILPGSGYIHYNEKFKGKATFTTDTSSNTAYMQLSSLTSED 90
Query: 156 AGIYKCEVIISL------NNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG 209
+ +Y C ++L S V PP + + S + V L C G
Sbjct: 91 SAVYYCSRALALYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVKG 149
Query: 210 -FPAP-TISWRRDNSAALSTG 228
FP P T++W NS +LS+G
Sbjct: 150 YFPEPVTVTW---NSGSLSSG 167
>pdb|1DJS|A Chain A, Ligand-binding Portion Of Fibroblast Growth Factor
Receptor 2 In Complex With Fgf1
Length = 216
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 44/187 (23%), Positives = 63/187 (33%), Gaps = 21/187 (11%)
Query: 191 RSVIVSEGQTVYLYCYANGFPAPTISWRRDNSA---ALSTGGSIYRGNILKI--PNITKT 245
R V TV C A G P PT W ++ GG R + ++ +
Sbjct: 19 RLHAVPAANTVKFRCPAGGNPXPTXRWLKNGKEFKQEHRIGGYKVRNQHWSLIXESVVPS 78
Query: 246 DRGTYYCVAQNGVG---RGMKRNIAVEVEFAPVITINRPRQGQA-LQYDAILECHVEAYP 301
D+G Y CV +N G ++ P++ P + D C V +
Sbjct: 79 DKGNYTCVVENEYGSINHTYHLDVVERSPHRPILQAGLPANASTVVGGDVEFVCKVYSDA 138
Query: 302 PPAIVWIKDGVQIMNNQHYSVSHF-------ATSDEFSDTSLRVITIERRQF---GQYAC 351
P I WIK + N Y A +D + V+ I F G+Y C
Sbjct: 139 QPHIQWIKHVEK--NGSKYGPDGLPYLKVLKAAGVNTTDKEIEVLYIRNVTFEDAGEYTC 196
Query: 352 KAANKYG 358
A N G
Sbjct: 197 LAGNSIG 203
>pdb|2C1O|A Chain A, Enaiihis Fab Fragment In The Free Form
pdb|2C1O|L Chain L, Enaiihis Fab Fragment In The Free Form
Length = 254
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 47/195 (24%), Positives = 77/195 (39%), Gaps = 14/195 (7%)
Query: 175 VELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT-----ISWRRDNSAALSTGG 229
+ + + +P IS S++S++ S G+T + +P +S TG
Sbjct: 48 LSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIYLVSKLDSGDPDRFTGS 107
Query: 230 SIYRGNILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQ 285
LKI + D G YYCV + G G K + + AP ++I P Q
Sbjct: 108 GSGTDFTLKISRVEAEDLGIYYCVQGSHFPPTFGAGTKLELK-RADAAPTVSIFPPSSEQ 166
Query: 286 ALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI- 341
A + C + + P I W DG + N S + + D +S +S +T
Sbjct: 167 LTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKD 226
Query: 342 ERRQFGQYACKAANK 356
E + Y C+A +K
Sbjct: 227 EYERHNSYTCEATHK 241
>pdb|3NZ8|B Chain B, Crystal Structure Of The Hiv-2 Neutralizing Fab Fragment
7c8
pdb|3NZ8|L Chain L, Crystal Structure Of The Hiv-2 Neutralizing Fab Fragment
7c8
Length = 218
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPFTFGSGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|3RNQ|A Chain A, Crystal Structure Of The Complex Between The Extracellular
Domains Of Mouse Pd-1 Mutant And Pd-L2
Length = 117
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 89 TADLKCSV-QYADDYPVIWMKMDTAKKMEPLPISMSG-SLIIHDSRFQLTTDPETSTYIL 146
A CS+ +++D + W ++ + + E +G S + D+RFQ+ P + +
Sbjct: 16 NATFTCSLSNWSEDLMLNWNRLSPSNQTEKQAAFSNGLSQPVQDARFQIIQLPNRHDFHM 75
Query: 147 SIKEIQETDAGIYKCEVI 164
+I + + D+GIY C I
Sbjct: 76 NILDTRRNDSGIYLCGAI 93
>pdb|1UZ6|E Chain E, Anti-Lewis X Fab Fragment Uncomplexed
pdb|1UZ6|L Chain L, Anti-Lewis X Fab Fragment Uncomplexed
pdb|1UZ6|M Chain M, Anti-Lewis X Fab Fragment Uncomplexed
pdb|1UZ6|V Chain V, Anti-Lewis X Fab Fragment Uncomplexed
Length = 218
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 55/190 (28%), Positives = 81/190 (42%), Gaps = 24/190 (12%)
Query: 185 ISDNSTRSVIVSEGQTVYLYCYAN--GFPAPTISWRRDNSAA-----LSTGGSIYRGN-- 235
IS S++S++ S G T YLY Y G + ++ N A+ S+ GS G
Sbjct: 21 ISCRSSKSLLYSNGIT-YLYWYLQKPGQSPQLLIYQMSNLASGVPDRFSSSGS---GTDF 76
Query: 236 ILKIPNITKTDRGTYYCVAQN-----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYD 290
L+I + D G YYC AQN G G K I + AP ++I P Q
Sbjct: 77 TLRISRVEAEDVGVYYC-AQNLEVPWTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGG 134
Query: 291 AILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQF 346
A + C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 135 ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERH 194
Query: 347 GQYACKAANK 356
Y C+A +K
Sbjct: 195 NSYTCEATHK 204
>pdb|1F90|L Chain L, Fab Fragment Of Monoclonal Antibody (Lnkb-2) Against Human
Interleukin-2 In Complex With Antigenic Peptide
pdb|1F8T|L Chain L, Fab (Lnkb-2) Of Monoclonal Antibody, Crystal Structure
pdb|1S5I|L Chain L, Fab (Lnkb-2) Of Monoclonal Antibody To Human
Interleukin-2, Crystal Structure
Length = 219
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 45/194 (23%), Positives = 76/194 (39%), Gaps = 12/194 (6%)
Query: 175 VELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT-----ISWRRDNSAALSTGG 229
+ + + +P IS S++S++ S G+T + +P +S TG
Sbjct: 11 LSVTIGQPASISCESSQSLLYSNGKTYLNWLLQRPGQSPKRLIYLVSKLDSGVPDRFTGS 70
Query: 230 SIYRGNILKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEV---EFAPVITINRPRQGQA 286
L+I + D G YYCV R +E+ + AP ++I P Q
Sbjct: 71 GSGTDFTLRISRVEAEDLGVYYCVQGTHFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQL 130
Query: 287 LQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-E 342
A + C + + P I W DG + N S + + D +S +S +T E
Sbjct: 131 TSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDE 190
Query: 343 RRQFGQYACKAANK 356
+ Y C+A +K
Sbjct: 191 YERHNSYTCEATHK 204
>pdb|1YEC|L Chain L, Structure Of A Catalytic Antibody Igg2a Fab Fragment
(D2.3)
pdb|1YEF|L Chain L, Structure Of Igg2a Fab Fragment (D2.3) Complexed With
Substrate Analogue
pdb|1YEG|L Chain L, Structure Of Igg2a Fab Fragment (D2.3) Complexed With
Reaction Product
pdb|1YEH|L Chain L, Structure Of Igg2a Fab Fragment
Length = 219
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 48/195 (24%), Positives = 77/195 (39%), Gaps = 14/195 (7%)
Query: 175 VELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT-----ISWRRDNSAALSTGG 229
+ + + +P IS S++S++ S G+T + +P +S TG
Sbjct: 11 LSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIHLVSKLDSGVPDRITGS 70
Query: 230 SIYRGNILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQ 285
LKI + D G YYCV G G K I + + AP ++I P Q
Sbjct: 71 GSGTDFTLKISRVEAADLGVYYCVQGTHFPYTFGGGTKLEI-LRGDAAPTVSIFPPSSEQ 129
Query: 286 ALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI- 341
A + C + + P I W DG + N S + + D +S +S +T
Sbjct: 130 LTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKD 189
Query: 342 ERRQFGQYACKAANK 356
E + Y C+A +K
Sbjct: 190 EYERHNSYTCEATHK 204
>pdb|1FPT|L Chain L, Three-Dimensional Structure Of The Complex Between The Fab
Fragment Of An Neutralizing Antibody For Type 1
Poliovirus And Its Viral Epitope
Length = 219
Score = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G Y+C V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYFCSQSTHVPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG ++ N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSEVQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|3MLR|L Chain L, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With A Ny5 V3 Peptide
pdb|3MLS|L Chain L, Crystal Structure Of Anti-Hiv-1 V3 Mab 2557 Fab In Complex
With A Hiv- 1 Gp120 V3 Mimotope
pdb|3MLS|M Chain M, Crystal Structure Of Anti-Hiv-1 V3 Mab 2557 Fab In Complex
With A Hiv- 1 Gp120 V3 Mimotope
pdb|3MLS|N Chain N, Crystal Structure Of Anti-Hiv-1 V3 Mab 2557 Fab In Complex
With A Hiv- 1 Gp120 V3 Mimotope
pdb|3MLS|O Chain O, Crystal Structure Of Anti-Hiv-1 V3 Mab 2557 Fab In Complex
With A Hiv- 1 Gp120 V3 Mimotope
pdb|3MLT|L Chain L, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With A Ug1033 V3 Peptide
pdb|3MLT|A Chain A, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With A Ug1033 V3 Peptide
pdb|3MLT|D Chain D, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With A Ug1033 V3 Peptide
pdb|3MLT|G Chain G, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With A Ug1033 V3 Peptide
Length = 219
Score = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 43/208 (20%), Positives = 78/208 (37%), Gaps = 35/208 (16%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISW---RRDNSAAL---------------STGGSIYR 233
SV VS GQT + C + +SW R S L +G +
Sbjct: 9 SVSVSPGQTASISCSGDKLDDKYVSWYYQRPGQSPVLLMYQDFKRPSGIPERLSGSKSGK 68
Query: 234 GNILKIPNITKTDRGTYYCVAQN---GV-----------GRGMKRNIAVEVEFAPVITIN 279
L I D G YYC A + GV G G + + + + AP +T+
Sbjct: 69 TATLTISGTQSLDEGDYYCQAWDASTGVSGGGTKLTVLFGDGTRLTVLGQPKAAPSVTLF 128
Query: 280 RPRQGQALQYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLR 337
P + A L C + + P A + W D + + ++++++ +S
Sbjct: 129 PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL 188
Query: 338 VITIER-RQFGQYACKAANKYGSAQKEI 364
+T E+ + Y+C+ ++ + +K +
Sbjct: 189 SLTPEQWKSHKSYSCQVTHEGSTVEKTV 216
>pdb|8FAB|A Chain A, Crystal Structure Of The Fab Fragment From The Human
Myeloma Immunoglobulin Igg Hil At 1.8 Angstroms
Resolution
pdb|8FAB|C Chain C, Crystal Structure Of The Fab Fragment From The Human
Myeloma Immunoglobulin Igg Hil At 1.8 Angstroms
Resolution
Length = 212
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 43/201 (21%), Positives = 77/201 (38%), Gaps = 31/201 (15%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISW--RRDNSAALSTGGSIYRGN-------------- 235
SV VS GQT + C AN P W ++ A + IY+
Sbjct: 9 SVSVSPGQTARITCSANALPNQYAYWYQQKPGRAPVMV---IYKDTQRPSGIPQRFSSST 65
Query: 236 -----ILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQA 286
L I + D YYC A + G G K + + + AP +T+ P +
Sbjct: 66 SGTTVTLTISGVQAEDEADYYCQAWDNSASIFGGGTKLTVLGQPKAAPSVTLFPPSSEEL 125
Query: 287 LQYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER- 343
A L C + + P A + W D I + ++++++ +S +T E+
Sbjct: 126 QANKATLVCLISDFYPGAVTVAWKADSSPIKAGVETTTPSKQSNNKYAASSYLSLTPEQW 185
Query: 344 RQFGQYACKAANKYGSAQKEI 364
+ Y+C+ ++ + +K +
Sbjct: 186 KSHRSYSCQVTHEGSTVEKTV 206
>pdb|4HC1|L Chain L, Crystal Structure Of A Loop Deleted Mutant Of Human
Madcam-1 D1d2 Complexed With Fab 10g3
pdb|4HC1|N Chain N, Crystal Structure Of A Loop Deleted Mutant Of Human
Madcam-1 D1d2 Complexed With Fab 10g3
Length = 214
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 52/200 (26%), Positives = 73/200 (36%), Gaps = 29/200 (14%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILK----- 238
I+ S S+ VS G TV C+A+ I W + S G IY G LK
Sbjct: 2 ILMTQSPSSMSVSLGDTVSFTCHASQGIGRNIGWLQQKPGK-SFKGLIYHGTNLKDGVPS 60
Query: 239 --------------IPNITKTDRGTYYCVAQ----NGVGRGMKRNIAVEVEFAPVITINR 280
I I D YYC+ G G K I + AP ++I
Sbjct: 61 RFSGSGSGADYSLTISRIESEDFADYYCIQYVQFPYTFGGGTKLEIK-RADAAPTVSIFP 119
Query: 281 PRQGQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLR 337
P Q A + C + + P I W DG + N S + + D +S +S
Sbjct: 120 PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTL 179
Query: 338 VITI-ERRQFGQYACKAANK 356
+T E + Y C+A +K
Sbjct: 180 TLTKDEYERHNSYTCEATHK 199
>pdb|4HK0|B Chain B, Uca Fab (unbound) From Ch65-ch67 Lineage
pdb|4HK0|D Chain D, Uca Fab (unbound) From Ch65-ch67 Lineage
pdb|4HK3|N Chain N, I2 Fab (unbound) From Ch65-ch67 Lineage
Length = 214
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 39/200 (19%), Positives = 78/200 (39%), Gaps = 27/200 (13%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRR------------DNSAALS------TGGSIYR 233
SV V+ GQT + C N + ++ W + D+S S +G +
Sbjct: 9 SVSVAPGQTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGN 68
Query: 234 GNILKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQGQAL 287
L I + D YYC + G G K + + + AP +T+ P +
Sbjct: 69 TATLTISRVEAGDEADYYCQVWDSSSDHVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQ 128
Query: 288 QYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-R 344
A L C + + P A + W D + + ++++++ +S +T E+ +
Sbjct: 129 ANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWK 188
Query: 345 QFGQYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 189 SHRSYSCQVTHEGSTVEKTV 208
>pdb|1TET|L Chain L, Crystal Structure Of An Anticholera Toxin Peptide Complex
At 2.3 Angstroms
Length = 216
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 54/128 (42%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + + G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHIPFTFGSGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITIERRQF-GQ 348
+ C + + P I W DG + N S + + D +S +S +T + ++
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYEWHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|2R0W|L Chain L, Pfa2 Fab Complexed With Abeta1-8
Length = 219
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1CLZ|L Chain L, Igg Fab (Igg3, Kappa) Fragment (Mbr96) Complexed With
Lewis Y Nonoate Methyl Ester
Length = 219
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPFTFGSGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1ZEA|L Chain L, Structure Of The Anti-Cholera Toxin Antibody Fab Fragment
Te33 In Complex With A D-Peptide
Length = 216
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + + G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHIPFTFGSGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1PLG|L Chain L, Evidence For The Extended Helical Nature Of Polysaccharide
Epitopes. The 2.8 Angstroms Resolution Structure And
Thermodynamics Of Ligand Binding Of An Antigen Binding
Fragment Specific For Alpha-(2->8)- Polysialic Acid
Length = 215
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 51/186 (27%), Positives = 74/186 (39%), Gaps = 16/186 (8%)
Query: 185 ISDNSTRSVIVSEGQTVYLYCY---ANGFPAPTI---SWRRDNSAALSTGGSIYRGNILK 238
IS S++S++ S G T YLY Y P P I S R +G LK
Sbjct: 21 ISCRSSQSLVHSNGNT-YLYWYLQKPGQSPKPLIYRVSNRFSGVPDRFSGSGSGTDFTLK 79
Query: 239 IPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
I + D G Y+C V G G + I + AP ++I P Q A +
Sbjct: 80 ISRVEAEDLGVYFCFQGTHVPYTFGGGTRLEIK-RADAAPTVSIFPPSSEQLTSGGASVV 138
Query: 295 CHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQYA 350
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 139 CFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYT 198
Query: 351 CKAANK 356
C+A +K
Sbjct: 199 CEATHK 204
>pdb|1IGF|L Chain L, Crystal Structures Of An Antibody To A Peptide And Its
Complex With Peptide Antigen At 2.8 Angstroms
pdb|1IGF|M Chain M, Crystal Structures Of An Antibody To A Peptide And Its
Complex With Peptide Antigen At 2.8 Angstroms
pdb|2IGF|L Chain L, Crystal Structures Of An Antibody To A Peptide And Its
Complex With Peptide Antigen At 2.8 Angstroms
Length = 219
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPPTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|2IPT|L Chain L, Pfa1 Fab Fragment
pdb|2IQA|L Chain L, Pfa2 Fab Fragment, Monoclinic Apo Form
pdb|2IQA|A Chain A, Pfa2 Fab Fragment, Monoclinic Apo Form
Length = 219
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1L7T|L Chain L, Crystal Structure Analysis Of The Anti-Testosterone Fab
Fragment
pdb|1VPO|L Chain L, Crystal Structure Analysis Of The Anti-testosterone Fab In
Complex With Testosterone
Length = 219
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 39/142 (27%), Positives = 60/142 (42%), Gaps = 10/142 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFDGSTVPPKFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANKYGSAQKEIELFDRE 370
Y C+A +K S ++ F+R+
Sbjct: 197 YTCEATHKT-STSPIVKSFNRD 217
>pdb|3U9U|B Chain B, Crystal Structure Of Extracellular Domain Of Human
Erbb4HER4 IN Complex With The Fab Fragment Of Mab1479
pdb|3U9U|D Chain D, Crystal Structure Of Extracellular Domain Of Human
Erbb4HER4 IN Complex With The Fab Fragment Of Mab1479
Length = 219
Score = 37.0 bits (84), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPWTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1A3L|L Chain L, Catalysis Of A Disfavored Reaction: An Antibody Exo Diels-
Alderase-Tsa-Inhibitor Complex At 1.95 A Resolution
pdb|1RUQ|L Chain L, Crystal Structure (H) Of U.V.-Irradiated Diels-Alder
Antibody 13g5 Fab At Ph 8.0 With A Data Set Collected In
House.
pdb|1RUR|L Chain L, Crystal Structure (i) Of Native Diels-alder Antibody 13g5
Fab At Ph 8.0 With A Data Set Collected At Ssrl Beamline
9- 1
Length = 217
Score = 37.0 bits (84), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 38/129 (29%), Positives = 54/129 (41%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQN-----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
L+I + D G YYC AQN G G K I + AP ++I P Q A
Sbjct: 78 LRISRVEAEDVGVYYC-AQNLELPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGA 135
Query: 292 ILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFG 347
+ C + + P I W DG + N S + T D +S +S +T E +
Sbjct: 136 SVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDTKDSTYSMSSTLTLTKDEYERHN 195
Query: 348 QYACKAANK 356
Y C+A +K
Sbjct: 196 SYTCEATHK 204
>pdb|1F3D|L Chain L, Catalytic Antibody 4b2 In Complex With Its Amidinium
Hapten.
pdb|1F3D|J Chain J, Catalytic Antibody 4b2 In Complex With Its Amidinium
Hapten
Length = 219
Score = 37.0 bits (84), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|2DQT|L Chain L, High Resolution Crystal Structure Of The Complex Of The
Hydrolytic Antibody Fab 6d9 And A Transition-State
Analog
pdb|2DQU|L Chain L, Crystal Form Ii: High Resolution Crystal Structure Of The
Complex Of The Hydrolytic Antibody Fab 6d9 And A
Transition-State Analog
pdb|2DTM|L Chain L, Thermodynamic And Structural Analyses Of Hydrolytic
Mechanism By Catalytic Antibodies
Length = 219
Score = 37.0 bits (84), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPPTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|2H1P|L Chain L, The Three-Dimensional Structures Of A Polysaccharide
Binding Antibody To Cryptococcus Neoformans And Its
Complex With A Peptide From A Phage Display Library:
Implications For The Identification Of Peptide Mimotopes
Length = 219
Score = 37.0 bits (84), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 50/190 (26%), Positives = 76/190 (40%), Gaps = 18/190 (9%)
Query: 182 PPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT-------ISWRRDNSAALSTGGSIYRG 234
P IS S++S++ S G T YL+ Y P + +S R +G
Sbjct: 18 PASISCRSSQSLVHSNGNT-YLHWYLQK-PGQSPKLLIYKVSNRFSGVPDKFSGSGSGTD 75
Query: 235 NILKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYD 290
LKI + D+G Y+C V G G K I + AP ++I P Q
Sbjct: 76 FTLKISRVEAEDQGVYFCSQSTHVPWTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGG 134
Query: 291 AILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQF 346
A + C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 135 ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDEDSKDSTYSMSSTLTLTKDEYERH 194
Query: 347 GQYACKAANK 356
Y C+A +K
Sbjct: 195 NSYTCEATHK 204
>pdb|3MA9|L Chain L, Crystal Structure Of Gp41 Derived Protein Complexed With
Fab 8066
pdb|3MAC|L Chain L, Crystal Structure Of Gp41-Derived Protein Complexed With
Fab 8062
Length = 213
Score = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 39/200 (19%), Positives = 76/200 (38%), Gaps = 27/200 (13%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRR-------------DNSAALS-----TGGSIYR 233
SV V GQT + C + P SW + DN+ +G +
Sbjct: 9 SVSVVPGQTARISCSGDNIPYEYASWYQQKPGQAPVLVIYGDNNRPSGIPERFSGSNSGN 68
Query: 234 GNILKIPNITKTDRGTYYCVAQNGV------GRGMKRNIAVEVEFAPVITINRPRQGQAL 287
L I D YYC + + + G G K + + + AP +T+ P +
Sbjct: 69 TATLTISGTQAEDEADYYCASWDSMTVDGVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQ 128
Query: 288 QYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-R 344
A L C + + P A + W D + + ++++++ +S +T E+ +
Sbjct: 129 ANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWK 188
Query: 345 QFGQYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 189 SHRSYSCQVTHEGSTVEKTV 208
>pdb|1KB5|L Chain L, Murine T-Cell Receptor Variable DomainFAB COMPLEX
Length = 214
Score = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 54/128 (42%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI ++ D G+YYC G G G K I + AP ++I P Q A
Sbjct: 73 LKINSLQPEDFGSYYCQHHYGTPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 131
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 132 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 191
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 192 YTCEATHK 199
>pdb|2VC2|L Chain L, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist L-739758
pdb|2VDK|L Chain L, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece
pdb|2VDL|L Chain L, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece
pdb|2VDM|L Chain L, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist Tirofiban
pdb|2VDN|L Chain L, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist Eptifibatide
pdb|2VDO|L Chain L, Integrin Alphaiibbeta3 Headpiece Bound To Fibrinogen Gamma
Chain Peptide, Hhlggakqagdv
pdb|2VDP|L Chain L, Integrin Alphaiibbeta3 Headpiece Bound To Fibrinogen Gamma
Chain Peptide,Lggakqagdv
pdb|2VDQ|L Chain L, Integrin Alphaiibbeta3 Headpiece Bound To A Chimeric
Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv
pdb|2VDR|L Chain L, Integrin Alphaiibbeta3 Headpiece Bound To A Chimeric
Fibrinogen Gamma Chain Peptide, Lggakqrgdv
pdb|3NID|F Chain F, The Closed Headpiece Of Integrin Alphaiib Beta3 And Its
Complex With An Alpahiib Beta3 -Specific Antagonist That
Does Not Induce Opening
pdb|3NID|L Chain L, The Closed Headpiece Of Integrin Alphaiib Beta3 And Its
Complex With An Alpahiib Beta3 -Specific Antagonist That
Does Not Induce Opening
pdb|3NIF|F Chain F, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIF|L Chain L, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIG|F Chain F, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIG|L Chain L, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3T3M|F Chain F, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3M|L Chain L, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3P|F Chain F, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3P|L Chain L, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
Length = 214
Score = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 49/199 (24%), Positives = 75/199 (37%), Gaps = 27/199 (13%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNI------- 236
I+ S S+ VS G TV + C+A+ + I W + G Y N+
Sbjct: 2 ILMTQSPSSMSVSLGDTVSITCHASQGISSNIGWLQQKPGKSFMGLIYYGTNLVDGVPSR 61
Query: 237 -----------LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRP 281
L I ++ D YYCV + G G K I + AP ++I P
Sbjct: 62 FSGSGSGADYSLTISSLDSEDFADYYCVQYAQLPYTFGGGTKLEIK-RADAAPTVSIFPP 120
Query: 282 RQGQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRV 338
Q A + C + + P I W DG + N S + + D +S +S
Sbjct: 121 SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT 180
Query: 339 ITI-ERRQFGQYACKAANK 356
+T E + Y C+A +K
Sbjct: 181 LTKDEYERHNSYTCEATHK 199
>pdb|1NL0|L Chain L, Crystal Structure Of Human Factor Ix Gla Domain In Complex
Of An Inhibitory Antibody, 10c12
Length = 213
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 27/137 (19%), Positives = 57/137 (41%), Gaps = 9/137 (6%)
Query: 237 LKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQGQALQYD 290
L I + D YYC A + G G K + + + AP +T+ P +
Sbjct: 74 LDISGLQSEDEADYYCAAWDDSLSEFLFGTGTKLTVLGQPKAAPSVTLFPPSSEELQANK 133
Query: 291 AILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQFG 347
A L C + + P A + W D + + ++++++ +S +T E+ +
Sbjct: 134 ATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHK 193
Query: 348 QYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 194 SYSCQVTHEGSTVEKTV 210
>pdb|1EHL|L Chain L, 64m-2 Antibody Fab Complexed With D(5ht)(6-4)t
Length = 217
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 36/127 (28%), Positives = 53/127 (41%), Gaps = 8/127 (6%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV---GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAIL 293
LKI + D G YYC + V G G K I + AP ++I P Q A +
Sbjct: 78 LKISRVEAEDLGVYYCFQGSLVPTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGASV 136
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 137 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 196
Query: 350 ACKAANK 356
C+A +K
Sbjct: 197 TCEATHK 203
>pdb|1FH5|L Chain L, Crystal Structure Of The Fab Fragment Of The Monoclonal
Antibody Mak33
Length = 213
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 49/199 (24%), Positives = 80/199 (40%), Gaps = 27/199 (13%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNS----------AALSTGG--SI 231
I+ S ++ V+ G++V L C A+ + + W + S A+ S G S
Sbjct: 2 IVLTQSPATLSVTPGESVSLSCRASQSISNNLHWYQQKSHESPRLLIKYASQSISGIPSR 61
Query: 232 YRGN------ILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRP 281
+ G+ L I ++ D G YYC N G G K + + AP ++I P
Sbjct: 62 FSGSGSGTDFTLSINSVETEDFGMYYCQQSNSWPLTFGAGTKLELK-RADAAPTVSIFPP 120
Query: 282 RQGQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRV 338
Q A + C + + P I W DG + N S + + D +S +S
Sbjct: 121 SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT 180
Query: 339 ITI-ERRQFGQYACKAANK 356
+T E + Y C+A +K
Sbjct: 181 LTKDEYERHNSYTCEATHK 199
Score = 28.5 bits (62), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 323 SHFATSDEFSDTSLRVITIERRQFGQYACKAANKY 357
S F+ S +D +L + ++E FG Y C+ +N +
Sbjct: 60 SRFSGSGSGTDFTLSINSVETEDFGMYYCQQSNSW 94
>pdb|1I9I|L Chain L, Native Crystal Structure Of The Recombinant Monoclonal
Wild Type Anti-Testosterone Fab Fragment
pdb|1I9J|L Chain L, Testosterone Complex Structure Of The Recombinant
Monoclonal Wild Type Anti-Testosterone Fab Fragment
Length = 219
Score = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPPTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1KEG|L Chain L, Antibody 64m-2 Fab Complexed With Dtt(6-4)tt
Length = 216
Score = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 36/127 (28%), Positives = 53/127 (41%), Gaps = 8/127 (6%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV---GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAIL 293
LKI + D G YYC + V G G K I + AP ++I P Q A +
Sbjct: 78 LKISRVEAEDLGVYYCFQGSLVPTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGASV 136
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 137 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 196
Query: 350 ACKAANK 356
C+A +K
Sbjct: 197 TCEATHK 203
>pdb|1NLD|L Chain L, Fab Fragment Of A Neutralizing Antibody Directed Against
An Epitope Of Gp41 From Hiv-1
Length = 219
Score = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 45/194 (23%), Positives = 76/194 (39%), Gaps = 12/194 (6%)
Query: 175 VELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT-----ISWRRDNSAALSTGG 229
+ + + +P IS S++S++ S+G+T + +P +S TG
Sbjct: 11 LSVTIGQPASISCKSSQSLLDSDGKTYLNWLLQRPGQSPKRLIYLVSKLDSGVPDRFTGS 70
Query: 230 SIYRGNILKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEV---EFAPVITINRPRQGQA 286
LKI + D G YYC R +E+ + AP ++I P Q
Sbjct: 71 GSGTDFTLKISRVEAEDLGVYYCWQGTHFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQL 130
Query: 287 LQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-E 342
A + C + + P I W DG + N S + + D +S +S +T E
Sbjct: 131 TSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDE 190
Query: 343 RRQFGQYACKAANK 356
+ Y C+A +K
Sbjct: 191 YERHNSYTCEATHK 204
>pdb|1C12|A Chain A, Insight In Odorant Perception: The Crystal Structure And
Binding Characteristics Of Antibody Fragments Directed
Against The Musk Odorant Traseolide
Length = 214
Score = 36.6 bits (83), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 50/195 (25%), Positives = 74/195 (37%), Gaps = 29/195 (14%)
Query: 189 STRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILK---------- 238
S S+ VS G TV + C+A+ + I W + S G IY G L+
Sbjct: 7 SPSSMSVSLGDTVSITCHASQGISSNIGWLQQKPGK-SFKGLIYHGTNLEDGVPSRFSGS 65
Query: 239 ---------IPNITKTDRGTYYCVAQ----NGVGRGMKRNIAVEVEFAPVITINRPRQGQ 285
I ++ D YYCV G G K I + AP ++I P Q
Sbjct: 66 GSGADYSLTISSLESEDFADYYCVQYVQFPFTFGSGTKLEIK-RADAAPTVSIFPPSSEQ 124
Query: 286 ALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI- 341
A + C + + P I W DG + N S + + D +S +S +T
Sbjct: 125 LTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKD 184
Query: 342 ERRQFGQYACKAANK 356
E + Y C+A +K
Sbjct: 185 EYERHNSYTCEATHK 199
>pdb|2WNG|A Chain A, Complete Extracellular Structure Of Human Signal
Regulatory Protein (Sirp) Alpha
Length = 327
Score = 36.6 bits (83), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 46/195 (23%), Positives = 75/195 (38%), Gaps = 34/195 (17%)
Query: 191 RSVIVSEGQTVYLYCYANGF-PAPTISWRRDNSAA---------------LSTGGSIYRG 234
+SV V+ G++ L+C P I W R A + S R
Sbjct: 11 KSVSVAAGESAILHCTVTSLIPVGPIQWFRGAGPARELIYNQKEGHFPRVTTVSESTKRE 70
Query: 235 NI---LKIPNITKTDRGTYYCV--------AQNGVGRGMKRNIAVEVEFAPVITINRPRQ 283
N+ + I NIT D GTYYCV + G G + ++ + APV++ P
Sbjct: 71 NMDFSISISNITPADAGTYYCVKFRKGSPDTEFKSGAGTELSVRAKPS-APVVS--GPAA 127
Query: 284 GQALQYDAILECHVEAYPPPAIV--WIKDGVQIMNNQHYSVSHFATSDEFS-DTSLRVIT 340
Q+ C + P I W K+G ++ + Q +V S +S ++ +V+
Sbjct: 128 RATPQHTVSFTCESHGFSPRDITLKWFKNGNELSDFQ-TNVDPVGESVSYSIHSTAKVVL 186
Query: 341 IERRQFGQYACKAAN 355
Q C+ A+
Sbjct: 187 TREDVHSQVICEVAH 201
>pdb|3D69|L Chain L, Crystal Structure Of The Fab Fragment Of An Anti-Factor Ix
Antibody 10c12
pdb|3D69|A Chain A, Crystal Structure Of The Fab Fragment Of An Anti-Factor Ix
Antibody 10c12
Length = 216
Score = 36.6 bits (83), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 27/137 (19%), Positives = 57/137 (41%), Gaps = 9/137 (6%)
Query: 237 LKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQGQALQYD 290
L I + D YYC A + G G K + + + AP +T+ P +
Sbjct: 74 LDISGLQSEDEADYYCAAWDDSLSEFLFGTGTKLTVLGQPKAAPSVTLFPPSSEELQANK 133
Query: 291 AILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQFG 347
A L C + + P A + W D + + ++++++ +S +T E+ +
Sbjct: 134 ATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHK 193
Query: 348 QYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 194 SYSCQVTHEGSTVEKTV 210
>pdb|2FGW|H Chain H, X-Ray Structures Of Fragments From Binding And Nonbinding
Versions Of A Humanized Anti-Cd18 Antibody: Structural
Indications Of The Key Role Of Vh Residues 59 To 65
Length = 232
Score = 36.6 bits (83), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 37/146 (25%), Positives = 60/146 (41%), Gaps = 21/146 (14%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
+Y + WM+ K +E + I+ H+ RF ++ D TST + + ++ D
Sbjct: 31 EYTMHWMRQAPGKGLEWVAGINPKNGGTSHNQRFMDRFTISVDKSTSTAYMQMNSLRAED 90
Query: 156 AGIYKCEVIISLNNKVSAEVELIVRRPPI--ISDNSTRSVIV---------SEGQTVYLY 204
+Y C LN + + + +S ST+ V + G T L
Sbjct: 91 TAVYYCARWRGLNYGFDVRYFDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALG 150
Query: 205 CYANG-FPAP-TISWRRDNSAALSTG 228
C FP P T+SW NS AL++G
Sbjct: 151 CLVKDYFPEPVTVSW---NSGALTSG 173
>pdb|4FQQ|L Chain L, Crystal Structure Of Germline Antibody Pgt121-Gl Fab
pdb|4FQQ|A Chain A, Crystal Structure Of Germline Antibody Pgt121-Gl Fab
pdb|4FQQ|C Chain C, Crystal Structure Of Germline Antibody Pgt121-Gl Fab
pdb|4FQQ|E Chain E, Crystal Structure Of Germline Antibody Pgt121-Gl Fab
Length = 215
Score = 36.6 bits (83), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 39/201 (19%), Positives = 78/201 (38%), Gaps = 28/201 (13%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRR------------DNSAALS------TGGSIYR 233
SV V+ GQT + C N + ++ W + D+S S +G +
Sbjct: 9 SVSVAPGQTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGN 68
Query: 234 GNILKIPNITKTDRGTYYCVAQNG-------VGRGMKRNIAVEVEFAPVITINRPRQGQA 286
L I + D YYC + G G K + + + AP +T+ P +
Sbjct: 69 TATLTISRVEAGDEADYYCQVWDSSSDHPWVFGGGTKLTVLGQPKAAPSVTLFPPSSEEL 128
Query: 287 LQYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER- 343
A L C + + P A + W D + + ++++++ +S +T E+
Sbjct: 129 QANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQW 188
Query: 344 RQFGQYACKAANKYGSAQKEI 364
+ Y+C+ ++ + +K +
Sbjct: 189 KSHRSYSCQVTHEGSTVEKTV 209
>pdb|3HG1|E Chain E, Germline-Governed Recognition Of A Cancer Epitope By An
Immunodominant Human T Cell Receptor
Length = 244
Score = 36.6 bits (83), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 28/139 (20%), Positives = 59/139 (42%), Gaps = 11/139 (7%)
Query: 83 IKDIAQTADLKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLT-TDPET 141
++ + L+C+V+ + + W + + ++ L S+ I + L+ + P+
Sbjct: 12 VQPVGSPLSLECTVEGTSNPNLYWYRQAAGRGLQLLFYSVGIGQISSEVPQNLSASRPQD 71
Query: 142 STYILSIKEIQETDAGIYKC----------EVIISLNNKVSAEVELIVRRPPIISDNSTR 191
+ILS K++ +D+G Y C E+ ++++ +L PP ++
Sbjct: 72 RQFILSSKKLLLSDSGFYLCAWSETGLGTGELFFGEGSRLTVLEDLKNVFPPEVAVFEPS 131
Query: 192 SVIVSEGQTVYLYCYANGF 210
+S Q L C A GF
Sbjct: 132 EAEISHTQKATLVCLATGF 150
>pdb|3QG7|L Chain L, Structural Basis For Ligand Recognition And Discrimination
Of A Quorum Quenching Antibody
Length = 216
Score = 36.6 bits (83), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVESEDLGIYYCSQTTHVPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|2R0Z|L Chain L, Pfa1 Fab Complexed With Gripi Peptide Fragment
pdb|3EYS|L Chain L, Pfa1 Fab Fragment Complexed With Pyro-Glu3-A-Beta (3-8)
pdb|3EYU|L Chain L, Pfa1 Fab Fragment Complexed With Ror2(518-525)
Length = 219
Score = 36.6 bits (83), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K + + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|2DDQ|L Chain L, Crystal Structure Of The Fab Fragment Of A R310 Antibody
Complexed With (R)-Hne-Histidine Adduct
Length = 218
Score = 36.6 bits (83), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K + + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|3QG6|A Chain A, Structural Basis For Ligand Recognition And Discrimination
Of A Quorum Quenching Antibody
pdb|3QG6|L Chain L, Structural Basis For Ligand Recognition And Discrimination
Of A Quorum Quenching Antibody
Length = 218
Score = 36.2 bits (82), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVESEDLGIYYCSQTTHVPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|2UYL|A Chain A, Crystal Structure Of A Monoclonal Antibody Directed
Against An Antigenic Determinant Common To Ogawa And
Inaba Serotypes Of Vibrio Cholerae O1
pdb|2UYL|M Chain M, Crystal Structure Of A Monoclonal Antibody Directed
Against An Antigenic Determinant Common To Ogawa And
Inaba Serotypes Of Vibrio Cholerae O1
pdb|2UYL|V Chain V, Crystal Structure Of A Monoclonal Antibody Directed
Against An Antigenic Determinant Common To Ogawa And
Inaba Serotypes Of Vibrio Cholerae O1
pdb|2UYL|X Chain X, Crystal Structure Of A Monoclonal Antibody Directed
Against An Antigenic Determinant Common To Ogawa And
Inaba Serotypes Of Vibrio Cholerae O1
Length = 219
Score = 36.2 bits (82), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 33/127 (25%), Positives = 53/127 (41%), Gaps = 7/127 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEV---EFAPVITINRPRQGQALQYDAIL 293
L+I + D G YYC + V R +E+ + AP ++I P Q A +
Sbjct: 78 LEISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASV 137
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 138 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 197
Query: 350 ACKAANK 356
C+A +K
Sbjct: 198 TCEATHK 204
>pdb|3V7A|G Chain G, Structural Basis For Broad Detection Of Genogroup Ii
Noroviruses By A Monoclonal Antibody That Binds To A
Site Occluded In The Viral Particle
pdb|3V7A|H Chain H, Structural Basis For Broad Detection Of Genogroup Ii
Noroviruses By A Monoclonal Antibody That Binds To A
Site Occluded In The Viral Particle
Length = 215
Score = 36.2 bits (82), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 36/129 (27%), Positives = 54/129 (41%), Gaps = 10/129 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG-----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
LKI ++ D G+YYC G G G K I + AP ++I P Q A
Sbjct: 73 LKINSLQPEDFGSYYCQHHYGSPPWTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGA 131
Query: 292 ILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFG 347
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 132 SVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHN 191
Query: 348 QYACKAANK 356
Y C+A +K
Sbjct: 192 SYTCEATHK 200
>pdb|3GNM|L Chain L, The Crystal Structure Of The Jaa-f11 Monoclonal Antibody
Fab Fragment
Length = 219
Score = 36.2 bits (82), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 35/133 (26%), Positives = 53/133 (39%), Gaps = 19/133 (14%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEADDLGVYYCFQGSHVPFTFGSGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMN-------NQHYSVSHFATSDEFSDTSLRVITIER 343
+ C + + P I W DG + N +Q S ++ S ++L + E
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNGWTDQDSKDSTYSMS-----STLTLTKDEY 191
Query: 344 RQFGQYACKAANK 356
+ Y C+A +K
Sbjct: 192 ERHNSYTCEATHK 204
>pdb|2IPU|L Chain L, Pfa1 Fab Fragment Complexed With Abeta 1-8 Peptide
pdb|2IPU|K Chain K, Pfa1 Fab Fragment Complexed With Abeta 1-8 Peptide
pdb|2IQ9|L Chain L, Pfa2 Fab Fragment, Triclinic Apo Form
Length = 219
Score = 36.2 bits (82), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K + + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1V7M|L Chain L, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|1V7M|M Chain M, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|1V7N|L Chain L, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|1V7N|M Chain M, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|1V7N|N Chain N, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|1V7N|O Chain O, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|2ZKH|L Chain L, Human Thrombopoietin Neutralizing Antibody Tn1 Fab
Length = 213
Score = 36.2 bits (82), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 33/127 (25%), Positives = 53/127 (41%), Gaps = 7/127 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEV---EFAPVITINRPRQGQALQYDAIL 293
L I + D TYYC ++G R +E+ + AP ++I P Q A +
Sbjct: 72 LTISRMEAEDAATYYCQQRSGYPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASV 131
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 132 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 191
Query: 350 ACKAANK 356
C+A +K
Sbjct: 192 TCEATHK 198
>pdb|1ZA6|B Chain B, The Structure Of An Antitumor Ch2-Domain-Deleted Humanized
Antibody
pdb|1ZA6|D Chain D, The Structure Of An Antitumor Ch2-Domain-Deleted Humanized
Antibody
pdb|1ZA6|F Chain F, The Structure Of An Antitumor Ch2-Domain-Deleted Humanized
Antibody
pdb|1ZA6|H Chain H, The Structure Of An Antitumor Ch2-Domain-Deleted Humanized
Antibody
Length = 344
Score = 36.2 bits (82), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 62/144 (43%), Gaps = 26/144 (18%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
D+ + W+K + +++E + S ++ RF+ LT D ST + + ++ D
Sbjct: 31 DHAIHWVKQNPGQRLEWIGYFSPGNDDFKYNERFKGKATLTADTSASTAYVELSSLRSED 90
Query: 156 AGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYCY 206
+Y C SLN + L+ +S ST+ V + G T L C
Sbjct: 91 TAVYFC--TRSLNMAYWGQGTLVT-----VSSASTKGPSVFPLAPSSKSTSGGTAALGCL 143
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 144 VKDYFPEPVTVSW---NSGALTSG 164
>pdb|4AEI|L Chain L, Crystal Structure Of The Aahii-Fab4c1 Complex
pdb|4AEI|M Chain M, Crystal Structure Of The Aahii-Fab4c1 Complex
pdb|4AEI|N Chain N, Crystal Structure Of The Aahii-Fab4c1 Complex
Length = 219
Score = 36.2 bits (82), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K + + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|4DAG|H Chain H, Structure Of The Human Metapneumovirus Fusion Protein With
Neutralizing Antibody Identifies A Pneumovirus Antigenic
Site
Length = 220
Score = 36.2 bits (82), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 34/139 (24%), Positives = 59/139 (42%), Gaps = 19/139 (13%)
Query: 106 WMKMDTAKKMEPLPISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETDAGIYKC 161
W++ K +E + + SG + RF ++ D +T L + ++ D IY C
Sbjct: 36 WVRQTPGKGLEWISVFYSGGTTYYADAVKGRFSISMDTSKNTLHLQMNSLRVEDTAIYYC 95
Query: 162 EVIISLNNKVSAEVELIVRRPPI-ISDNSTR---------SVIVSEGQTVYLYCYANG-F 210
++S + + ++ + +S ST+ S + G T L C F
Sbjct: 96 ARVLSRASGMPDAFDIWGPGTMVTVSSASTKGPSVFPLAPSSAATSGGTAALGCLVKDYF 155
Query: 211 PAP-TISWRRDNSAALSTG 228
P P T+SW NS AL++G
Sbjct: 156 PEPVTVSW---NSGALTSG 171
>pdb|1I8M|L Chain L, Crystal Structure Of A Recombinant Anti-Single-Stranded
Dna Antibody Fragment Complexed With Dt5
pdb|1I8M|A Chain A, Crystal Structure Of A Recombinant Anti-Single-Stranded
Dna Antibody Fragment Complexed With Dt5
pdb|1P7K|L Chain L, Crystal Structure Of An Anti-Ssdna Antigen-Binding
Fragment (Fab) Bound To
4-(2-Hydroxyethyl)piperazine-1-Ethanesulfonic Acid
(Hepes)
pdb|1P7K|A Chain A, Crystal Structure Of An Anti-Ssdna Antigen-Binding
Fragment (Fab) Bound To
4-(2-Hydroxyethyl)piperazine-1-Ethanesulfonic Acid
(Hepes)
pdb|1XF2|L Chain L, Structure Of Fab Dna-1 Complexed With Dt3
pdb|1XF2|A Chain A, Structure Of Fab Dna-1 Complexed With Dt3
pdb|1XF3|L Chain L, Structure Of Ligand-Free Fab Dna-1 In Space Group P65
pdb|1XF3|A Chain A, Structure Of Ligand-Free Fab Dna-1 In Space Group P65
pdb|1XF4|L Chain L, Structure Of Ligand-Free Fab Dna-1 In Space Group P321
Solved From Crystals With Perfect Hemihedral Twinning
pdb|1XF4|A Chain A, Structure Of Ligand-Free Fab Dna-1 In Space Group P321
Solved From Crystals With Perfect Hemihedral Twinning
pdb|2FR4|L Chain L, Structure Of Fab Dna-1 Complexed With A Stem-loop Dna
Ligand
pdb|2FR4|A Chain A, Structure Of Fab Dna-1 Complexed With A Stem-loop Dna
Ligand
Length = 214
Score = 36.2 bits (82), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 54/128 (42%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI ++ D G+YYC G G G K + + AP ++I P Q A
Sbjct: 73 LKINSLQPEDFGSYYCQHHYGTPLTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 131
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 132 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 191
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 192 YTCEATHK 199
>pdb|3UJJ|L Chain L, Crystal Structure Of Anti-Hiv-1 V3 Fab 4025 In Complex
With Con A Peptide
Length = 213
Score = 36.2 bits (82), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 38/200 (19%), Positives = 71/200 (35%), Gaps = 27/200 (13%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALS------------------TGGSIYR 233
SV VS GQT + C + P W + S +G
Sbjct: 9 SVSVSPGQTARITCSGDALPEKYAYWYQQKSGQAPVLIIYEDSKRPSGIPERFSGSRSGT 68
Query: 234 GNILKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQGQAL 287
L I D YYC + N G G K + + + P +T+ P +
Sbjct: 69 MATLTISGAQVDDEADYYCYSTNSGGTFFVFGTGTKVTVLGQPKANPTVTLFPPSSEELQ 128
Query: 288 QYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-R 344
A L C + + P A + W D + + ++++++ +S +T E+ +
Sbjct: 129 ANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWK 188
Query: 345 QFGQYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 189 SHRSYSCQVTHEGSTVEKTV 208
>pdb|3IFP|L Chain L, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
7:12b4) Complex
pdb|3IFP|B Chain B, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
7:12b4) Complex
pdb|3IFP|D Chain D, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
7:12b4) Complex
pdb|3IFP|F Chain F, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
7:12b4) Complex
Length = 219
Score = 36.2 bits (82), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K + + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|4H20|H Chain H, Crystal Structure And Computational Modeling Of The Fab
Fragment From The Protective Anti-ricin Monoclonal
Antibody Rac18
Length = 220
Score = 36.2 bits (82), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 38/152 (25%), Positives = 62/152 (40%), Gaps = 38/152 (25%)
Query: 101 DYPVIWMKMDTAKKMEPLPISM-SGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY V W+K K +E L + + S ++ +F+ LT D +ST + + + D
Sbjct: 31 DYYVNWVKQSRGKSLEWLGLIIPSNGGTTYNQKFRGKATLTVDKSSSTAYMELNSLTSED 90
Query: 156 AGIYKCE-----------------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEG 198
+ +Y C V +S + V + P+ D + G
Sbjct: 91 SAVYYCARRGLTGALFAYWGQGTLVTVSAAKTTAPSVYPLA---PVCGDTT--------G 139
Query: 199 QTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+V L C G FP P T++W NS +LS+G
Sbjct: 140 SSVTLGCLVKGYFPEPVTLTW---NSGSLSSG 168
>pdb|3GO1|L Chain L, Crystal Structure Of Anti-Hiv-1 Fab 268-D In Complex With
V3 Peptide Mn
Length = 209
Score = 36.2 bits (82), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 42/202 (20%), Positives = 76/202 (37%), Gaps = 32/202 (15%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISW--RRDNSAAL-------------------STGGS 230
SV VS GQT + C A W +R A L ST G+
Sbjct: 9 SVSVSPGQTARITCSAEALSNQYAYWYRQRPGQAPLLIIYKDTKRPSGIPERFSGSTSGT 68
Query: 231 IYRGNILKIPNITKTDRGTYYCVAQNG-----VGRGMKRNIAVEVEFAPVITINRPRQGQ 285
L I + D YYC + + G G K + + + P +T+ P +
Sbjct: 69 TV---TLTISGVQAEDEADYYCQSADSSGDYVFGGGTKVTVLGQPKANPTVTLFPPSSEE 125
Query: 286 ALQYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER 343
A L C + + P A + W DG + + ++++++ +S +T E+
Sbjct: 126 LQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQ 185
Query: 344 -RQFGQYACKAANKYGSAQKEI 364
+ Y+C+ ++ + +K +
Sbjct: 186 WKSHRSYSCQVTHEGSTVEKTV 207
>pdb|1AQK|H Chain H, Three-Dimensional Structure Of A Human Fab With High
Affinity For Tetanus Toxoid
Length = 226
Score = 36.2 bits (82), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 37/146 (25%), Positives = 64/146 (43%), Gaps = 20/146 (13%)
Query: 100 DDYPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQET 154
++Y + W++ K +E + IS GS + RF ++ D +T L + ++
Sbjct: 30 NNYAIHWVRQAPGKGLEWVAFISYDGSKNYYADSVKGRFTISRDNSKNTLFLQMNSLRPE 89
Query: 155 DAGIYKCEVIISLNNKVSAEVELIVRRPPI-ISDNSTRSVIV---------SEGQTVYLY 204
D IY C ++ + A ++ + + +S ST+ V + G T L
Sbjct: 90 DTAIYYCARVLFQQLVLYAPFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALG 149
Query: 205 CYANG-FPAP-TISWRRDNSAALSTG 228
C FP P T+SW NS AL++G
Sbjct: 150 CLVKDYFPQPVTVSW---NSGALTSG 172
>pdb|3C5Z|A Chain A, Crystal Structure Of Mouse Mhc Class Ii I-Ab3K PEPTIDE
COMPLEXED WITH Mouse Tcr B3k506
pdb|3C5Z|E Chain E, Crystal Structure Of Mouse Mhc Class Ii I-Ab3K PEPTIDE
COMPLEXED WITH Mouse Tcr B3k506
Length = 202
Score = 36.2 bits (82), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 25/39 (64%)
Query: 133 FQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKV 171
F+ T D T+++ L +QE+D+ +Y C ++IS NKV
Sbjct: 61 FEATYDKGTTSFHLRKASVQESDSAVYYCALVISNTNKV 99
>pdb|3U2S|L Chain L, Crystal Structure Of Pg9 Fab In Complex With V1v2 Region
From Hiv-1 Strain Zm109
pdb|3U2S|B Chain B, Crystal Structure Of Pg9 Fab In Complex With V1v2 Region
From Hiv-1 Strain Zm109
pdb|3U36|L Chain L, Crystal Structure Of Pg9 Fab
pdb|3U36|B Chain B, Crystal Structure Of Pg9 Fab
pdb|3U36|D Chain D, Crystal Structure Of Pg9 Fab
pdb|3U36|F Chain F, Crystal Structure Of Pg9 Fab
pdb|3U4E|L Chain L, Crystal Structure Of Pg9 Fab In Complex With V1v2 Region
From Hiv-1 Strain Cap45
pdb|3U4E|B Chain B, Crystal Structure Of Pg9 Fab In Complex With V1v2 Region
From Hiv-1 Strain Cap45
Length = 216
Score = 36.2 bits (82), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 27/136 (19%), Positives = 57/136 (41%), Gaps = 8/136 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV-----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
L I + D G YYC + G G K + + + AP +T+ P + A
Sbjct: 75 LTISGLQAEDEGDYYCKSLTSTRRRVFGTGTKLTVLGQPKAAPSVTLFPPSSEELQANKA 134
Query: 292 ILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQFGQ 348
L C + + P A + W D + + ++++++ +S +T E+ +
Sbjct: 135 TLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKS 194
Query: 349 YACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 195 YSCQVTHEGSTVEKTV 210
>pdb|3MUH|L Chain L, Crystal Structure Of Pg9 Light Chain
Length = 216
Score = 36.2 bits (82), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 27/136 (19%), Positives = 57/136 (41%), Gaps = 8/136 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV-----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
L I + D G YYC + G G K + + + AP +T+ P + A
Sbjct: 75 LTISGLQAEDEGDYYCKSLTSTRRRVFGTGTKLTVLGQPKAAPSVTLFPPSSEELQANKA 134
Query: 292 ILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQFGQ 348
L C + + P A + W D + + ++++++ +S +T E+ +
Sbjct: 135 TLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKS 194
Query: 349 YACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 195 YSCQVTHEGSTVEKTV 210
>pdb|3MJ9|L Chain L, Crystal Structure Of Jaml In Complex With The Stimulatory
Antibody Hl4e10
pdb|3MJ8|L Chain L, Crystal Structure Of Hl4e10 Fab, A Hamster Ab Stimulatory
For Gammadelta T Cells
pdb|3MJ8|A Chain A, Crystal Structure Of Hl4e10 Fab, A Hamster Ab Stimulatory
For Gammadelta T Cells
Length = 213
Score = 35.8 bits (81), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 30/141 (21%), Positives = 52/141 (36%), Gaps = 10/141 (7%)
Query: 234 GNI--LKIPNITKTDRGTYYCVAQNGV------GRGMKRNIAVEVEFAPVITINRPRQGQ 285
GN+ L I D YYC + +G G G K + + AP +T+ P +
Sbjct: 67 GNMATLTISKAQAGDEADYYCQSWDGTNSAWVFGSGTKVTVLGQPNAAPSVTLFPPSSEE 126
Query: 286 ALQYDAILECHVEAYPPP--AIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER 343
A L C + + P A+ W DG I + + S + + L +
Sbjct: 127 LKTNQATLVCMINGFYPADVAVTWEADGTPITQGVKTTQPSKSDSKYMATSYLTMTADAW 186
Query: 344 RQFGQYACKAANKYGSAQKEI 364
+ + CK + + +K +
Sbjct: 187 KSRNTFICKVTHGGNTVEKSL 207
>pdb|3P30|L Chain L, Crystal Structure Of The Cluster Ii Fab 1281 In Complex
With Hiv-1 Gp41 Ectodomain
Length = 213
Score = 35.8 bits (81), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 28/138 (20%), Positives = 57/138 (41%), Gaps = 10/138 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG-------VGRGMKRNIAVEVEFAPVITINRPRQGQALQY 289
L I + D YYC A + G G K + + + AP +T+ P +
Sbjct: 74 LAISGLRSEDEADYYCAAWDDSLSGPYVFGAGTKLTVLGQPKAAPSVTLFPPSSEELQAN 133
Query: 290 DAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQF 346
A L C + + P A + W D I + ++++++ +S +T E+ +
Sbjct: 134 KATLVCLISDFYPGAVTVAWKADSSPIKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSH 193
Query: 347 GQYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 194 RSYSCQVTHEGSTVEKTV 211
>pdb|3O6K|L Chain L, Crystal Structure Of Anti-Tat Hiv Fab'11h6h1
pdb|3O6L|L Chain L, Anti-Tat Hiv 11h6h1 Fab' Complexed With A 15-Mer Tat
Peptide
pdb|3O6M|L Chain L, Anti-Tat Hiv 11h6h1 Fab' Complexed With A 9-Mer Tat
Peptide
Length = 219
Score = 35.8 bits (81), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 45/194 (23%), Positives = 75/194 (38%), Gaps = 12/194 (6%)
Query: 175 VELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT-----ISWRRDNSAALSTGG 229
+ + + +P IS S +S++ S+G+T + +P +S TG
Sbjct: 11 LSVTIGQPASISCKSGQSLLYSDGKTYLNWLLQRPGQSPKRLIYLVSKLDSGVPDRFTGS 70
Query: 230 SIYRGNILKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEV---EFAPVITINRPRQGQA 286
LKI + D G YYC R +E+ + AP ++I P Q
Sbjct: 71 GSGTDFTLKISRVEAEDLGIYYCWQGTHFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQL 130
Query: 287 LQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-E 342
A + C + + P I W DG + N S + + D +S +S +T E
Sbjct: 131 TSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDE 190
Query: 343 RRQFGQYACKAANK 356
+ Y C+A +K
Sbjct: 191 YERHNSYTCEATHK 204
>pdb|1MH5|A Chain A, The Structure Of The Complex Of The Fab Fragment Of The
Esterolytic Antibody Ms6-164 And A Transition-State
Analog
pdb|1MH5|L Chain L, The Structure Of The Complex Of The Fab Fragment Of The
Esterolytic Antibody Ms6-164 And A Transition-State
Analog
Length = 219
Score = 35.8 bits (81), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 48/186 (25%), Positives = 76/186 (40%), Gaps = 16/186 (8%)
Query: 185 ISDNSTRSVIVSEGQTVYLYCYAN--GFPAPTISWRRDNSAA----LSTGGSIYRGNILK 238
IS S++S++ S G T YLY + G + +R N A+ +G L+
Sbjct: 21 ISCRSSKSLLHSNGNT-YLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLR 79
Query: 239 IPNITKTDRGTYYCVAQ----NGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
I + D G YYC+ G G K + + AP ++I P Q A +
Sbjct: 80 ISRVEAEDVGVYYCLQHLEYPFTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGASVV 138
Query: 295 CHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQYA 350
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 139 CFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYT 198
Query: 351 CKAANK 356
C+A +K
Sbjct: 199 CEATHK 204
>pdb|2J88|L Chain L, Hyaluronidase In Complex With A Monoclonal Igg Fab
Fragment
Length = 213
Score = 35.8 bits (81), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 35/127 (27%), Positives = 53/127 (41%), Gaps = 8/127 (6%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV---GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAIL 293
LKI ++ D G YYC G G G + I + AP ++I P Q A +
Sbjct: 73 LKISSLQPEDFGNYYCQHHYGTRTFGGGTRLEIK-RADAAPTVSIFPPSSEQLTSGGASV 131
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 132 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 191
Query: 350 ACKAANK 356
C+A +K
Sbjct: 192 TCEATHK 198
>pdb|1MJ8|L Chain L, High Resolution Crystal Structure Of The Fab Fragment Of
The Esterolytic Antibody Ms6-126
Length = 219
Score = 35.8 bits (81), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 48/186 (25%), Positives = 76/186 (40%), Gaps = 16/186 (8%)
Query: 185 ISDNSTRSVIVSEGQTVYLYCYAN--GFPAPTISWRRDNSAA----LSTGGSIYRGNILK 238
IS S++S++ S G T YLY + G + +R N A+ +G L+
Sbjct: 21 ISCRSSKSLLHSNGNT-YLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLR 79
Query: 239 IPNITKTDRGTYYCVAQ----NGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
I + D G YYC+ G G K + + AP ++I P Q A +
Sbjct: 80 ISRVEAEDVGVYYCLQHLEYPFTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGASVV 138
Query: 295 CHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQYA 350
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 139 CFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYT 198
Query: 351 CKAANK 356
C+A +K
Sbjct: 199 CEATHK 204
>pdb|3SGD|L Chain L, Crystal Structure Of The Mouse Mab 17.2
pdb|3SGD|I Chain I, Crystal Structure Of The Mouse Mab 17.2
pdb|3SGE|L Chain L, Crystal Structure Of Mab 17.2 In Complex With R13 Peptide
pdb|3SGE|I Chain I, Crystal Structure Of Mab 17.2 In Complex With R13 Peptide
Length = 219
Score = 35.8 bits (81), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 47/195 (24%), Positives = 77/195 (39%), Gaps = 14/195 (7%)
Query: 175 VELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT-----ISWRRDNSAALSTGG 229
+ + + +P IS S++S++ S+G+T + +P +S TG
Sbjct: 11 LSVTIGQPASISCKSSQSLLDSDGKTYLNWLLQRPGQSPKRLIYLVSKLDSGVPDRFTGS 70
Query: 230 SIYRGNILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQ 285
LKI + D G YYC + G G K I + AP ++I P Q
Sbjct: 71 GSGTDFTLKISRVEAEDLGVYYCWQGSHFPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQ 129
Query: 286 ALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI- 341
A + C + + P I W DG + N S + + D +S +S +T
Sbjct: 130 LTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKD 189
Query: 342 ERRQFGQYACKAANK 356
E + Y C+A +K
Sbjct: 190 EYERHNSYTCEATHK 204
>pdb|1YC8|A Chain A, Caban33- Y37vE44GR45L TRIPLE MUTANT
pdb|1YC8|B Chain B, Caban33- Y37vE44GR45L TRIPLE MUTANT
pdb|1YZZ|A Chain A, Humanized Caban33 At Room Temperature
pdb|1YZZ|B Chain B, Humanized Caban33 At Room Temperature
Length = 124
Score = 35.8 bits (81), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 92 LKCSVQYADDYPVI--WMKMDTAKKMEPLP-ISMSGSLIIHDS---RFQLTTDPETSTYI 145
L C+V + P W++ K +E + IS G++ DS RF ++ D +T
Sbjct: 20 LSCAVSGSTYSPCTTGWVRQAPGKGLEWVSSISSPGTIYYQDSVKGRFTISRDNAKNTVY 79
Query: 146 LSIKEIQETDAGIYKCEV 163
L + +Q D G+Y C++
Sbjct: 80 LQMNSLQREDTGMYYCQI 97
>pdb|1MJJ|A Chain A, High Resolution Crystal Structure Of The Complex Of The
Fab Fragment Of Esterolytic Antibody Ms6-12 And A
Transition- State Analog
pdb|1MJJ|L Chain L, High Resolution Crystal Structure Of The Complex Of The
Fab Fragment Of Esterolytic Antibody Ms6-12 And A
Transition- State Analog
pdb|1MJU|L Chain L, 1.22 Angstrom Resolution Crystal Structure Of The Fab
Fragment Of Esterolytic Antibody Ms6-12
Length = 219
Score = 35.8 bits (81), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 48/186 (25%), Positives = 76/186 (40%), Gaps = 16/186 (8%)
Query: 185 ISDNSTRSVIVSEGQTVYLYCYAN--GFPAPTISWRRDNSAA----LSTGGSIYRGNILK 238
IS S++S++ S G T YLY + G + +R N A+ +G L+
Sbjct: 21 ISCRSSKSLLHSNGNT-YLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLR 79
Query: 239 IPNITKTDRGTYYCVAQ----NGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
I + D G YYC+ G G K + + AP ++I P Q A +
Sbjct: 80 ISRVEAEDVGVYYCLQHLEYPFTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGASVV 138
Query: 295 CHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQYA 350
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 139 CFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYT 198
Query: 351 CKAANK 356
C+A +K
Sbjct: 199 CEATHK 204
>pdb|3R4D|A Chain A, Crystal Structure Of Mouse Coronavirus Receptor-Binding
Domain Complexed With Its Murine Receptor
pdb|3R4D|C Chain C, Crystal Structure Of Mouse Coronavirus Receptor-Binding
Domain Complexed With Its Murine Receptor
Length = 208
Score = 35.8 bits (81), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 34/131 (25%), Positives = 53/131 (40%), Gaps = 3/131 (2%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYC 205
L + I D G+Y ++ + A V V +P + V E +V L C
Sbjct: 73 LLFQMITMKDMGVYTLDMTDENYRRTQATVRFHVHQPVTQPFLQVTNTTVKELDSVTLTC 132
Query: 206 YANGFPAPTISWR-RDNSAALSTGGSIYRGN-ILKIPNITKTDRGTYYCVAQNGVGRGMK 263
+N A I W S L+ ++ + N IL+I I + D G Y C N V
Sbjct: 133 LSNDIGA-NIQWLFNSQSLQLTERMTLSQNNSILRIDPIKREDAGEYQCEISNPVSVRRS 191
Query: 264 RNIAVEVEFAP 274
+I +++ F P
Sbjct: 192 NSIKLDIIFDP 202
>pdb|3IFO|L Chain L, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
7:10d5) Complex
pdb|3IFO|B Chain B, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
7:10d5) Complex
Length = 219
Score = 35.8 bits (81), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K + + AP ++I P Q A
Sbjct: 78 LKIKKVEAEDLGIYYCFQGSHVPLTFGAGTKLELE-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1MRC|L Chain L, Preparation, Characterization And Crystallization Of An
Antibody Fab Fragment That Recognizes Rna. Crystal
Structures Of Native Fab And Three Fab-Mononucleotide
Complexes
pdb|1MRD|L Chain L, Preparation, Characterization And Crystallization Of An
Antibody Fab Fragment That Recognizes Rna. Crystal
Structures Of Native Fab And Three Fab-Mononucleotide
Complexes
pdb|1MRE|L Chain L, Preparation, Characterization And Crystallization Of An
Antibody Fab Fragment That Recognizes Rna. Crystal
Structures Of Native Fab And Three Fab-Mononucleotide
Complexes
pdb|1MRF|L Chain L, Preparation, Characterization And Crystallization Of An
Antibody Fab Fragment That Recognizes Rna. Crystal
Structures Of Native Fab And Three Fab-Mononucleotide
Complexes
Length = 219
Score = 35.8 bits (81), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 33/127 (25%), Positives = 52/127 (40%), Gaps = 7/127 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEV---EFAPVITINRPRQGQALQYDAIL 293
LKI + D G Y+C V R +E+ + AP ++I P Q A +
Sbjct: 78 LKISRVEAEDLGVYFCSQSTHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASV 137
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 138 VCFLNNFYPKDINVKWKIDGKERQNGVLNSWTDQNSKDSTYSMSSTLTLTKDEYERHNSY 197
Query: 350 ACKAANK 356
C+A +K
Sbjct: 198 TCEATHK 204
>pdb|1PSK|L Chain L, The Crystal Structure Of An Fab Fragment That Binds To The
Melanoma-Associated Gd2 Ganglioside
Length = 213
Score = 35.8 bits (81), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I + D TYYC ++G G G K I + AP ++I P Q A
Sbjct: 72 LTISRMGAEDAATYYCQQRSGYPFTFGSGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 130
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 131 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 190
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 191 YTCEATHK 198
>pdb|3IFL|L Chain L, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
7:12a11) Complex
pdb|3IFN|L Chain L, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
40:12a11) Complex
Length = 219
Score = 35.8 bits (81), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K + + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGIYYCFQSSHVPLTFGAGTKLELK-GADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|3V4P|L Chain L, Crystal Structure Of A4b7 Headpiece Complexed With Fab
Act-1
pdb|3V4P|N Chain N, Crystal Structure Of A4b7 Headpiece Complexed With Fab
Act-1
pdb|3V4V|L Chain L, Crystal Structure Of A4b7 Headpiece Complexed With Fab
Act-1 And Ro0505376
pdb|3V4V|N Chain N, Crystal Structure Of A4b7 Headpiece Complexed With Fab
Act-1 And Ro0505376
Length = 217
Score = 35.8 bits (81), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI I D G YYC+ G G K I + AP ++I P Q A
Sbjct: 78 LKISTIKPEDLGMYYCLQGTHQPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWNIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|3QUM|L Chain L, Crystal Structure Of Human Prostate Specific Antigen (Psa)
In Fab Sandwich With A High Affinity And A Pca Selective
Antibody
pdb|3QUM|M Chain M, Crystal Structure Of Human Prostate Specific Antigen (Psa)
In Fab Sandwich With A High Affinity And A Pca Selective
Antibody
Length = 219
Score = 35.8 bits (81), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 49/186 (26%), Positives = 76/186 (40%), Gaps = 16/186 (8%)
Query: 185 ISDNSTRSVIVSEGQTVYLYCYAN--GFPAPTISWRRDNSAA----LSTGGSIYRGNILK 238
IS S++S++ S G T YLY + G + +R N A+ +G L+
Sbjct: 21 ISCRSSKSLLHSNGNT-YLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTDFTLR 79
Query: 239 IPNITKTDRGTYYCVAQ----NGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
I + D G YYC+ G G K I + AP ++I P Q A +
Sbjct: 80 ISRVEAEDVGVYYCMQHLEYPVTFGAGTKVEIK-RADAAPTVSIFPPSSEQLTSGGASVV 138
Query: 295 CHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQYA 350
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 139 CFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYT 198
Query: 351 CKAANK 356
C+A +K
Sbjct: 199 CEATHK 204
>pdb|1L6Z|A Chain A, Crystal Structure Of Murine Ceacam1a[1,4]: A Coronavirus
Receptor And Cell Adhesion Molecule In The Cea Family
Length = 216
Score = 35.8 bits (81), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 34/131 (25%), Positives = 53/131 (40%), Gaps = 3/131 (2%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYC 205
L + I D G+Y ++ + A V V +P + V E +V L C
Sbjct: 73 LLFQMITMKDMGVYTLDMTDENYRRTQATVRFHVHQPVTQPFLQVTNTTVKELDSVTLTC 132
Query: 206 YANGFPAPTISWR-RDNSAALSTGGSIYRGN-ILKIPNITKTDRGTYYCVAQNGVGRGMK 263
+N A I W S L+ ++ + N IL+I I + D G Y C N V
Sbjct: 133 LSNDIGA-NIQWLFNSQSLQLTERMTLSQNNSILRIDPIKREDAGEYQCEISNPVSVRRS 191
Query: 264 RNIAVEVEFAP 274
+I +++ F P
Sbjct: 192 NSIKLDIIFDP 202
>pdb|2PCP|A Chain A, Antibody Fab Complexed With Phencyclidine
pdb|2PCP|C Chain C, Antibody Fab Complexed With Phencyclidine
Length = 216
Score = 35.8 bits (81), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCV----AQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC A G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGTHAPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1IGC|H Chain H, Igg1 Fab Fragment (Mopc21) Complex With Domain Iii Of
Protein G From Streptococcus
Length = 222
Score = 35.8 bits (81), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 35/138 (25%), Positives = 55/138 (39%), Gaps = 19/138 (13%)
Query: 106 WMKMDTAKKMEPLPISMSGSLIIH-----DSRFQLTTDPETSTYILSIKEIQETDAGIYK 160
W++ K +E + SGS +H RF ++ D +T L + ++ D G+Y
Sbjct: 36 WVRQAPEKGLEWVAYISSGSSTLHYADTVKGRFTISRDNPKNTLFLQMTSLRSEDTGMYY 95
Query: 161 CE--------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FP 211
C + S V PP + + S + V L C G FP
Sbjct: 96 CARWGNYPYYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTN-SMVTLGCLVKGYFP 154
Query: 212 AP-TISWRRDNSAALSTG 228
P T++W NS +LS+G
Sbjct: 155 EPVTVTW---NSGSLSSG 169
>pdb|4D9Q|E Chain E, Inhibiting Alternative Pathway Complement Activation By
Targeting The Exosite On Factor D
pdb|4D9Q|H Chain H, Inhibiting Alternative Pathway Complement Activation By
Targeting The Exosite On Factor D
Length = 217
Score = 35.8 bits (81), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 60/144 (41%), Gaps = 26/144 (18%)
Query: 101 DYPVIWMKMDTAKKMEPLPI--SMSGSLIIHD---SRFQLTTDPETSTYILSIKEIQETD 155
+Y + W++ + +E + + +G D RF + D ST L I ++ D
Sbjct: 31 NYGMNWVRQAPGQGLEWMGWINTYTGETTYADDFKGRFVFSLDTSVSTAYLQISSLKAED 90
Query: 156 AGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYCY 206
+Y CE +NN + L+ +S ST+ V + G T L C
Sbjct: 91 TAVYYCEREGGVNNW--GQGTLVT-----VSSASTKGPSVFPLAPSSKSTSGGTAALGCL 143
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 144 VKDYFPEPVTVSW---NSGALTSG 164
>pdb|1K6Q|L Chain L, Crystal Structure Of Antibody Fab Fragment D3
Length = 210
Score = 35.8 bits (81), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 35/129 (27%), Positives = 55/129 (42%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNG-----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
L I ++ D TYYC+ Q+G G G K + + AP ++I P Q A
Sbjct: 73 LTISSLESDDTATYYCL-QHGESPFTFGSGTKLELK-RADAAPTVSIFPPSSEQLTSGGA 130
Query: 292 ILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFG 347
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 131 SVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHN 190
Query: 348 QYACKAANK 356
Y C+A +K
Sbjct: 191 SYTCEATHK 199
>pdb|1C1E|L Chain L, Crystal Structure Of A Diels-alderase Catalytic Antibody
1e9 In Complex With Its Hapten
Length = 216
Score = 35.4 bits (80), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 35/129 (27%), Positives = 52/129 (40%), Gaps = 9/129 (6%)
Query: 236 ILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
ILKI + D G Y+C G G K I + AP ++I P Q A
Sbjct: 77 ILKISRVEAEDLGVYFCFQSTHFFPTFGGGTKLEIK-SADAAPTVSIFPPSSEQLTSGGA 135
Query: 292 ILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFG 347
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 136 SVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHN 195
Query: 348 QYACKAANK 356
Y C+A +K
Sbjct: 196 SYTCEATHK 204
>pdb|2DD8|L Chain L, Crystal Structure Of Sars-Cov Spike Receptor-Binding
Domain Complexed With Neutralizing Antibody
pdb|2G75|B Chain B, Crystal Structure Of Anti-Sars M396 Antibody
pdb|2G75|D Chain D, Crystal Structure Of Anti-Sars M396 Antibody
Length = 213
Score = 35.4 bits (80), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 38/199 (19%), Positives = 78/199 (39%), Gaps = 26/199 (13%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRR------------DNSAALS------TGGSIYR 233
SV V+ G+T + C N + ++ W + D+S S +G +
Sbjct: 9 SVSVAPGKTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGN 68
Query: 234 GNILKIPNITKTDRGTYYCVAQNG-----VGRGMKRNIAVEVEFAPVITINRPRQGQALQ 288
L I + D YYC + G G K + + + P +T+ P +
Sbjct: 69 TATLTISRVEAGDEADYYCQVWDSSSDYVFGTGTKVTVLGQPKANPTVTLFPPSSEEFQA 128
Query: 289 YDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQ 345
A L C + + P A + W DG + + ++++++ +S +T E+ +
Sbjct: 129 NKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKS 188
Query: 346 FGQYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 189 HRSYSCQVTHEGSTVEKTV 207
>pdb|2C5D|C Chain C, Structure Of A Minimal Gas6-Axl Complex
pdb|2C5D|D Chain D, Structure Of A Minimal Gas6-Axl Complex
Length = 195
Score = 35.4 bits (80), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 44/192 (22%), Positives = 71/192 (36%), Gaps = 29/192 (15%)
Query: 89 TADLKCSVQYADDYP-VIWMK-------MDTAKKMEPLPISMSGSLIIHDSRFQLTTDPE 140
T L+C +Q + P V W++ D+ + PL I+
Sbjct: 19 TGTLRCQLQVQGEPPEVHWLRDGQILELADSTQTQVPLGEDEQDDWIV------------ 66
Query: 141 TSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPP-IISDNSTRSVIVSEGQ 199
L I +Q +D G Y+C V + VS + + P + + R+V +
Sbjct: 67 --VSQLRITSLQLSDTGQYQCLVFLGHQTFVSQPGYVGLEGLPYFLEEPEDRTVAANT-- 122
Query: 200 TVYLYCYANGFPAPT-ISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQNGV 258
L C A G P P + W +D + L+T L +P + KT ++ C A N
Sbjct: 123 PFNLSCQAQGPPEPVDLLWLQD-AVPLATAPGHGPQRSLHVPGLNKTS--SFSCEAHNAK 179
Query: 259 GRGMKRNIAVEV 270
G R + V
Sbjct: 180 GVTTSRTATITV 191
>pdb|2HKF|L Chain L, Crystal Structure Of The Complex Fab M75- Peptide
pdb|2HKH|L Chain L, Crystal Structure Of The Fab M75
Length = 219
Score = 35.4 bits (80), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G Y+C V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYFCSQSTHVPFTFGSGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|3SO3|C Chain C, Structures Of Fab-Protease Complexes Reveal A Highly
Specific Non- Canonical Mechanism Of Inhibition
Length = 228
Score = 35.4 bits (80), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 41/148 (27%), Positives = 66/148 (44%), Gaps = 22/148 (14%)
Query: 100 DDYPVIWMKMDTAKKMEPL-PISMSG-SLIIHDS---RFQLTTDPETSTYILSIKEIQET 154
Y + W++ K +E + IS SG S DS RF ++ D +T L + ++
Sbjct: 30 SSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMSSLRAE 89
Query: 155 DAGIYKC--EVIISLNNKVSAEVELIVRRPPI-ISDNSTRSVIV---------SEGQTVY 202
D +Y C ++ I+ VS ++ + + +S ST+ V + G T
Sbjct: 90 DTAVYYCVKDLGIAARRFVSGAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAA 149
Query: 203 LYCYANG-FPAP-TISWRRDNSAALSTG 228
L C FP P T+SW NS AL++G
Sbjct: 150 LGCLVKDYFPEPVTVSW---NSGALTSG 174
>pdb|3SM5|L Chain L, Influenza Hemagglutinin In Complex With A Neutralizing
Antibody
pdb|3SM5|M Chain M, Influenza Hemagglutinin In Complex With A Neutralizing
Antibody
pdb|3SM5|N Chain N, Influenza Hemagglutinin In Complex With A Neutralizing
Antibody
Length = 211
Score = 35.4 bits (80), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 37/200 (18%), Positives = 76/200 (38%), Gaps = 27/200 (13%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRR---------------DNSAALS---TGGSIYR 233
SV V+ GQT + C N ++ W + D + + +G +
Sbjct: 9 SVSVAPGQTARITCGGNDIGRKSVHWNQQKPGQAPVLVVCYDSDRPSGIPERFSGSNSGN 68
Query: 234 GNILKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQGQAL 287
L I + D YYC + G G K + + + AP +T+ P +
Sbjct: 69 TATLTISRVEAGDEADYYCQVWDSSSDHVIFGGGTKLTVLGQPKAAPSVTLFPPSSEELQ 128
Query: 288 QYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-R 344
A L C + + P A + W D + + ++++++ +S +T E+ +
Sbjct: 129 ANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWK 188
Query: 345 QFGQYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 189 SHRSYSCQVTHEGSTVEKTV 208
>pdb|4D9R|H Chain H, Inhibiting Alternative Pathway Complement Activation By
Targeting The Exosite On Factor D
pdb|4D9R|E Chain E, Inhibiting Alternative Pathway Complement Activation By
Targeting The Exosite On Factor D
Length = 218
Score = 35.4 bits (80), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 60/144 (41%), Gaps = 26/144 (18%)
Query: 101 DYPVIWMKMDTAKKMEPLPI--SMSGSLIIHD---SRFQLTTDPETSTYILSIKEIQETD 155
+Y + W++ + +E + + +G D RF + D ST L I ++ D
Sbjct: 31 NYGMNWVRQAPGQGLEWMGWINTYTGETTYADDFKGRFVFSLDTSVSTAYLQISSLKAED 90
Query: 156 AGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYCY 206
+Y CE +NN + L+ +S ST+ V + G T L C
Sbjct: 91 TAVYYCEREGGVNNW--GQGTLVT-----VSSASTKGPSVFPLAPSSKSTSGGTAALGCL 143
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 144 VKDYFPEPVTVSW---NSGALTSG 164
>pdb|1KOA|A Chain A, Twitchin Kinase Fragment (C.Elegans), Autoregulated
Protein Kinase And Immunoglobulin Domains
Length = 491
Score = 35.4 bits (80), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 28/115 (24%), Positives = 48/115 (41%), Gaps = 16/115 (13%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSI--YRGNI--LKIPNITKTDRGTY 250
V EGQ+ YC P ++W +D+ + + Y GN L I + D+G Y
Sbjct: 388 VGEGQSANFYCRVIASSPPVVTWHKDDRELKQSVKYMKRYNGNDYGLTINRVKGDDKGEY 447
Query: 251 YCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAI 305
A+N G + ++ +N R + L+++ LE +A PP +
Sbjct: 448 TVRAKNSYGTKEE-----------IVFLNVTRHSEPLKFEP-LEPMKKAPSPPRV 490
Score = 33.1 bits (74), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 295 CHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAA 354
C V A PP + W KD ++ + Y + +D L + ++ G+Y +A
Sbjct: 398 CRVIASSPPVVTWHKDDRELKQSVKYMKRYNG-----NDYGLTINRVKGDDKGEYTVRAK 452
Query: 355 NKYGSAQK 362
N YG+ ++
Sbjct: 453 NSYGTKEE 460
>pdb|1W72|L Chain L, Crystal Structure Of Hla-A1:mage-A1 In Complex With Fab-
Hyb3
pdb|1W72|M Chain M, Crystal Structure Of Hla-A1:mage-A1 In Complex With Fab-
Hyb3
Length = 210
Score = 35.4 bits (80), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 39/200 (19%), Positives = 78/200 (39%), Gaps = 27/200 (13%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRR------------DNSAALS------TGGSIYR 233
SV V+ GQT + C N + ++ W + D+S S +G +
Sbjct: 9 SVSVAPGQTARITCGGNNIGSRSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGN 68
Query: 234 GNILKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQGQAL 287
L I + D YYC + G G + + + AP +T+ P +
Sbjct: 69 MATLTISRVEAGDEADYYCQVWDSRTDHWVFGGGTDLTVLGQPKAAPSVTLFPPSSEELQ 128
Query: 288 QYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-R 344
A L C + + P A + W DG + + ++++++ +S +T E+ +
Sbjct: 129 ANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWK 188
Query: 345 QFGQYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 189 SHRSYSCQVTHEGSTVEKTV 208
>pdb|1M71|A Chain A, Crystal Structure Of A Monoclonal Fab Specific For
Shigella Flexneri Y Lipopolysaccharide
pdb|1M7D|A Chain A, Crystal Structure Of A Monoclonal Fab Specific For
Shigella Flexneri Y Lipopolysaccharide Complexed With A
Trisaccharide
pdb|1M7I|A Chain A, Crystal Structure Of A Monoclonal Fab Specific For
Shigella Flexneri Y Lipopolysaccharide Complexed With A
Pentasaccharide
pdb|1PZ5|A Chain A, Structural Basis Of Peptide-Carbohydrate Mimicry In An
Antibody Combining Site
Length = 215
Score = 35.4 bits (80), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 35/127 (27%), Positives = 52/127 (40%), Gaps = 8/127 (6%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV---GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAIL 293
LKI + D G Y+C V G G K I + AP ++I P Q A +
Sbjct: 78 LKISRVEAEDLGVYFCSQTTHVPTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGASV 136
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 137 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 196
Query: 350 ACKAANK 356
C+A +K
Sbjct: 197 TCEATHK 203
>pdb|3UO1|L Chain L, Structure Of A Monoclonal Antibody Complexed With Its
Mhc-I Antigen
pdb|3UYR|L Chain L, Structure Of A Monoclonal Antibody Complexed With Its
Mhc-I Antigen
pdb|3V4U|L Chain L, Structure Of A Monoclonal Antibody Complexed With Its
Mhc-I Antigen
pdb|3V52|L Chain L, Structure Of A Monoclonal Antibody Complexed With Its
Mhc-I Antigen
Length = 218
Score = 35.4 bits (80), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 35/127 (27%), Positives = 52/127 (40%), Gaps = 8/127 (6%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV---GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAIL 293
LKI + D G Y+C V G G K I + AP ++I P Q A +
Sbjct: 78 LKISRVEAEDLGVYFCSQSTHVPTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGASV 136
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 137 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 196
Query: 350 ACKAANK 356
C+A +K
Sbjct: 197 TCEATHK 203
>pdb|1MCB|A Chain A, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCB|B Chain B, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCC|A Chain A, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCC|B Chain B, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCD|A Chain A, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCD|B Chain B, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCE|A Chain A, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCE|B Chain B, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCF|A Chain A, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCF|B Chain B, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCH|A Chain A, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCH|B Chain B, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCI|A Chain A, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCI|B Chain B, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCJ|A Chain A, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCJ|B Chain B, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCK|A Chain A, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCK|B Chain B, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCL|A Chain A, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCL|B Chain B, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCN|A Chain A, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCN|B Chain B, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCQ|A Chain A, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCQ|B Chain B, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCR|A Chain A, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCR|B Chain B, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCS|A Chain A, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
pdb|1MCS|B Chain B, Principles And Pitfalls In Designing Site Directed Peptide
Ligands
Length = 216
Score = 35.4 bits (80), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 26/136 (19%), Positives = 57/136 (41%), Gaps = 8/136 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNG-----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
L + + D YYC + G G G K + + + P +T+ P + A
Sbjct: 75 LTVSGLQAEDEADYYCSSYEGSDNFVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKA 134
Query: 292 ILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQFGQ 348
L C + + P A + W DG + + ++++++ +S +T E+ +
Sbjct: 135 TLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRS 194
Query: 349 YACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 195 YSCQVTHEGSTVEKTV 210
>pdb|2XKN|A Chain A, Crystal Structure Of The Fab Fragment Of The Anti-Egfr
Antibody 7a7
pdb|2XKN|C Chain C, Crystal Structure Of The Fab Fragment Of The Anti-Egfr
Antibody 7a7
Length = 223
Score = 35.4 bits (80), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 54/128 (42%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I N+ + D TY+C N + G G K I + AP ++I P Q A
Sbjct: 73 LTISNLEQEDIATYFCQQGNTLPWTFGGGTKVEIK-RADAAPTVSIFPPSSEQLTSGGAS 131
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 132 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 191
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 192 YTCEATHK 199
>pdb|3CXD|L Chain L, Crystal Structure Of Anti-Osteopontin Antibody 23c3 In
Complex With Its Epitope Peptide
pdb|3DSF|L Chain L, Crystal Structure Of Anti-Osteopontin Antibody 23c3 In
Complex With W43a Mutated Epitope Peptide
Length = 213
Score = 35.4 bits (80), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 35/132 (26%), Positives = 54/132 (40%), Gaps = 17/132 (12%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI ++ D GTYYC G G G K I + AP ++I P Q
Sbjct: 73 LKINSLQSEDFGTYYCQHFWGTPFTFGSGTKLEIK-RSDAAPTVSIFPPSAAQLSSGGGS 131
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITI------ERR 344
+ C + + P I W DG + N V + TS + +D++ + + E
Sbjct: 132 VVCFLNNFYPKDINVKWKIDGAERGNG----VLNSWTSQDSADSTYSMSSTLTSGGDEYE 187
Query: 345 QFGQYACKAANK 356
+ Y C+A +K
Sbjct: 188 RHNSYTCEATHK 199
>pdb|2OJZ|L Chain L, Anti-Dna Antibody Ed10
pdb|2OJZ|M Chain M, Anti-Dna Antibody Ed10
pdb|2OK0|L Chain L, Fab Ed10-Dna Complex
Length = 219
Score = 35.4 bits (80), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + + G G K + + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHIPLTFGAGTKLEVK-RSDAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|2GJZ|L Chain L, Structure Of Catalytic Elimination Antibody 13g5 From A
Crystal In Space Group P2(1)
pdb|2GJZ|A Chain A, Structure Of Catalytic Elimination Antibody 13g5 From A
Crystal In Space Group P2(1)
pdb|2GK0|L Chain L, Structure Of Catalytic Elimination Antibody 13g5 From A
Twinned Crystal In Space Group C2
pdb|2GK0|A Chain A, Structure Of Catalytic Elimination Antibody 13g5 From A
Twinned Crystal In Space Group C2
Length = 217
Score = 35.4 bits (80), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + + G G K I + AP ++I P Q A
Sbjct: 78 LKINRVEAEDLGVYYCFQGSHLPPTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|2R15|A Chain A, Crystal Structure Of The Myomesin Domains 12 And 13
pdb|2R15|B Chain B, Crystal Structure Of The Myomesin Domains 12 And 13
Length = 212
Score = 35.4 bits (80), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 11/85 (12%)
Query: 275 VITINRPRQGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDT 334
V+TI ++G+AL L C+V PPP + W+K+ + H ++ A +
Sbjct: 126 VVTI---QEGKALN----LTCNVWGDPPPEVSWLKNEKALAQTDHCNLKFEAGRTAY--- 175
Query: 335 SLRVITIERRQFGQYACKAANKYGS 359
+ + G+Y NKYGS
Sbjct: 176 -FTINGVSTADSGKYGLVVKNKYGS 199
Score = 32.0 bits (71), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 29/72 (40%), Gaps = 5/72 (6%)
Query: 193 VIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGG-----SIYRGNILKIPNITKTDR 247
V + EG+ + L C G P P +SW ++ A T R I ++ D
Sbjct: 127 VTIQEGKALNLTCNVWGDPPPEVSWLKNEKALAQTDHCNLKFEAGRTAYFTINGVSTADS 186
Query: 248 GTYYCVAQNGVG 259
G Y V +N G
Sbjct: 187 GKYGLVVKNKYG 198
>pdb|3RKD|L Chain L, Hepatitis E Virus E2s Domain (Genotype I) In Complex With
A Neutralizing Antibody
pdb|3RKD|C Chain C, Hepatitis E Virus E2s Domain (Genotype I) In Complex With
A Neutralizing Antibody
Length = 214
Score = 35.4 bits (80), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 50/194 (25%), Positives = 77/194 (39%), Gaps = 33/194 (17%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISW---RRDNSAAL------------------STGGS 230
S+ VS G+TV + C A+ ++W ++ S L S G+
Sbjct: 10 SLSVSVGETVTITCRASEIIYSNLAWYQQKQGKSPQLLVYSATNLAEGVPSRFSGSGSGT 69
Query: 231 IYRGNILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQA 286
Y LKI ++ D G+YYC G G G K I + AP ++I P Q
Sbjct: 70 QYS---LKINSLQSEDFGSYYCQHFWGNPWTFGGGTKLEIK-RADAAPTVSIFPPSSEQL 125
Query: 287 LQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-E 342
A + C + + P I W DG + N S + + D +S +S +T E
Sbjct: 126 TSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDE 185
Query: 343 RRQFGQYACKAANK 356
+ Y C+A +K
Sbjct: 186 YERHNSYTCEATHK 199
>pdb|2Z4Q|A Chain A, Crystal Structure Of A Murine Antibody Fab 528
Length = 219
Score = 35.4 bits (80), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + + G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGIYYCFQGSHIPPTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPRDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1MCW|M Chain M, Three-Dimensional Structure Of A Hybrid Light Chain Dimer.
Protein Engineering Of A Binding Cavity
pdb|2MCG|1 Chain 1, Three-Dimensional Structure Of A Light Chain Dimer
Crystallized In Water. Conformational Flexibility Of A
Molecule In Two Crystal Forms
pdb|2MCG|2 Chain 2, Three-Dimensional Structure Of A Light Chain Dimer
Crystallized In Water. Conformational Flexibility Of A
Molecule In Two Crystal Forms
pdb|3MCG|1 Chain 1, Three-Dimensional Structure Of A Light Chain Dimer
Crystallized In Water. Conformational Flexibility Of A
Molecule In Two Crystal Forms
pdb|3MCG|2 Chain 2, Three-Dimensional Structure Of A Light Chain Dimer
Crystallized In Water. Conformational Flexibility Of A
Molecule In Two Crystal Forms
pdb|1A8J|L Chain L, Immunoglobulin Lambda Light Chain Dimer (Mcg) Complex With
Aspartame
pdb|1A8J|H Chain H, Immunoglobulin Lambda Light Chain Dimer (Mcg) Complex With
Aspartame
Length = 216
Score = 35.4 bits (80), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 26/136 (19%), Positives = 57/136 (41%), Gaps = 8/136 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNG-----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
L + + D YYC + G G G K + + + P +T+ P + A
Sbjct: 75 LTVSGLQAEDEADYYCSSYEGSDNFVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKA 134
Query: 292 ILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQFGQ 348
L C + + P A + W DG + + ++++++ +S +T E+ +
Sbjct: 135 TLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRS 194
Query: 349 YACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 195 YSCQVTHEGSTVEKTV 210
>pdb|1JGL|L Chain L, Crystal Structure Of Immunoglobulin Fab Fragment Complexed
With 17-Beta-Estradiol
pdb|1JHK|L Chain L, Crystal Structure Of The Anti-Estradiol Antibody 57-2
Length = 214
Score = 35.4 bits (80), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 49/194 (25%), Positives = 77/194 (39%), Gaps = 33/194 (17%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRRD-----------NSAALSTG----------GS 230
S+ S G+TV + C A+G ++W + N+ L+ G G+
Sbjct: 10 SLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYNAKTLADGVPSRFSGSGSGT 69
Query: 231 IYRGNILKIPNITKTDRGTYYC----VAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQA 286
Y LKI ++ D GTYYC G G K + + AP ++I P Q
Sbjct: 70 QYS---LKINSLQPEDFGTYYCHHFWSTPWTFGGGTKLEVK-RADAAPTVSIFPPSSEQL 125
Query: 287 LQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-E 342
A + C + + P I W DG + N S + + D +S +S +T E
Sbjct: 126 TSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDE 185
Query: 343 RRQFGQYACKAANK 356
+ Y C+A +K
Sbjct: 186 YERHNSYTCEATHK 199
>pdb|1DCL|A Chain A, Mcg, A Lambda V Type Light-Chain Dimer (Bence-Jones
Protein), Crystallized From Ammonium Sulfate
pdb|1DCL|B Chain B, Mcg, A Lambda V Type Light-Chain Dimer (Bence-Jones
Protein), Crystallized From Ammonium Sulfate
Length = 216
Score = 35.4 bits (80), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 26/136 (19%), Positives = 57/136 (41%), Gaps = 8/136 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNG-----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
L + + D YYC + G G G K + + + P +T+ P + A
Sbjct: 75 LTVSGLQAEDEADYYCSSYEGSDNFVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKA 134
Query: 292 ILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQFGQ 348
L C + + P A + W DG + + ++++++ +S +T E+ +
Sbjct: 135 TLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRS 194
Query: 349 YACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 195 YSCQVTHEGSTVEKTV 210
>pdb|3QG6|B Chain B, Structural Basis For Ligand Recognition And Discrimination
Of A Quorum Quenching Antibody
pdb|3QG6|H Chain H, Structural Basis For Ligand Recognition And Discrimination
Of A Quorum Quenching Antibody
pdb|3QG7|H Chain H, Structural Basis For Ligand Recognition And Discrimination
Of A Quorum Quenching Antibody
Length = 213
Score = 35.4 bits (80), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 40/162 (24%), Positives = 66/162 (40%), Gaps = 34/162 (20%)
Query: 87 AQTADLKCSV---QYADDYPVIWMKMDTAKKMEPLP-ISMSGSLIIH---DSRFQLTTDP 139
+Q+ L C+V +Y W++ K+E + IS G+ + SRF +T D
Sbjct: 15 SQSLSLTCTVTGYSITSNYAWNWIRQFPGNKLEWMGFISSYGTTTYNPSLKSRFSITRDT 74
Query: 140 ETSTYILSIKEIQETDAGIYKC-----------EVIISLNNKVSAEVELIVRRPPIISDN 188
+ + L + + D G Y C + +S + V + P+ D
Sbjct: 75 SKNQFFLQLHSVTIEDTGTYFCTREGDYWGQGTTLTVSSAKTTAPSVYPLA---PVCGDT 131
Query: 189 STRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ G +V L C G FP P T++W NS +LS+G
Sbjct: 132 T--------GSSVTLGCLVKGYFPEPVTLTW---NSGSLSSG 162
Score = 32.0 bits (71), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 1/85 (1%)
Query: 236 ILKIPNITKTDRGTYYCVAQNGV-GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
L++ ++T D GTY+C + G+G ++ AP + P G L
Sbjct: 80 FLQLHSVTIEDTGTYFCTREGDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLG 139
Query: 295 CHVEAYPPPAIVWIKDGVQIMNNQH 319
C V+ Y P + + + + H
Sbjct: 140 CLVKGYFPEPVTLTWNSGSLSSGVH 164
>pdb|2G60|L Chain L, Structure Of Anti-Flag M2 Fab Domain
Length = 216
Score = 35.4 bits (80), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCV----AQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC A G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGAHAPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1ORQ|A Chain A, X-Ray Structure Of A Voltage-Dependent Potassium Channel
In Complex With An Fab
Length = 215
Score = 35.0 bits (79), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I ++ D TYYC +G G G K I + AP ++I P Q A
Sbjct: 74 LTISSVEAEDTATYYCQQYSGNPWTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 132
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 133 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 192
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 193 YTCEATHK 200
>pdb|2ADF|L Chain L, Crystal Structure And Paratope Determination Of 82d6a3, An
Antithrombotic Antibody Directed Against The Von
Willebrand Factor A3-Domain
Length = 209
Score = 35.0 bits (79), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 36/137 (26%), Positives = 56/137 (40%), Gaps = 8/137 (5%)
Query: 227 TGGSIYRGNILKIPNITKTDRGTYYCVAQNGV---GRGMKRNIAVEVEFAPVITINRPRQ 283
+G R I N+ D TYYC+ + + G G K I + AP ++I P
Sbjct: 63 SGSGSGRDYSFSISNLEPEDIATYYCLQYDNLRTFGGGTKLEIK-RADAAPTVSIFPPSS 121
Query: 284 GQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVIT 340
Q A + C + + P I W DG + N S + + D +S +S +T
Sbjct: 122 EQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLT 181
Query: 341 I-ERRQFGQYACKAANK 356
E + Y C+A +K
Sbjct: 182 KDEYERHNSYTCEATHK 198
>pdb|1T66|L Chain L, The Structure Of Fab With Intermediate Affinity For
Fluorescein.
pdb|1T66|C Chain C, The Structure Of Fab With Intermediate Affinity For
Fluorescein
Length = 219
Score = 35.0 bits (79), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G Y+C V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYFCSQSTHVPWTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQNSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|2W60|B Chain B, Anti Citrullinated Collagen Type 2 Antibody Acc4
pdb|2W65|B Chain B, Anti Citrullinated Collagen Type 2 Antibody Acc4 In
Complex With A Citrullinated Peptide
pdb|2W65|D Chain D, Anti Citrullinated Collagen Type 2 Antibody Acc4 In
Complex With A Citrullinated Peptide
Length = 217
Score = 35.0 bits (79), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 46/195 (23%), Positives = 76/195 (38%), Gaps = 14/195 (7%)
Query: 175 VELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT-----ISWRRDNSAALSTGG 229
+ + + +P IS S++S++ S+G+T + +P +S TG
Sbjct: 11 LSVTIGQPASISCKSSQSLLDSDGKTYLNWLLQRPGQSPKRLIYLVSKLDSGVPDRFTGS 70
Query: 230 SIYRGNILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQ 285
LKI + D G YYC G G K + + AP ++I P Q
Sbjct: 71 GSGTDFTLKISRVEAEDLGVYYCWQGTHFPLTFGAGTKLELK-RADAAPTVSIFPPSSEQ 129
Query: 286 ALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI- 341
A + C + + P I W DG + N S + + D +S +S +T
Sbjct: 130 LTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKD 189
Query: 342 ERRQFGQYACKAANK 356
E + Y C+A +K
Sbjct: 190 EYERHNSYTCEATHK 204
>pdb|4FAB|L Chain L, Three-Dimensional Structure Of A Fluorescein-Fab Complex
Crystallized In 2-Methyl-2,4-Pentanediol
Length = 219
Score = 35.0 bits (79), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G Y+C V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYFCSQSTHVPWTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1FLR|L Chain L, 4-4-20 Fab Fragment
Length = 219
Score = 35.0 bits (79), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G Y+C V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYFCSQSTHVPWTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1EGJ|H Chain H, Domain 4 Of The Beta Common Chain In Complex With An
Antibody
Length = 220
Score = 35.0 bits (79), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 37/152 (24%), Positives = 63/152 (41%), Gaps = 38/152 (25%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K K +E + I+ S +++ +F+ LT D +ST + + + D
Sbjct: 31 DYYMKWVKHSHGKSLEWIGDINPSNGGTLYNQKFKGKATLTVDKSSSTASMQLSRLTSED 90
Query: 156 AGIYKCE-----------------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEG 198
+ +Y C V +S + V + P+ D + G
Sbjct: 91 SAVYYCSRGDGIHGGFAYWGQGTTVTVSSAKTTAPSVYPLA---PVCGDTT--------G 139
Query: 199 QTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+V L C G FP P T++W NS +LS+G
Sbjct: 140 SSVTLGCLVKGYFPEPVTLTW---NSGSLSSG 168
>pdb|1U9K|A Chain A, Crystal Structure Of Mouse Triggering Receptor Expressed
On Myeloid Cells 1 (Trem-1) At 1.76
pdb|1U9K|B Chain B, Crystal Structure Of Mouse Triggering Receptor Expressed
On Myeloid Cells 1 (Trem-1) At 1.76
Length = 114
Score = 35.0 bits (79), Expect = 0.069, Method: Composition-based stats.
Identities = 24/93 (25%), Positives = 45/93 (48%), Gaps = 11/93 (11%)
Query: 87 AQTADLKCS---VQYADDYPVIWMKMDTAKKMEPLPISMSGSLI-----IHDSRFQLTTD 138
QT +KC ++YA+ W ++ K EPL + ++ +H +F L D
Sbjct: 14 GQTLTVKCPFNIMKYANSQKA-WQRLPDGK--EPLTLVVTQRPFTRPSEVHMGKFTLKHD 70
Query: 139 PETSTYILSIKEIQETDAGIYKCEVIISLNNKV 171
P + + + ++Q TD+G+Y+C + N+ V
Sbjct: 71 PSEAMLQVQMTDLQVTDSGLYRCVIYHPPNDPV 103
>pdb|3MCK|L Chain L, Crystal Structure Of Anti-Beta-Amyloid Antibody C705
pdb|3MCK|A Chain A, Crystal Structure Of Anti-Beta-Amyloid Antibody C705
Length = 219
Score = 35.0 bits (79), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 54/128 (42%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI ++ D G +YC + V G G K + + AP ++I P Q A
Sbjct: 78 LKISSVEAEDLGVFYCFQGSRVPLTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1RMF|L Chain L, Structures Of A Monoclonal Anti-Icam-1 Antibody R6.5
Fragment At 2.8 Angstroms Resolution
Length = 219
Score = 35.0 bits (79), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G Y+C V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYFCSQSTHVPLTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1AE6|L Chain L, Igg-Fab Fragment Of Mouse Monoclonal Antibody Ctm01
Length = 219
Score = 35.0 bits (79), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 45/185 (24%), Positives = 75/185 (40%), Gaps = 14/185 (7%)
Query: 185 ISDNSTRSVIVSEGQT-VYLYCYANGFPAPTISWRRDNSAA----LSTGGSIYRGNILKI 239
IS S++S++ S G T +Y + G + +R N A+ +G L++
Sbjct: 21 ISCRSSKSLLHSNGDTFLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLRV 80
Query: 240 PNITKTDRGTYYCVAQ----NGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILEC 295
+ D G YYC+ G G K + + AP ++I P Q A + C
Sbjct: 81 SRVEAEDVGVYYCMQHLEYPFTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGASVVC 139
Query: 296 HVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQYAC 351
+ + P I W DG + N S + + D +S +S +T E + Y C
Sbjct: 140 FLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTC 199
Query: 352 KAANK 356
+A +K
Sbjct: 200 EATHK 204
>pdb|1AXT|L Chain L, Immune Versus Natural Selection: Antibody Aldolases With
The Rates Of Natural Enzymes
Length = 216
Score = 35.0 bits (79), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G Y+C V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYFCSQGTHVPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1HKF|A Chain A, The Three Dimensional Structure Of Nk Cell Receptor Nkp44,
A Triggering Partner In Natural Cytotoxicity
Length = 122
Score = 35.0 bits (79), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 34/74 (45%)
Query: 106 WMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYILSIKEIQETDAGIYKCEVII 165
W K +A L S + SRF + DP+ + +++ +++E D+G Y C +
Sbjct: 46 WCKEASALVCIRLVTSSKPRTMAWTSRFTIWDDPDAGFFTVTMTDLREEDSGHYWCRIYR 105
Query: 166 SLNNKVSAEVELIV 179
+N VS V +
Sbjct: 106 PSDNSVSKSVRFYL 119
>pdb|2BRR|L Chain L, Complex Of The Neisserial Pora P1.4 Epitope Peptide And
Two Fab-Fragments (Antibody Mn20b9.34)
pdb|2BRR|X Chain X, Complex Of The Neisserial Pora P1.4 Epitope Peptide And
Two Fab-Fragments (Antibody Mn20b9.34)
Length = 215
Score = 35.0 bits (79), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I ++ D TYYC +G G G K I + AP ++I P Q A
Sbjct: 74 LTISSVEAEDAATYYCQQYSGYPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 132
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 133 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 192
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 193 YTCEATHK 200
>pdb|1FJ1|A Chain A, Lyme Disease Antigen Ospa In Complex With Neutralizing
Antibody Fab La-2
pdb|1FJ1|C Chain C, Lyme Disease Antigen Ospa In Complex With Neutralizing
Antibody Fab La-2
Length = 213
Score = 35.0 bits (79), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 34/137 (24%), Positives = 55/137 (40%), Gaps = 7/137 (5%)
Query: 227 TGGSIYRGNILKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEV---EFAPVITINRPRQ 283
+G R I N+ D YYC+ + + R VE+ + AP ++I P
Sbjct: 63 SGSGSGRDYSFSISNLEAEDIAIYYCLQYDNLQRTFGGGTKVEIKRADAAPTVSIFPPSS 122
Query: 284 GQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVIT 340
Q A + C + + P I W DG + N S + + D +S +S +T
Sbjct: 123 EQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLT 182
Query: 341 I-ERRQFGQYACKAANK 356
E + Y C+A +K
Sbjct: 183 KDEYERHNSYTCEATHK 199
>pdb|3RJD|A Chain A, Crystal Structure Of Fc Ri And Its Implication To High
Affinity Immunoglobulin G Binding
Length = 262
Score = 35.0 bits (79), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 55/239 (23%), Positives = 102/239 (42%), Gaps = 30/239 (12%)
Query: 137 TDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVS 196
T +TST I D+G Y+C+ +S S ++L + R ++ S+R + +
Sbjct: 41 TATQTSTPSYRITSASVNDSGEYRCQRGLS---GRSDPIQLEIHRGWLLLQVSSR--VFT 95
Query: 197 EGQTVYLYCYA--NGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVA 254
EG+ + L C+A + + +R + + + L I + GTY+C
Sbjct: 96 EGEPLALRCHAWKDKLVYNVLYYRNGKAFKF-----FHWNSNLTILKTNISHNGTYHCSG 150
Query: 255 QNGVGRGMKRNIAVEV-EFAPVITINRPRQGQALQYDAI-LECHVEAYPPPAIVWIKDGV 312
G R I+V V E P +N L+ + + L C + ++ + G+
Sbjct: 151 M-GKHRYTSAGISVTVKELFPAPVLNASVTSPLLEGNLVTLSCETK------LLLQRPGL 203
Query: 313 QIMNNQHYSVSHFATSDEFSDTS--LRVITIERRQFGQYACKAANKYGSAQK---EIEL 366
Q+ ++S + + +TS +++T R G Y C+AA + G+ K E+EL
Sbjct: 204 QL----YFSFYMGSKTLRGRNTSSEYQILTARREDSGLYWCEAATEDGNVLKRSPELEL 258
>pdb|1QFU|L Chain L, Influenza Virus Hemagglutinin Complexed With A
Neutralizing Antibody
Length = 217
Score = 35.0 bits (79), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G Y+C V G G K I + AP ++I P + Q A
Sbjct: 78 LKISRVEAEDLGVYFCSQNTHVPYTFGGGTKLEIK-RADAAPTVSIFPPSKIQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|3I75|A Chain A, Antibody Structure
Length = 212
Score = 35.0 bits (79), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 35/138 (25%), Positives = 56/138 (40%), Gaps = 9/138 (6%)
Query: 227 TGGSIYRGNILKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPR 282
+G R I N+ D TYYC+ + + G G K + + AP ++I P
Sbjct: 63 SGSGSGRDYSFSISNLEPEDTATYYCLQYDDLLLTFGAGTKLELK-RADAAPTVSIFPPS 121
Query: 283 QGQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVI 339
Q A + C + + P I W DG + N S + + D +S +S +
Sbjct: 122 SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSETDQDSKDSTYSMSSTLTL 181
Query: 340 TI-ERRQFGQYACKAANK 356
T E + Y C+A +K
Sbjct: 182 TKDEYERHNTYTCEATHK 199
>pdb|1LO0|X Chain X, Catalytic Retro-Diels-Alderase Transition State Analogue
Complex
pdb|1LO0|L Chain L, Catalytic Retro-Diels-Alderase Transition State Analogue
Complex
pdb|1LO2|X Chain X, Retro-Diels-Alderase Catalytic Antibody
pdb|1LO2|L Chain L, Retro-Diels-Alderase Catalytic Antibody
pdb|1LO3|X Chain X, Retro-Diels-Alderase Catalytic Antibody: Product Analogue
pdb|1LO3|L Chain L, Retro-Diels-Alderase Catalytic Antibody: Product Analogue
Length = 219
Score = 35.0 bits (79), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQN----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + G G K + + AP ++I P Q A
Sbjct: 78 LKISRVETEDLGIYYCFQGSHFPLAFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|3CMO|L Chain L, Hiv Neutralizing Monoclonal Antibody Yz18
pdb|3CMO|X Chain X, Hiv Neutralizing Monoclonal Antibody Yz18
Length = 210
Score = 35.0 bits (79), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 35/127 (27%), Positives = 53/127 (41%), Gaps = 8/127 (6%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV---GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAIL 293
L I N+ D TYYC + + G G K I + AP ++I P Q A +
Sbjct: 73 LTISNLVPEDIATYYCQQYSKLFTFGSGTKLEIK-RADAAPTVSIFPPSSEQLTSGGASV 131
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 132 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 191
Query: 350 ACKAANK 356
C+A +K
Sbjct: 192 TCEATHK 198
>pdb|3QEH|A Chain A, Crystal Structure Of Human N12-I15, An Adcc And
Non-Neutralizing Anti- Hiv-1 Env Antibody
pdb|3QEH|C Chain C, Crystal Structure Of Human N12-I15, An Adcc And
Non-Neutralizing Anti- Hiv-1 Env Antibody
pdb|3QEH|E Chain E, Crystal Structure Of Human N12-I15, An Adcc And
Non-Neutralizing Anti- Hiv-1 Env Antibody
pdb|3QEH|G Chain G, Crystal Structure Of Human N12-I15, An Adcc And
Non-Neutralizing Anti- Hiv-1 Env Antibody
Length = 232
Score = 35.0 bits (79), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 32/111 (28%), Positives = 48/111 (43%), Gaps = 17/111 (15%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISL--NNKVSAEVELIVRRPPI-ISDN 188
R LT D TST + + ++ D IY C + + N + +E + + +S
Sbjct: 67 RVTLTRDTSTSTVFMELSSLRSDDTAIYYCARDLEMRDGNNHGSHLEFWGQGTLVTVSSA 126
Query: 189 STRSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
ST+ V + G T L C FP P T+SW NS AL++G
Sbjct: 127 STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 174
>pdb|1MNU|L Chain L, Unliganded Bactericidal Antibody Against Neisseria
Meningitidis
pdb|2MPA|L Chain L, Bactericidal Antibody Against Neisseria Meningitidis
pdb|1MPA|L Chain L, Bactericidal Antibody Against Neisseria Meningitidis
Length = 219
Score = 34.7 bits (78), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 32/127 (25%), Positives = 52/127 (40%), Gaps = 7/127 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEV---EFAPVITINRPRQGQALQYDAIL 293
LKI + D G ++C V R +E+ + AP ++I P Q A +
Sbjct: 78 LKISRVEAEDLGVFFCSQSTHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASV 137
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 138 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 197
Query: 350 ACKAANK 356
C+A +K
Sbjct: 198 TCEATHK 204
>pdb|2WP3|T Chain T, Crystal Structure Of The Titin M10-Obscurin Like 1 Ig
Complex
pdb|2WWK|T Chain T, Crystal Structure Of The Titin M10-Obscurin Like 1 Ig F17r
Mutant Complex
pdb|2WWM|D Chain D, Crystal Structure Of The Titin M10-Obscurin Like 1 Ig
Complex In Space Group P1
pdb|2WWM|T Chain T, Crystal Structure Of The Titin M10-Obscurin Like 1 Ig
Complex In Space Group P1
pdb|2Y9R|T Chain T, Crystal Structure Of The M10 Domain Of Titin
Length = 102
Score = 34.7 bits (78), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 26/110 (23%), Positives = 50/110 (45%), Gaps = 11/110 (10%)
Query: 261 GMKRNIAVEVEFAPV-ITINRPRQGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQH 319
G R I ++E P I+I+ +G+ L + C P P + W G +I ++Q
Sbjct: 1 GSSRGIPPKIEALPSDISID---EGKVL----TVACAFTGEPTPEVTWSCGGRKI-HSQE 52
Query: 320 YSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIELFDR 369
H +D+ T+L ++ ++++ G Y N++GS + + R
Sbjct: 53 QGRFHIENTDDL--TTLIIMDVQKQDGGLYTLSLGNEFGSDSATVNIHIR 100
>pdb|1AHW|A Chain A, A Complex Of Extracellular Domain Of Tissue Factor With An
Inhibitory Fab (5g9)
pdb|1AHW|D Chain D, A Complex Of Extracellular Domain Of Tissue Factor With An
Inhibitory Fab (5g9)
pdb|1FGN|L Chain L, Monoclonal Murine Antibody 5g9-Anti-Human Tissue Factor
Length = 214
Score = 34.7 bits (78), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 36/129 (27%), Positives = 55/129 (42%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNG-----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
L I ++ D TYYC+ Q+G G G K I + AP ++I P Q A
Sbjct: 73 LTISSLESDDTATYYCL-QHGESPYTFGGGTKLEIN-RADAAPTVSIFPPSSEQLTSGGA 130
Query: 292 ILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFG 347
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 131 SVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHN 190
Query: 348 QYACKAANK 356
Y C+A +K
Sbjct: 191 SYTCEATHK 199
>pdb|2RCJ|A Chain A, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|B Chain B, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|E Chain E, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|F Chain F, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|I Chain I, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|J Chain J, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|M Chain M, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|N Chain N, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|Q Chain Q, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|R Chain R, Solution Structure Of Human Immunoglobulin M
Length = 218
Score = 34.7 bits (78), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 36/143 (25%), Positives = 57/143 (39%), Gaps = 23/143 (16%)
Query: 102 YPVIWMKMDTAKKMEPLPISMSGSLIIH-----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K +E + I H RF ++ + +T L + ++ D
Sbjct: 32 YAMYWVRQAPGKGLEWVAIIWDDGSDQHYADSVKGRFTISRNDSKNTLFLQMDSLRPEDT 91
Query: 157 GIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYCYA 207
G+Y C + + SA P +S ST+ V + G T L C
Sbjct: 92 GVYFC----ARDGGSSAPDYWGQGTPVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLV 147
Query: 208 NG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 148 KDYFPQPVTVSW---NSGALTSG 167
>pdb|4FFZ|L Chain L, Crystal Structure Of Denv1-E111 Fab Fragment Bound To
Denv-1 Diii (Western Pacific-74 Strain).
pdb|4FFZ|Y Chain Y, Crystal Structure Of Denv1-E111 Fab Fragment Bound To
Denv-1 Diii (Western Pacific-74 Strain)
Length = 216
Score = 34.7 bits (78), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQN----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I ++ D TYYC N G G K I + AP ++I P Q A
Sbjct: 77 LTIDSVETDDAATYYCQQNNEDPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 135
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 136 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 195
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 196 YTCEATHK 203
>pdb|3BKC|L Chain L, Crystal Structure Of Anti-Amyloid Beta Fab Wo2 (P21,
Formb)
pdb|3BKJ|L Chain L, Crystal Structure Of Fab Wo2 Bound To The N Terminal
Domain Of Amyloid Beta Peptide (1-16)
pdb|3BKM|L Chain L, Structure Of Anti-Amyloid-Beta Fab Wo2 (Form A, P212121)
Length = 252
Score = 34.7 bits (78), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L+I + D G YYC + V G G K + + AP ++I P Q A
Sbjct: 111 LRISRVEAEDLGVYYCFQASLVPLTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 169
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 170 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 229
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 230 YTCEATHK 237
>pdb|1CL7|L Chain L, Anti Hiv1 Protease Fab
Length = 216
Score = 34.7 bits (78), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGIYYCFQGSHFPPTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|4DGI|H Chain H, Structure Of Pom1 Fab Fragment Complexed With Human Prpc
Fragment 120- 230
Length = 218
Score = 34.7 bits (78), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 39/165 (23%), Positives = 65/165 (39%), Gaps = 36/165 (21%)
Query: 101 DYPVIWMKMDTAKKMEPL-PISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K + +E + I S S H+ +F+ LT D +ST + + + D
Sbjct: 31 DYWMHWVKQRPGQGLEWIGSIDPSDSYTSHNEKFKGKATLTVDESSSTAYMQLSSLTSED 90
Query: 156 AGIYKCE-------VIISLNNKVSAEVELIVRRPPII-----SDNSTRSVIVSEGQTVYL 203
+ +Y C + S V PP + +T S++ L
Sbjct: 91 SAVYFCSRSGYGYYAMEYWGQGTSVTVSSAKTTPPSVYPLAPGGGATNSMVT-------L 143
Query: 204 YCYANG-FPAP-TISWRRDNSAALSTGGSIYRGNILKIPNITKTD 246
C G FP P T++W NS +LS G + P + ++D
Sbjct: 144 GCLVKGYFPEPVTVTW---NSGSLS-------GGVHTFPAVLQSD 178
>pdb|1WEJ|L Chain L, Igg1 Fab Fragment (Of E8 Antibody) Complexed With Horse
Cytochrome C At 1.8 A Resolution
pdb|1QBL|L Chain L, Fab E8 (Fabe8a) X-Ray Structure At 2.26 Angstrom
Resolution
pdb|1QBM|L Chain L, Fab E8b Antibody, X-Ray Structure At 2.37 Angstroms
Resolution
Length = 214
Score = 34.7 bits (78), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 49/194 (25%), Positives = 77/194 (39%), Gaps = 33/194 (17%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRRD-----------NSAALSTG----------GS 230
S+ S G+TV + C A+G ++W + N+ L+ G G+
Sbjct: 10 SLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYNAKTLADGVPSRFSGSGSGT 69
Query: 231 IYRGNILKIPNITKTDRGTYYC----VAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQA 286
Y LKI ++ D G+YYC G G K I + AP ++I P Q
Sbjct: 70 QYS---LKINSLQPEDFGSYYCQHFWSTPWTFGGGTKLEIK-RADAAPTVSIFPPSSEQL 125
Query: 287 LQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-E 342
A + C + + P I W DG + N S + + D +S +S +T E
Sbjct: 126 TSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDE 185
Query: 343 RRQFGQYACKAANK 356
+ Y C+A +K
Sbjct: 186 YERHNSYTCEATHK 199
>pdb|3FO9|L Chain L, Crystal Structure Of Aldolase Antibody 33f12 Fab' In
Complex With Hapten 1,3-Diketone
pdb|3FO9|A Chain A, Crystal Structure Of Aldolase Antibody 33f12 Fab' In
Complex With Hapten 1,3-Diketone
Length = 219
Score = 34.7 bits (78), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G Y+C V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYFCSQGTHVPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|4HCR|L Chain L, Crystal Structure Of Human Madcam-1 D1d2 Complexed With
Fab Pf-547659
pdb|4HCR|N Chain N, Crystal Structure Of Human Madcam-1 D1d2 Complexed With
Fab Pf-547659
Length = 219
Score = 34.7 bits (78), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 49/192 (25%), Positives = 76/192 (39%), Gaps = 20/192 (10%)
Query: 181 RPPIISDNSTRSVIVSEGQTVYLYCYANGFPAP------TISWRRDNSAALSTGGSIYRG 234
+P IS S++S++ ++G T YLY Y P +S R +G
Sbjct: 17 QPASISCKSSQSLLHTDG-TTYLYWYLQKPGQPPQLLIYEVSNRFSGVPDRFSGSGSGTD 75
Query: 235 NILKIPNITKTDRGTYYCVAQN-----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQY 289
LKI + D G YYC+ QN G+G K I V AP + I P Q
Sbjct: 76 FTLKISRVEAEDVGIYYCM-QNIQLPWTFGQGTKVEIKRTVA-APSVFIFPPSDEQLKSG 133
Query: 290 DAILECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFG 347
A + C + + P + W D N SV+ + D S +T+ + +
Sbjct: 134 TASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYE 192
Query: 348 Q---YACKAANK 356
+ YAC+ ++
Sbjct: 193 KHKVYACEVTHQ 204
>pdb|3G5V|A Chain A, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
Length = 212
Score = 34.7 bits (78), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 51/200 (25%), Positives = 76/200 (38%), Gaps = 29/200 (14%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRG-NI------ 236
I+ S S+ VS G TV + C+++ I W + S G IY G N+
Sbjct: 2 ILMTQSPSSMSVSLGDTVSITCHSSQDINSNIGWLQQKPGK-SFKGLIYHGTNLDDEVPS 60
Query: 237 ------------LKIPNITKTDRGTYYCVAQN----GVGRGMKRNIAVEVEFAPVITINR 280
L I ++ D YYCV G G K I + AP ++I
Sbjct: 61 RFSGSGSGADYSLTISSLESEDFADYYCVQYAQFPWTFGGGTKLEIK-RADAAPTVSIFP 119
Query: 281 PRQGQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLR 337
P Q A + C + + P I W DG + N S + + D +S +S
Sbjct: 120 PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTL 179
Query: 338 VITI-ERRQFGQYACKAANK 356
+T E + Y C+A +K
Sbjct: 180 TLTKDEYERHNSYTCEATHK 199
>pdb|3BAE|L Chain L, Crystal Structure Of Fab Wo2 Bound To The N Terminal
Domain Of Amyloid Beta Peptide (1-28)
Length = 218
Score = 34.7 bits (78), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L+I + D G YYC + V G G K + + AP ++I P Q A
Sbjct: 78 LRISRVEAEDLGVYYCFQASLVPLTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1XED|A Chain A, Crystal Structure Of A Ligand-Binding Domain Of The Human
Polymeric Ig Receptor, Pigr
pdb|1XED|B Chain B, Crystal Structure Of A Ligand-Binding Domain Of The Human
Polymeric Ig Receptor, Pigr
pdb|1XED|C Chain C, Crystal Structure Of A Ligand-Binding Domain Of The Human
Polymeric Ig Receptor, Pigr
pdb|1XED|D Chain D, Crystal Structure Of A Ligand-Binding Domain Of The Human
Polymeric Ig Receptor, Pigr
pdb|1XED|E Chain E, Crystal Structure Of A Ligand-Binding Domain Of The Human
Polymeric Ig Receptor, Pigr
pdb|1XED|F Chain F, Crystal Structure Of A Ligand-Binding Domain Of The Human
Polymeric Ig Receptor, Pigr
Length = 117
Score = 34.7 bits (78), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 3/50 (6%)
Query: 129 HDSRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIIS---LNNKVSAEV 175
+ R LT PE T++++I ++ + D+G YKC + I+ L+ VS EV
Sbjct: 60 YAGRANLTNFPENGTFVVNIAQLSQDDSGRYKCGLGINSRGLSFDVSLEV 109
>pdb|4BJL|A Chain A, Locw, A Lambda 1 Type Light-Chain Dimer (Bence-Jones
Protein) Crystallized In Distilled Water
pdb|4BJL|B Chain B, Locw, A Lambda 1 Type Light-Chain Dimer (Bence-Jones
Protein) Crystallized In Distilled Water
pdb|3BJL|A Chain A, Loc, A Lambda 1 Type Light-Chain Dimer (Bence-Jones
Protein) Crystallized In Ammonium Sulfate
pdb|3BJL|B Chain B, Loc, A Lambda 1 Type Light-Chain Dimer (Bence-Jones
Protein) Crystallized In Ammonium Sulfate
pdb|1BJM|A Chain A, Loc Naks, A Lambda 1 Type Light-Chain Dimer (Bence-Jones
Protein) Crystallized In Nakso4
pdb|1BJM|B Chain B, Loc Naks, A Lambda 1 Type Light-Chain Dimer (Bence-Jones
Protein) Crystallized In Nakso4
Length = 216
Score = 34.7 bits (78), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 27/137 (19%), Positives = 57/137 (41%), Gaps = 9/137 (6%)
Query: 237 LKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQGQALQYD 290
L I + D YYC A + G G K + + + P +T+ P +
Sbjct: 74 LAISGLQPEDETDYYCAAWDDSLDVAVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANK 133
Query: 291 AILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQFG 347
A L C + + P A + W DG + + ++++++ +S +T E+ +
Sbjct: 134 ATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHR 193
Query: 348 QYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 194 SYSCQVTHEGSTVEKTV 210
>pdb|3GJE|H Chain H, Rational Development Of High-Affinity T-Cell Receptor-Like
Antibodies
pdb|3GJE|B Chain B, Rational Development Of High-Affinity T-Cell Receptor-Like
Antibodies
pdb|3GJF|H Chain H, Rational Development Of High-Affinity T-Cell Receptor-Like
Antibodies
pdb|3GJF|M Chain M, Rational Development Of High-Affinity T-Cell Receptor-Like
Antibodies
Length = 220
Score = 34.7 bits (78), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 38/145 (26%), Positives = 61/145 (42%), Gaps = 26/145 (17%)
Query: 102 YPVIWMKMDTAKKMEPLP--ISMSGSLIIHDS---RFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K +E + +S GS DS RF ++ D +T L + ++ D
Sbjct: 32 YQMSWVRQAPGKGLEWVSGIVSSGGSTAYADSVKGRFTISRDNSKNTLYLQMNSLRAEDT 91
Query: 157 GIYKC--EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYC 205
+Y C E++ V + + +S ST+ V + G T L C
Sbjct: 92 AVYYCAGELLPYYGMDVWGQGTTVT-----VSSASTKGPSVFPLAPSSKSTSGGTAALGC 146
Query: 206 YANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 147 LVKDYFPEPVTVSW---NSGALTSG 168
>pdb|1FIG|L Chain L, Routes To Catalysis: Structure Of A Catalytic Antibody And
Comparison With Its Natural Counterpart
Length = 215
Score = 34.7 bits (78), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I ++ D TYYC +G G G K + + AP ++I P Q A
Sbjct: 74 LTISSVEAEDAATYYCQQYSGYPLTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 132
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 133 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 192
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 193 YTCEATHK 200
>pdb|3G5X|A Chain A, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
pdb|3G5X|C Chain C, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
Length = 214
Score = 34.7 bits (78), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 51/200 (25%), Positives = 76/200 (38%), Gaps = 29/200 (14%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRG-NI------ 236
I+ S S+ VS G TV + C+++ I W + S G IY G N+
Sbjct: 2 ILMTQSPSSMSVSLGDTVSITCHSSQDINSNIGWLQQKPGK-SFKGLIYHGTNLDDEVPS 60
Query: 237 ------------LKIPNITKTDRGTYYCVAQN----GVGRGMKRNIAVEVEFAPVITINR 280
L I ++ D YYCV G G K I + AP ++I
Sbjct: 61 RFSGSGSGADYSLTISSLESEDFADYYCVQYAQFPWTFGGGTKLEIK-RADAAPTVSIFP 119
Query: 281 PRQGQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLR 337
P Q A + C + + P I W DG + N S + + D +S +S
Sbjct: 120 PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTL 179
Query: 338 VITI-ERRQFGQYACKAANK 356
+T E + Y C+A +K
Sbjct: 180 TLTKDEYERHNSYTCEATHK 199
>pdb|4FFV|D Chain D, Crystal Structure Of Dipeptidyl Peptidase Iv (Dpp4,
Dpp-Iv, Cd26) In Complex With 11a19 Fab
pdb|4FFV|H Chain H, Crystal Structure Of Dipeptidyl Peptidase Iv (Dpp4,
Dpp-Iv, Cd26) In Complex With 11a19 Fab
pdb|4FFW|D Chain D, Crystal Structure Of Dipeptidyl Peptidase Iv (Dpp4,
Dpp-Iv, Cd26) In Complex With Fab + Sitagliptin
pdb|4FFW|H Chain H, Crystal Structure Of Dipeptidyl Peptidase Iv (Dpp4,
Dpp-Iv, Cd26) In Complex With Fab + Sitagliptin
Length = 217
Score = 34.7 bits (78), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 36/144 (25%), Positives = 60/144 (41%), Gaps = 24/144 (16%)
Query: 101 DYPVIWMKMDTAKKMEPLPISMSG-SLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + WMK K +E + + + ++ +FQ LT D +ST + + + D
Sbjct: 31 DYNINWMKQSNGKSLEWIGVVIPKYGTTNYNQKFQGKATLTVDQSSSTAYIQLNSLTSED 90
Query: 156 AGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYCY 206
+ +Y C + V + +S T + V + G +V L C
Sbjct: 91 SAVYYCTRFRDVFFDVWGTGTTVT-----VSSAKTTAPSVYPLAPVCGGTTGSSVTLGCL 145
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 146 VKGYFPEPVTLTW---NSGSLSSG 166
>pdb|1YC7|A Chain A, Caban33 Vhh Fragment Against Vsg
pdb|1YC7|B Chain B, Caban33 Vhh Fragment Against Vsg
Length = 124
Score = 34.7 bits (78), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 92 LKCSVQYADDYPVI--WMKMDTAKKMEPLP-ISMSGSLIIHDS---RFQLTTDPETSTYI 145
L C+V + P W + K+ E + IS G++ DS RF ++ D +T
Sbjct: 20 LSCAVSGSTYSPCTTGWYRQAPGKEREWVSSISSPGTIYYQDSVKGRFTISRDNAKNTVY 79
Query: 146 LSIKEIQETDAGIYKCEV 163
L + +Q D G+Y C++
Sbjct: 80 LQMNSLQREDTGMYYCQI 97
>pdb|3K0W|A Chain A, Crystal Structure Of The Tandem Ig-Like C2-Type 2 Domains
Of The Human Mucosa-Associated Lymphoid Tissue Lymphoma
Translocation Protein 1
Length = 218
Score = 34.7 bits (78), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 36/160 (22%), Positives = 56/160 (35%), Gaps = 20/160 (12%)
Query: 112 AKKMEPLPISMSGSLIIHDSRFQLTTD-PETSTYILSIKEIQETDAGIYKCEVIISLNNK 170
A + L +G + F++ + P +T L + DAG Y C V + +
Sbjct: 32 AGQFVKLCCRATGHPFVQYQWFKMNKEIPNGNTSELIFNAVHVKDAGFYVCRVNNNFTFE 91
Query: 171 VSAEVELIVRRPPIISDNSTRSVIVSE--------------GQTVYLYCYANGFPAPTIS 216
S +L V P S V S+ G T+ L C A G P P
Sbjct: 92 FSQWSQLDVCDIPESFQRSVDGVSESKLQICVEPTSQKLMPGSTLVLQCVAVGSPIPHYQ 151
Query: 217 WRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQN 256
W ++ +Y +P + +GTY+C N
Sbjct: 152 WFKNELPLTHETKKLYM-----VPYVDLEHQGTYWCHVYN 186
>pdb|1RU9|L Chain L, Crystal Structure (A) Of U.V.-Irradiated Cationic
Cyclization Antibody 4c6 Fab At Ph 4.6 With A Data Set
Collected In-House.
pdb|1RUA|L Chain L, Crystal Structure (b) Of U.v.-irradiated Cationic
Cyclization Antibody 4c6 Fab At Ph 4.6 With A Data Set
Collected At Ssrl Beamline 11-1.
pdb|1RUL|L Chain L, Crystal Structure (d) Of U.v.-irradiated Cationic
Cyclization Antibody 4c6 Fab At Ph 5.6 With A Data Set
Collected At Ssrl Beamline 11-1.
pdb|1RUM|L Chain L, Crystal Structure (F) Of H2o2-Soaked Cationic Cyclization
Antibody 4c6 Fab At Ph 8.5 With A Data Set Collected At
Ssrl Beamline 9-1
Length = 219
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 51/128 (39%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCWQGTHFPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSXTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1F11|A Chain A, F124 Fab Fragment From A Monoclonal Anti-Pres2 Antibody
pdb|1F11|C Chain C, F124 Fab Fragment From A Monoclonal Anti-Pres2 Antibody
Length = 218
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQN----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I + + D TYYC N G G K I + AP ++I P Q A
Sbjct: 77 LNIHPVEEEDAATYYCQQSNEDPFTFGSGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 135
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 136 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 195
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 196 YTCEATHK 203
>pdb|1CBV|L Chain L, An Autoantibody To Single-Stranded Dna: Comparison Of The
Three-Dimensional Structures Of The Unliganded Fab And A
Deoxynucleotide-Fab Complex
pdb|1NBV|L Chain L, An Autoantibody To Single-Stranded Dna: Comparison Of The
Three-Dimensional Structures Of The Unliganded Fab And A
Deoxynucleotide-Fab Complex
Length = 219
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G Y+C V G G K + + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYFCSQSTHVPLTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1BLN|A Chain A, Anti-P-Glycoprotein Fab Mrk-16
pdb|1BLN|C Chain C, Anti-P-Glycoprotein Fab Mrk-16
Length = 214
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 32/126 (25%), Positives = 51/126 (40%), Gaps = 7/126 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEV---EFAPVITINRPRQGQALQYDAIL 293
LKI + D G YYC + R +E+ + AP ++I P Q A +
Sbjct: 78 LKISRVEAEDLGVYYCFQASHAPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASV 137
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 138 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 197
Query: 350 ACKAAN 355
C+A +
Sbjct: 198 TCEATS 203
>pdb|3U0T|D Chain D, Fab-Antibody Complex
pdb|3U0T|B Chain B, Fab-Antibody Complex
Length = 217
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 40/164 (24%), Positives = 67/164 (40%), Gaps = 19/164 (11%)
Query: 79 SQEQIKDIAQTADLKC--SVQYADDYPVIWMKMDTAKKME------PLPISMSGSLIIHD 130
S ++K + + C S Y + Y + W++ + +E P + + + D
Sbjct: 7 SGAEVKKPGASVKVSCKASGYYTEAYYIHWVRQAPGQGLEWMGRIDPATGNTKYAPRLQD 66
Query: 131 SRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISL----NNKVSAEVELIVRRPPIIS 186
R +T D TST + + ++ D +Y C + SL + V + P +
Sbjct: 67 -RVTMTRDTSTSTVYMELSSLRSEDTAVYYCASLYSLPVYWGQGTTVTVSSASTKGPSVF 125
Query: 187 DNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ S SE T L C FP P T+SW NS AL++G
Sbjct: 126 PLAPCSRSTSE-STAALGCLVKDYFPEPVTVSW---NSGALTSG 165
>pdb|3LEY|L Chain L, 2f5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal
Antibody 6a7 In Complex With Hiv-1 Gp41
Length = 219
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 47/195 (24%), Positives = 76/195 (38%), Gaps = 14/195 (7%)
Query: 175 VELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT-----ISWRRDNSAALSTGG 229
+ + + +P IS S++S++ S+G+T + +P +S TG
Sbjct: 11 LSVTLGQPASISCKSSQSLLDSDGKTYLNWLLQRPGQSPKRLIYLVSKLASGVPDRFTGS 70
Query: 230 SIYRGNILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQ 285
LKI + D G YYC G G K I + AP ++I P Q
Sbjct: 71 GSGTDFTLKINRVEAEDLGIYYCWQGTHFPWTFGGGTKLEIK-RADAAPTVSIFPPSSEQ 129
Query: 286 ALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI- 341
A + C + + P I W DG + N S + + D +S +S +T
Sbjct: 130 LTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKD 189
Query: 342 ERRQFGQYACKAANK 356
E + Y C+A +K
Sbjct: 190 EYERHNSYTCEATHK 204
>pdb|1UWG|H Chain H, Molecular Mechanism Of Enantioselective Proton Transfer To
Carbon In Catalytic Antibody 14d9
pdb|1UWG|Y Chain Y, Molecular Mechanism Of Enantioselective Proton Transfer To
Carbon In Catalytic Antibody 14d9
Length = 225
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 36/148 (24%), Positives = 59/148 (39%), Gaps = 16/148 (10%)
Query: 93 KCSVQYADDYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILS 147
K S D+ + W+K K +E + I +++ +F LT D +ST +
Sbjct: 23 KASAYSITDFNIYWVKQSHGKNLEWIGGIDPHNGGPVYNQKFNGKATLTVDKSSSTAFMH 82
Query: 148 IKEIQETDAGIYKCEVIIS-----LNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVY 202
+ + D+ +Y C + + V + P + + S S G T
Sbjct: 83 LNSLTSEDSAVYYCAIFYGNFFDYWGPGTTVTVSSASTKGPSVFPLAPSSKSTS-GGTAA 141
Query: 203 LYCYANG-FPAP-TISWRRDNSAALSTG 228
L C FP P T+SW NS AL++G
Sbjct: 142 LGCLVKDYFPEPVTVSW---NSGALTSG 166
>pdb|2ZCH|L Chain L, Crystal Structure Of Human Prostate Specific Antigen
Complexed With An Activating Antibody
Length = 215
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQN----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I + + D TYYC N G G K I + AP ++I P Q A
Sbjct: 77 LNIQPVEEEDAATYYCQQSNEDPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 135
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 136 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 195
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 196 YTCEATHK 203
>pdb|1S3K|H Chain H, Crystal Structure Of A Humanized Fab (Hu3s193) In Complex
With The Lewis Y Tetrasaccharide
pdb|3EYV|H Chain H, Anti-Lewis Y Fab Fragment With Lewis Y Antigen In The
Presence Of Zinc Ions
pdb|3EYV|B Chain B, Anti-Lewis Y Fab Fragment With Lewis Y Antigen In The
Presence Of Zinc Ions
Length = 222
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 38/146 (26%), Positives = 61/146 (41%), Gaps = 26/146 (17%)
Query: 101 DYPVIWMKMDTAKKMEPLPISMSGSLIIHD------SRFQLTTDPETSTYILSIKEIQET 154
DY + W++ K +E + MS I D RF ++ D +T L + ++
Sbjct: 31 DYYMYWVRQAPGKGLEWVAY-MSNVGAITDYPDTVKGRFTISRDNSKNTLFLQMDSLRPE 89
Query: 155 DAGIYKCEVIISLNNKVSAEVELIVRRPPI-ISDNSTRSVIV---------SEGQTVYLY 204
D G+Y C + + + + P+ +S ST+ V + G T L
Sbjct: 90 DTGVYFC----ARGTRDGSWFAYWGQGTPVTVSSASTKGPSVFPLAPSSKSTSGGTAALG 145
Query: 205 CYANG-FPAP-TISWRRDNSAALSTG 228
C FP P T+SW NS AL++G
Sbjct: 146 CLVKDYFPQPVTVSW---NSGALTSG 168
>pdb|3E8U|L Chain L, Crystal Structure And Thermodynamic Analysis Of Diagnostic
Fab 106.3 Complexed With Bnp 5-13 (C10a) Reveal Basis Of
Selective Molecular Recognition
Length = 216
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQN----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I + + D TYYC N G G K I + AP ++I P Q A
Sbjct: 77 LNIHPVEEEDAATYYCQQSNEDPFTFGSGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 135
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 136 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 195
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 196 YTCEATHK 203
>pdb|1IT9|H Chain H, Crystal Structure Of An Antigen-Binding Fragment From A
Humanized Version Of The Anti-Human Fas Antibody Hfe7a
Length = 219
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 40/147 (27%), Positives = 62/147 (42%), Gaps = 28/147 (19%)
Query: 102 YPVIWMKMDTAKKMEPL-PISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETDA 156
Y + W+K + +E + I S S ++ +F+ LT D TST + + ++ D
Sbjct: 32 YWMQWVKQAPGQGLEWMGEIDPSDSYTNYNQKFKGKATLTVDTSTSTAYMELSSLRSEDT 91
Query: 157 GIYKCEVIISLNNK----VSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYL 203
+Y C +N V E L+ +S ST+ V + G T L
Sbjct: 92 AVYYCARNRDYSNNWYFDVWGEGTLVT-----VSSASTKGPSVFPLAPSSKSTSGGTAAL 146
Query: 204 YCYANG-FPAP-TISWRRDNSAALSTG 228
C FP P T+SW NS AL++G
Sbjct: 147 GCLVKDYFPEPVTVSW---NSGALTSG 170
>pdb|2JEL|L Chain L, Jel42 FabHPR COMPLEX
Length = 217
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 36/133 (27%), Positives = 56/133 (42%), Gaps = 19/133 (14%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VW-IKDGVQ---IMN---NQHYSVSHFATSDEFSDTSLRVITIER 343
+ C + + P I W I DG + ++N +Q S ++ S ++L + E
Sbjct: 137 VVCFLNNFYPKDINVKWKIGDGARQNGVLNSWTDQDSKDSTYSMS-----STLTLTKDEY 191
Query: 344 RQFGQYACKAANK 356
+ Y C+A +K
Sbjct: 192 ERHNSYTCEATHK 204
>pdb|3E8U|H Chain H, Crystal Structure And Thermodynamic Analysis Of Diagnostic
Fab 106.3 Complexed With Bnp 5-13 (C10a) Reveal Basis Of
Selective Molecular Recognition
Length = 217
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 39/164 (23%), Positives = 64/164 (39%), Gaps = 17/164 (10%)
Query: 79 SQEQIKDIAQTADLKC--SVQYADDYPVIWMKMDTAKKMEPLPI--SMSGSLIIHD---S 131
S +++ +T + C S Y + W+K +K ++ + + +G I D
Sbjct: 7 SGPELRKPGETVKISCKGSGYTFTHYGINWVKQTPSKDLKWMGWINTHTGEPIYADDFKG 66
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCE-----VIISLNNKVSAEVELIVRRPPIIS 186
RF + + +T L I + D G Y C + S V PP +
Sbjct: 67 RFAFSLETSANTAYLQINNLNNGDMGTYFCTRSHRFGLDYWGQGTSVTVSSAKTTPPSVY 126
Query: 187 DNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ S + V L C G FP P T++W NS +LS+G
Sbjct: 127 PLAPGSAAAAAASMVTLGCLVKGYFPEPVTVTW---NSGSLSSG 167
>pdb|3GIZ|H Chain H, Crystal Structure Of The Fab Fragment Of Anti-Cd20
Antibody Ofatumumab
Length = 222
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 40/145 (27%), Positives = 59/145 (40%), Gaps = 19/145 (13%)
Query: 100 DDYPVIWMKMDTAKKMEPLP-ISM-SGSLIIHDS---RFQLTTDPETSTYILSIKEIQET 154
+DY + W++ K +E + IS SGS+ DS RF ++ D + L + ++
Sbjct: 30 NDYAMHWVRQAPGKGLEWVSTISWNSGSIGYADSVKGRFTISRDNAKKSLYLQMNSLRAE 89
Query: 155 DAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYC 205
D +Y C I N +S ST+ V S T L C
Sbjct: 90 DTALYYCAKDIQYGNYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPGSSKSTSGTAALGC 149
Query: 206 YANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 150 LVKDYFPEPVTVSW---NSGALTSG 171
>pdb|2ZCK|L Chain L, Crystal Structure Of A Ternary Complex Between Psa, A
Substrat-Acyl Intermediate And An Activating Antibody
pdb|2ZCL|L Chain L, Crystal Structure Of Human Prostate Specific Antigen
Complexed With An Activating Antibody
Length = 218
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQN----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I + + D TYYC N G G K I + AP ++I P Q A
Sbjct: 77 LNIQPVEEEDAATYYCQQSNEDPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 135
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 136 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 195
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 196 YTCEATHK 203
>pdb|3CAF|A Chain A, Crystal Structure Of Hfgfr2 D2 Domain
pdb|3CU1|A Chain A, Crystal Structure Of 2:2:2 Fgfr2d2:fgf1:sos Complex
pdb|3CU1|C Chain C, Crystal Structure Of 2:2:2 Fgfr2d2:fgf1:sos Complex
pdb|3EUU|A Chain A, Crystal Structure Of The Fgfr2 D2 Domain
pdb|3EUU|B Chain B, Crystal Structure Of The Fgfr2 D2 Domain
Length = 100
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 30/70 (42%), Gaps = 5/70 (7%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDN---SAALSTGGSIYRGN--ILKIPNITKTDRGT 249
V TV C A G P PT+ W ++ GG R L + ++ +D+G
Sbjct: 20 VPAANTVKFRCPAGGNPMPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPSDKGN 79
Query: 250 YYCVAQNGVG 259
Y CV +N G
Sbjct: 80 YTCVVENEYG 89
Score = 28.1 bits (61), Expect = 8.8, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACK 352
C P P + W+K+G + Q + + + ++ SL + ++ G Y C
Sbjct: 28 FRCPAGGNPMPTMRWLKNGKEF--KQEHRIGGYKVRNQ--HWSLIMESVVPSDKGNYTCV 83
Query: 353 AANKYGS 359
N+YGS
Sbjct: 84 VENEYGS 90
>pdb|1WVZ|A Chain A, Solution Structure Of The D2 Domain Of The Fibroblast
Growth Factor
Length = 104
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 30/70 (42%), Gaps = 5/70 (7%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDN---SAALSTGGSIYRGN--ILKIPNITKTDRGT 249
V TV C A G P PT+ W ++ GG R L + ++ +D+G
Sbjct: 24 VPAANTVKFRCPAGGNPMPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPSDKGN 83
Query: 250 YYCVAQNGVG 259
Y CV +N G
Sbjct: 84 YTCVVENEYG 93
Score = 28.1 bits (61), Expect = 9.1, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACK 352
C P P + W+K+G + Q + + + ++ SL + ++ G Y C
Sbjct: 32 FRCPAGGNPMPTMRWLKNGKEF--KQEHRIGGYKVRNQ--HWSLIMESVVPSDKGNYTCV 87
Query: 353 AANKYGS 359
N+YGS
Sbjct: 88 VENEYGS 94
>pdb|3DAR|A Chain A, Crystal Structure Of D2 Domain From Human Fgfr2
pdb|3DAR|B Chain B, Crystal Structure Of D2 Domain From Human Fgfr2
Length = 105
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 30/70 (42%), Gaps = 5/70 (7%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDN---SAALSTGGSIYRGN--ILKIPNITKTDRGT 249
V TV C A G P PT+ W ++ GG R L + ++ +D+G
Sbjct: 25 VPAANTVKFRCPAGGNPMPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPSDKGN 84
Query: 250 YYCVAQNGVG 259
Y CV +N G
Sbjct: 85 YTCVVENEYG 94
Score = 28.1 bits (61), Expect = 9.0, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACK 352
C P P + W+K+G + Q + + + ++ SL + ++ G Y C
Sbjct: 33 FRCPAGGNPMPTMRWLKNGKEF--KQEHRIGGYKVRNQ--HWSLIMESVVPSDKGNYTCV 88
Query: 353 AANKYGS 359
N+YGS
Sbjct: 89 VENEYGS 95
>pdb|3MAC|H Chain H, Crystal Structure Of Gp41-Derived Protein Complexed With
Fab 8062
Length = 245
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 39/173 (22%), Positives = 68/173 (39%), Gaps = 32/173 (18%)
Query: 79 SQEQIKDIAQTADLKCSVQYA--DDYPVIWMKMDTAKKMEPLP--ISMSGSLIIHDSRFQ 134
S ++K + + C + Y W++ + +E + I + G +++ +FQ
Sbjct: 7 SGAEVKKPGSSVKVSCKASGGTFNSYAFSWVRQAPGQGLEWMGSIIPLFG-FVVYAQKFQ 65
Query: 135 ----LTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVS----AEVELIVRRPPIIS 186
+T D TST + + ++ D +Y C N + L+ +S
Sbjct: 66 GRVTITADESTSTAYMELSSLRSEDTAVYYCARYFDTYNNYGFANWGQGTLVT-----VS 120
Query: 187 DNSTRSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
ST+ V + G T L C FP P T+SW NS AL++G
Sbjct: 121 SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 170
>pdb|2R4R|H Chain H, Crystal Structure Of The Human Beta2 Adrenoceptor
pdb|2R4S|H Chain H, Crystal Structure Of The Human Beta2 Adrenoceptor
pdb|3KJ6|H Chain H, Crystal Structure Of A Methylated Beta2 Adrenergic
Receptor- Fab Complex
Length = 217
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 36/136 (26%), Positives = 58/136 (42%), Gaps = 12/136 (8%)
Query: 101 DYPVIWMKMDTAKKMEPLPISMSGSL-IIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W++ T + E + GS I ++ RF+ LT D +ST + + + D
Sbjct: 31 DYYINWVRQRTGQGFEWIGEIYPGSGNIDYNERFKDKATLTADKSSSTAYMQLSSLTSED 90
Query: 156 AGIYKC-EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FPAP 213
+ +Y C + V PP + + S + V L C G FP P
Sbjct: 91 SAVYFCVRGFGYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTN-SAVTLGCLVKGYFPEP 149
Query: 214 -TISWRRDNSAALSTG 228
T++W NS +LS+G
Sbjct: 150 VTVTW---NSGSLSSG 162
>pdb|1W72|H Chain H, Crystal Structure Of Hla-A1:mage-A1 In Complex With Fab-
Hyb3
pdb|1W72|I Chain I, Crystal Structure Of Hla-A1:mage-A1 In Complex With Fab-
Hyb3
Length = 223
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 39/145 (26%), Positives = 60/145 (41%), Gaps = 19/145 (13%)
Query: 100 DDYPVIWMKMDTAKKMEPLP-ISM-SGSLIIHDS---RFQLTTDPETSTYILSIKEIQET 154
DDY + W++ K +E + IS SGS+ DS RF ++ D ++ L + ++
Sbjct: 30 DDYAMHWVRQAPGKGLEWVSGISWNSGSIGYADSVKGRFTISRDNAKNSLYLQMNSLRAE 89
Query: 155 DAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYC 205
D +Y C + +S ST+ V + G T L C
Sbjct: 90 DTAVYYCARGRGFHYYYYGMDIWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGC 149
Query: 206 YANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 150 LVKDYFPEPVTVSW---NSGALTSG 171
>pdb|1NC2|D Chain D, Crystal Structure Of Monoclonal Antibody 2d12.5 Fab
Complexed With Y- Dota
pdb|1NC4|D Chain D, Crystal Structure Of Monoclonal Antibody 2d12.5 Fab
Complexed With Gd- Dota
Length = 221
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 38/158 (24%), Positives = 60/158 (37%), Gaps = 20/158 (12%)
Query: 87 AQTADLKCSVQ--YADDYPVIWMKMDTAKKMEPLPISMSGSLIIHD----SRFQLTTDPE 140
+Q+ + C+V DY V W++ K +E L + SG + SR + D
Sbjct: 15 SQSLSITCTVSGFSLTDYGVHWVRQSPGKGLEWLGVIWSGGGTAYTAAFISRLNIYKDNS 74
Query: 141 TSTYILSIKEIQETDAGIYKCEVIIS--------LNNKVSAEVELIVRRPPIISDNSTRS 192
+ + +Q D +Y C S + V PP + + S
Sbjct: 75 KNQVFFEMNSLQANDTAMYYCARRGSYPYNYFDVWGQGTTVTVSSAKTTPPSVYPLAPGS 134
Query: 193 VIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ V L C G FP P T++W NS +LS+G
Sbjct: 135 AAQTN-SMVTLGCLVKGYFPEPVTVTW---NSGSLSSG 168
>pdb|1JGV|L Chain L, Structural Basis For Disfavored Elimination Reaction In
Catalytic Antibody 1d4
pdb|1JGU|L Chain L, Structural Basis For Disfavored Elimination Reaction In
Catalytic Antibody 1d4
Length = 220
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 34/129 (26%), Positives = 52/129 (40%), Gaps = 10/129 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV-----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
LKI + D G Y+C V G G K + + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYFCSQSTHVPPLTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGA 136
Query: 292 ILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFG 347
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 SVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHN 196
Query: 348 QYACKAANK 356
Y C+A +K
Sbjct: 197 SYTCEATHK 205
>pdb|1IQW|L Chain L, Crystal Structure Of The Fab Fragment Of The Mouse Anti-
Human Fas Antibody Hfe7a
Length = 218
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 33/127 (25%), Positives = 52/127 (40%), Gaps = 7/127 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEV---EFAPVITINRPRQGQALQYDAIL 293
L I + + D TYYC N R +E+ + AP ++I P Q A +
Sbjct: 77 LNIHPVEEEDAATYYCQQSNEDPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASV 136
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 137 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 196
Query: 350 ACKAANK 356
C+A +K
Sbjct: 197 TCEATHK 203
>pdb|1LO4|L Chain L, Retro-Diels-Alderase Catalytic Antibody 9d9
Length = 217
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + G G K + + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGLYYCFQGSHSPWTFGGGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1NC2|B Chain B, Crystal Structure Of Monoclonal Antibody 2d12.5 Fab
Complexed With Y- Dota
pdb|1NC4|B Chain B, Crystal Structure Of Monoclonal Antibody 2d12.5 Fab
Complexed With Gd- Dota
Length = 221
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 38/158 (24%), Positives = 60/158 (37%), Gaps = 20/158 (12%)
Query: 87 AQTADLKCSVQ--YADDYPVIWMKMDTAKKMEPLPISMSGSLIIHD----SRFQLTTDPE 140
+Q+ + C+V DY V W++ K +E L + SG + SR + D
Sbjct: 15 SQSLSITCTVSGFSLTDYGVHWVRQSPGKGLEWLGVIWSGGGTAYTAAFISRLNIYKDNS 74
Query: 141 TSTYILSIKEIQETDAGIYKCEVIIS--------LNNKVSAEVELIVRRPPIISDNSTRS 192
+ + +Q D +Y C S + V PP + + S
Sbjct: 75 KNQVFFEMNSLQANDTAMYYCARRGSYPYNYFDVWGQGTTVTVSSAKTTPPSVYPLAPGS 134
Query: 193 VIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ V L C G FP P T++W NS +LS+G
Sbjct: 135 AAQTN-SMVTLGCLVKGYFPEPVTVTW---NSGSLSSG 168
>pdb|1NCW|L Chain L, Cationic Cyclization Antibody 4c6 In Complex With Benzoic
Acid
pdb|1ND0|A Chain A, Cationic Cyclization Antibody 4c6 Complex With Transition
State Analog
pdb|1ND0|C Chain C, Cationic Cyclization Antibody 4c6 Complex With Transition
State Analog
pdb|1ND0|E Chain E, Cationic Cyclization Antibody 4c6 Complex With Transition
State Analog
pdb|1ND0|G Chain G, Cationic Cyclization Antibody 4c6 Complex With Transition
State Analog
pdb|1RUK|L Chain L, Crystal Structure (C) Of Native Cationic Cyclization
Antibody 4c6 Fab At Ph 4.6 With A Data Set Collected At
Ssrl Beamline 9-1
pdb|1RUP|L Chain L, Crystal Structure (g) Of Native Cationic Cyclization
Antibody 4c6 Fab At Ph 8.5 With A Data Set Collected At
Aps Beamline 19-id
Length = 219
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 51/128 (39%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC G G K I + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCWQGTHFPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|2GFB|B Chain B, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
pdb|2GFB|D Chain D, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
pdb|2GFB|F Chain F, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
pdb|2GFB|H Chain H, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
pdb|2GFB|J Chain J, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
pdb|2GFB|L Chain L, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
pdb|2GFB|N Chain N, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
pdb|2GFB|P Chain P, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
Length = 219
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 34/145 (23%), Positives = 60/145 (41%), Gaps = 35/145 (24%)
Query: 106 WMKMDTAKKMEPLPISMSGSLIIH-----DSRFQLTTDPETSTYILSIKEIQETDAGIYK 160
W++ K +E + SGS I+ RF ++ D +T L + ++ D +Y
Sbjct: 36 WVRQAPEKGLEWVAYISSGSSTIYYADTVKGRFTISRDNPKNTLFLQMTSLRSEDTAMYY 95
Query: 161 CE---------------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYC 205
C +++++ K +A + P+ D + G +V L C
Sbjct: 96 CARGDYYGSRGAYWGQGTLVTVSAKTTAPS--VYPLAPVCGDTT--------GSSVTLGC 145
Query: 206 YANG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 146 LVKGYFPEPVTLTW---NSGSLSSG 167
>pdb|4AEH|L Chain L, Crystal Structure Of The Anti-Aahi Fab9c2 Antibody
Length = 214
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 54/128 (42%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI ++ D G+YYC + G G K I + AP ++I P Q A
Sbjct: 73 LKINSLQSEDFGSYYCQHFWNIPFTFGSGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 131
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 132 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 191
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 192 YTCEATHK 199
>pdb|2JEL|H Chain H, Jel42 FabHPR COMPLEX
Length = 218
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 37/139 (26%), Positives = 60/139 (43%), Gaps = 15/139 (10%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETDA 156
Y + W+K AK +E + IS ++ +F+ +T D +ST + + + D+
Sbjct: 32 YAMHWVKQSHAKSLEWIGLISTYSGYTNYNQKFKGKATMTVDKSSSTAYMELARLTSEDS 91
Query: 157 GIYKCEVIISLN--NKVSAEVELIVRRPPIISDNSTRSVIVSEGQ---TVYLYCYANG-F 210
IY C ++ + A +IV + S GQ V L C G F
Sbjct: 92 AIYYCARVMGEQYFDVWGAGTTVIVSSAATTPPSVYPLAPGSGGQGNSMVTLGCLVKGYF 151
Query: 211 PAP-TISWRRDNSAALSTG 228
P P T++W NS +LS+G
Sbjct: 152 PEPVTVTW---NSGSLSSG 167
>pdb|1KFA|L Chain L, Crystal Structure Of Fab Fragment Complexed With
Gibberellin A4
pdb|1KFA|M Chain M, Crystal Structure Of Fab Fragment Complexed With
Gibberellin A4
Length = 217
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 51/128 (39%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G Y+C V G G K I + P ++ P Q A
Sbjct: 78 LKISRVEAEDLGVYFCSQSTHVPFTFGSGTKLEIK-RADAGPTVSSFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHAS 196
Query: 349 YACKAANK 356
Y C+AA+K
Sbjct: 197 YTCEAAHK 204
>pdb|1YNT|B Chain B, Structure Of The Immunodominant Epitope Displayed By The
Surface Antigen 1 (Sag1) Of Toxoplasma Gondii Complexed
To A Monoclonal Antibody
pdb|1YNT|D Chain D, Structure Of The Immunodominant Epitope Displayed By The
Surface Antigen 1 (Sag1) Of Toxoplasma Gondii Complexed
To A Monoclonal Antibody
Length = 218
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 38/152 (25%), Positives = 64/152 (42%), Gaps = 39/152 (25%)
Query: 101 DYPVIWMKMDTAKKMEPLPI--SMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQET 154
DY + W+K AK +E + I + SG ++ +F+ +T D +ST + + +
Sbjct: 31 DYGMHWVKQSHAKSLEWIGIISTYSGD-ASYNQKFKGKATMTVDKSSSTAYMELARLTSE 89
Query: 155 DAGIYKCE----------------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEG 198
D+ IY C + +S + V + P+ D + G
Sbjct: 90 DSAIYYCARSSTWYYFDYWGQGTTLTVSSAKTTAPSVYPLA---PVCGDTT--------G 138
Query: 199 QTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+V L C G FP P T++W NS +LS+G
Sbjct: 139 SSVTLGCLVKGYFPEPVTLTW---NSGSLSSG 167
>pdb|1FJ1|B Chain B, Lyme Disease Antigen Ospa In Complex With Neutralizing
Antibody Fab La-2
pdb|1FJ1|D Chain D, Lyme Disease Antigen Ospa In Complex With Neutralizing
Antibody Fab La-2
Length = 213
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 41/159 (25%), Positives = 65/159 (40%), Gaps = 14/159 (8%)
Query: 79 SQEQIKDIAQTADLKC--SVQYADDYPVIWMKMDTAKKMEPLPI--SMSGSLIIHD---S 131
S ++K +T + C S DY + W+K K ++ + + +G D
Sbjct: 7 SGPELKKPGETVKISCKASGYTFTDYSMYWVKQAPGKGLKRMGWINTETGEPTYADDFKG 66
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKC-EVIISLNNKVSAEVELIVRRPPIISDNST 190
RF L+ D ST L I ++ D Y C + S S V PP + +
Sbjct: 67 RFALSLDTSASTAYLHISNLKNEDTATYFCARGLDSWGQGTSVTVSSAKTTPPSVYPLA- 125
Query: 191 RSVIVSEGQTVYLYCYANG-FP-APTISWRRDNSAALST 227
+ G +V L C G FP + T++W NS +LS+
Sbjct: 126 PGCGDTTGSSVTLGCLVKGYFPESVTVTW---NSGSLSS 161
>pdb|3TT1|L Chain L, Crystal Structure Of Leut In The Outward-Open Conformation
In Complex With Fab
pdb|3TT1|M Chain M, Crystal Structure Of Leut In The Outward-Open Conformation
In Complex With Fab
Length = 218
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQN----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I + + D TYYC N G G K I + AP ++I P Q A
Sbjct: 77 LNIHPVEEEDAATYYCQQSNEDPYTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 135
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 136 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 195
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 196 YTCEATHK 203
>pdb|2R56|H Chain H, Crystal Structure Of A Recombinant Ige Fab Fragment In
Complex With Bovine Beta-Lactoglobulin Allergen
pdb|2R56|I Chain I, Crystal Structure Of A Recombinant Ige Fab Fragment In
Complex With Bovine Beta-Lactoglobulin Allergen
Length = 221
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 39/145 (26%), Positives = 63/145 (43%), Gaps = 24/145 (16%)
Query: 102 YPVIWMKMDTAKKMEPLPISMSGSLI---IHDS---RFQLTTDPETSTYILSIKEIQETD 155
+ + W++ K +E + S+SGS DS RF ++ D +T L + +++ D
Sbjct: 32 HGMTWVRQAPGKGLEWV-ASLSGSGTKTHFADSVKGRFTISRDNSNNTLYLQMDNVRDED 90
Query: 156 AGIYKCEVIISLNNKVSAEVELIVRRPPI-ISDNSTRSVIV---------SEGQTVYLYC 205
IY C + + +L R + +S ST+ V + G T L C
Sbjct: 91 TAIYYCAKAKRVG--ATGYFDLWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGC 148
Query: 206 YANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 149 LVKDYFPEPVTVSW---NSGALTSG 170
>pdb|2FB4|L Chain L, Dir Primaerstruktur Des Kristallisierbaren Monoklonalen
Immunoglobulins Igg1 Kol. Ii. Aminosaeuresequenz Der L-
Kette, Lambda-Typ, Subgruppe I (German)
pdb|2IG2|L Chain L, Dir Primaerstruktur Des Kristallisierbaren Monoklonalen
Immunoglobulins Igg1 Kol. Ii. Aminosaeuresequenz Der L-
Kette, Lambda-Typ, Subgruppe I (German)
Length = 216
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 27/137 (19%), Positives = 57/137 (41%), Gaps = 9/137 (6%)
Query: 237 LKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQGQALQYD 290
L I + D YYC A + G G K + + + P +T+ P +
Sbjct: 74 LAIGGLQSEDETDYYCAAWDVSLNAYVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANK 133
Query: 291 AILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQFG 347
A L C + + P A + W DG + + ++++++ +S +T E+ +
Sbjct: 134 ATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHR 193
Query: 348 QYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 194 SYSCQVTHEGSTVEKTV 210
>pdb|4DW2|H Chain H, The Crystal Structure Of Upa In Complex With The Fab
Fragment Of Mab- 112
Length = 212
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 41/166 (24%), Positives = 67/166 (40%), Gaps = 27/166 (16%)
Query: 80 QEQIKDIAQ---TADLKCSVQ--YADDYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDS-- 131
QE D+ + + L CS Y + W++ K++E + I+ GS DS
Sbjct: 5 QESGGDLVKPGGSLKLSCSASGFTFSRYAMSWVRQTPEKRLEWVASITNGGSTYYSDSVK 64
Query: 132 -RFQLTTDPETSTYILSIKEIQETDAGIYKCE------VIISLNNKVSAEVELIVRRPPI 184
RF ++ D + L + ++ D +Y CE + + V PP
Sbjct: 65 GRFIISRDNARNILSLQMSSLRSEDTAMYYCERGELTYAMDYWGQGTTVTVSSAKTTPPS 124
Query: 185 ISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ ++ G V L C G FP P T++W NS +LS+G
Sbjct: 125 VYP-------LAPGSMVTLGCLVKGYFPEPVTVTW---NSGSLSSG 160
>pdb|1FDL|L Chain L, Crystallographic Refinement Of The Three-Dimensional
Structure Of The Fab D1.3-Lysozyme Complex At 2.5-
Angstroms Resolution
Length = 214
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 49/194 (25%), Positives = 76/194 (39%), Gaps = 33/194 (17%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISW---RRDNSAAL------------------STGGS 230
S+ S G+TV + C A+G ++W ++ S L S G+
Sbjct: 10 SLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYYTTTLADGVPSRFSGSGSGT 69
Query: 231 IYRGNILKIPNITKTDRGTYYC----VAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQA 286
Y LKI ++ D G+YYC G G K I + AP ++I P Q
Sbjct: 70 QYS---LKINSLQPEDFGSYYCQHFWSTPRTFGGGTKLEIK-RADAAPTVSIFPPSSEQL 125
Query: 287 LQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-E 342
A + C + + P I W DG + N S + + D +S +S +T E
Sbjct: 126 TSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDE 185
Query: 343 RRQFGQYACKAANK 356
+ Y C+A +K
Sbjct: 186 YERHNSYTCEATHK 199
>pdb|1FRG|H Chain H, Crystal Structure, Sequence, And Epitope Mapping Of A
Peptide Complex Of An Anti-Influenza Ha Peptide Antibody
Fab 26(Slash)9: Fine-Tuning Antibody Specificity
Length = 220
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 36/152 (23%), Positives = 61/152 (40%), Gaps = 39/152 (25%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIHD----SRFQLTTDPETSTYILSIKEIQETDA 156
+ + W++ K++E + IS G + RF ++ D +T L + ++ DA
Sbjct: 32 FGMSWVRHTPDKRLEWVATISNGGGYTYYQDSVKGRFTISRDNAKNTLFLEMTSLKSEDA 91
Query: 157 GIYKCE------------------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEG 198
G+Y C V +S + V + P+ D + G
Sbjct: 92 GLYYCARRERYDEKGFAYWGRGTLVTVSAAKTTAPSVYPLA---PVCGDTT--------G 140
Query: 199 QTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+V L C G FP P T++W NS +LS+G
Sbjct: 141 SSVTLGCLVKGYFPEPVTLTW---NSGSLSSG 169
>pdb|1QKZ|L Chain L, 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
Length = 217
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 49/186 (26%), Positives = 73/186 (39%), Gaps = 17/186 (9%)
Query: 185 ISDNSTRSVIVSEGQTVYLYCYANGFPAP-------TISWRRDNSAALSTGGSIYRGNIL 237
IS S++S++ S G T YL+ Y P T+S R +G L
Sbjct: 21 ISCRSSQSLVHSNGNT-YLHWYLQK-PGQSPKLLIYTVSNRFSGVPDRFSGSGSGTDFTL 78
Query: 238 KIPNITKTDRGTYYCVAQNG---VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
KI + D G Y+C G G K I + AP ++I P Q A +
Sbjct: 79 KISRVEAEDLGVYFCSQSTHFPTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGASVV 137
Query: 295 CHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQYA 350
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 138 CFLNNFYPKDINVKWKIDGKERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYT 197
Query: 351 CKAANK 356
C+A +K
Sbjct: 198 CEATHK 203
>pdb|2Y6S|D Chain D, Structure Of An Ebolavirus-Protective Antibody In Complex
With Its Mucin-Domain Linear Epitope
pdb|2Y6S|H Chain H, Structure Of An Ebolavirus-Protective Antibody In Complex
With Its Mucin-Domain Linear Epitope
Length = 213
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 33/136 (24%), Positives = 54/136 (39%), Gaps = 12/136 (8%)
Query: 101 DYPVIWMKMDTAKKMEPLPISMSGSLIIH-----DSRFQLTTDPETSTYILSIKEIQETD 155
DY + W+K T + +E + G+ + R LT D + T + + + D
Sbjct: 31 DYVISWVKQRTGQGLEWIGEFYPGTDSTYYTENFKGRATLTADKSSKTAYMQLSSLTSED 90
Query: 156 AGIYKCEVIIS-LNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FPAP 213
+ +Y C + V PP + + S + V L C G FP P
Sbjct: 91 SAVYFCATAFDYWGQGTTLTVSSAATTPPSVYPLAPGSAAQTNSM-VTLGCLVKGYFPEP 149
Query: 214 -TISWRRDNSAALSTG 228
T++W NS +LS+G
Sbjct: 150 VTVTW---NSGSLSSG 162
>pdb|3UTO|A Chain A, Twitchin Kinase Region From C.Elegans
(Fn31-Nl-Kin-Crd-Ig26)
pdb|3UTO|B Chain B, Twitchin Kinase Region From C.Elegans
(Fn31-Nl-Kin-Crd-Ig26)
Length = 573
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 30/69 (43%), Gaps = 4/69 (5%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSI--YRGNI--LKIPNITKTDRGTY 250
V EGQ+ YC P ++W +D+ + + Y GN L I + D+G Y
Sbjct: 494 VGEGQSANFYCRVIASSPPVVTWHKDDRELKQSVKYMKRYNGNDYGLTINRVKGDDKGEY 553
Query: 251 YCVAQNGVG 259
A+N G
Sbjct: 554 TVRAKNSYG 562
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 295 CHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAA 354
C V A PP + W KD ++ + Y + +D L + ++ G+Y +A
Sbjct: 504 CRVIASSPPVVTWHKDDRELKQSVKYMKRYNG-----NDYGLTINRVKGDDKGEYTVRAK 558
Query: 355 NKYGSAQK 362
N YG+ ++
Sbjct: 559 NSYGTKEE 566
>pdb|2HMI|C Chain C, Hiv-1 Reverse TranscriptaseFRAGMENT OF FAB 28DNA COMPLEX
pdb|1J5O|L Chain L, Crystal Structure Of Met184ile Mutant Of Hiv-1 Reverse
Transcriptase In Complex With Double Stranded Dna
Template- Primer
Length = 214
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 50/128 (39%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I N+ D TYYC + G G K I + AP ++I P Q A
Sbjct: 73 LTISNLEPEDFATYYCQQYSKFPWTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 131
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITIERRQFGQ- 348
+ C + + P I W DG N S + + D +S +S +T + +
Sbjct: 132 VVCFLNNFYPKDINVAWAIDGSAAANGVLNSWTDQDSKDSTYSMSSTLTLTADEYEAANS 191
Query: 349 YACKAANK 356
Y C A +K
Sbjct: 192 YTCAATHK 199
>pdb|2IFF|H Chain H, Structure Of An Antibody-Lysozyme Complex: Effect Of A
Conservative Mutation
pdb|1BQL|H Chain H, Structure Of An Anti-Hel Fab Fragment Complexed With
Bobwhite Quail Lysozyme
Length = 215
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 37/140 (26%), Positives = 58/140 (41%), Gaps = 17/140 (12%)
Query: 101 DYPVIWMKMDTAKKMEPLP--ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQET 154
DY + W+K +E + + SGS H+ RF+ T D +ST + + +
Sbjct: 31 DYWIEWVKQRPGHGLEWIGEILPGSGSTNYHE-RFKGKATFTADTSSSTAYMQLNSLTSE 89
Query: 155 DAGIYKCEV----IISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG- 209
D+G+Y C + V PP + + S + V L C G
Sbjct: 90 DSGVYYCLHGNYDFDGWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTN-SMVTLGCLVKGY 148
Query: 210 FPAP-TISWRRDNSAALSTG 228
FP P T++W NS +LS+G
Sbjct: 149 FPEPVTVTW---NSGSLSSG 165
>pdb|1CGS|L Chain L, Local And Transmitted Conformational Changes On
Complexation Of An Anti-Sweetener Fab
pdb|2CGR|L Chain L, Local And Transmitted Conformational Changes On
Complexation Of An Anti-Sweetener Fab
pdb|1YNK|L Chain L, Identification Of Key Residues Of The Nc6.8 Fab Antibody
Fragment Binding To Synthetic Sweeteners: Crystal
Structure Of Nc6.8 Co-Crystalized With High Potency
Sweetener Compound Sc45647
pdb|1YNL|L Chain L, Identification Of Key Residues Of The Nc6.8 Fab Antibody
Fragment Binding To Synthetic Sweeterners: Crystal
Structure Of Nc6.8 Co-Crystalized With High Potency
Sweetener Compound Sc45647
Length = 219
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G Y+C V G G K + + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGVYFCSQGTHVPYTFGGGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1YQV|H Chain H, The Crystal Structure Of The Antibody Fab Hyhel5 Complex
With Lysozyme At 1.7a Resolution
Length = 215
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 37/140 (26%), Positives = 58/140 (41%), Gaps = 17/140 (12%)
Query: 101 DYPVIWMKMDTAKKMEPLP--ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQET 154
DY + W+K +E + + SGS H+ RF+ T D +ST + + +
Sbjct: 31 DYWIEWVKQRPGHGLEWIGEILPGSGSTNYHE-RFKGKATFTADTSSSTAYMQLNSLTSE 89
Query: 155 DAGIYKC----EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG- 209
D+G+Y C + V PP + + S + V L C G
Sbjct: 90 DSGVYYCLHGNYDFDGWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTN-SMVTLGCLVKGY 148
Query: 210 FPAP-TISWRRDNSAALSTG 228
FP P T++W NS +LS+G
Sbjct: 149 FPEPVTVTW---NSGSLSSG 165
>pdb|1NDG|B Chain B, Crystal Structure Of Fab Fragment Of Antibody Hyhel-8
Complexed With Its Antigen Lysozyme
Length = 210
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 2/87 (2%)
Query: 235 NILKIPNITKTDRGTYYCVAQNGV--GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
+ L++ ++T D TYYC +G G G ++ AP + P G
Sbjct: 78 HYLQLSSVTTEDTATYYCANWDGTYWGEGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSVT 137
Query: 293 LECHVEAYPPPAIVWIKDGVQIMNNQH 319
L C V+ Y P + + + + H
Sbjct: 138 LGCLVKGYFPEPVTLTWNSGSLSSGVH 164
>pdb|3MLW|L Chain L, Crystal Structure Of Anti-Hiv-1 V3 Fab 1006-15d In Complex
With An Mn V3 Peptide
pdb|3MLW|M Chain M, Crystal Structure Of Anti-Hiv-1 V3 Fab 1006-15d In Complex
With An Mn V3 Peptide
Length = 215
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 26/139 (18%), Positives = 57/139 (41%), Gaps = 11/139 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG--------VGRGMKRNIAVEVEFAPVITINRPRQGQALQ 288
L I + D YYC + + G G K + + + P +T+ P +
Sbjct: 74 LAISGLRSEDEADYYCASWDDSRGGPDYVFGTGTKVTVLGQPKANPTVTLFPPSSEELQA 133
Query: 289 YDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQ 345
A L C + + P A + W DG + + ++++++ +S +T E+ +
Sbjct: 134 NKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKS 193
Query: 346 FGQYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 194 HRSYSCQVTHEGSTVEKTV 212
>pdb|1JNN|H Chain H, Crystal Structure Of Fab-Estradiol Complexes
Length = 214
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 40/149 (26%), Positives = 65/149 (43%), Gaps = 17/149 (11%)
Query: 92 LKCSV---QYADDYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETST 143
L CS D Y + W+K + ++ + I+ + + +D RFQ LT D ++T
Sbjct: 20 LSCSASGFNIKDTY-MFWVKQRPEQGLDWIGRINPANGISKYDPRFQGKATLTADTSSNT 78
Query: 144 YILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRR--PPIISDNSTRSVIVSEGQTV 201
L + + D +Y C + L V + V + PP + + S + V
Sbjct: 79 AYLQLDNLTSEDTAVYYCAIEKDLPWGQGTLVTVSVAKTTPPSVYPLAPGSAAQTNSM-V 137
Query: 202 YLYCYANG-FPAP-TISWRRDNSAALSTG 228
L C G FP P T++W NS +LS+G
Sbjct: 138 TLGCLVKGYFPEPVTVTW---NSGSLSSG 163
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 36/150 (24%), Positives = 58/150 (38%), Gaps = 34/150 (22%)
Query: 194 IVSEGQTVYLYCYANGF-------------PAPTISW--RRDNSAALSTGGSIYRGNI-- 236
+V G +V L C A+GF P + W R + + +S ++G
Sbjct: 11 LVKPGASVRLSCSASGFNIKDTYMFWVKQRPEQGLDWIGRINPANGISKYDPRFQGKATL 70
Query: 237 ----------LKIPNITKTDRGTYYCVAQNGV--GRGMKRNIAVEVEFAPVITINRPRQG 284
L++ N+T D YYC + + G+G ++V P + P G
Sbjct: 71 TADTSSNTAYLQLDNLTSEDTAVYYCAIEKDLPWGQGTLVTVSVAKTTPPSVYPLAP--G 128
Query: 285 QALQYDAI--LECHVEAY-PPPAIVWIKDG 311
A Q +++ L C V+ Y P P V G
Sbjct: 129 SAAQTNSMVTLGCLVKGYFPEPVTVTWNSG 158
>pdb|2A1W|L Chain L, Anti-Cocaine Antibody 7.5.21, Crystal Form I
pdb|2A1W|M Chain M, Anti-Cocaine Antibody 7.5.21, Crystal Form I
Length = 216
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 33/128 (25%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L+I + D G YYC + + G G K + + AP ++I P Q A
Sbjct: 78 LRISRVEAEDLGVYYCFQGSHIPWTFGGGTKLE-SKRADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1MJJ|B Chain B, High Resolution Crystal Structure Of The Complex Of The
Fab Fragment Of Esterolytic Antibody Ms6-12 And A
Transition- State Analog
pdb|1MJJ|H Chain H, High Resolution Crystal Structure Of The Complex Of The
Fab Fragment Of Esterolytic Antibody Ms6-12 And A
Transition- State Analog
pdb|1MJU|H Chain H, 1.22 Angstrom Resolution Crystal Structure Of The Fab
Fragment Of Esterolytic Antibody Ms6-12
Length = 227
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 37/149 (24%), Positives = 61/149 (40%), Gaps = 35/149 (23%)
Query: 101 DYPVIWMKMDTAKKMEPLPISMSGSLIIH-DSRFQ----LTTDPETSTYILSIKEIQETD 155
+Y + W+K + +E + GS H + +F+ LT D +ST + + + D
Sbjct: 31 NYWINWVKQRPGQGLEWIGNIYPGSSYTHYNEKFKNKATLTVDTSSSTAYMQLSSLTSDD 90
Query: 156 AGIYKCE--------------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTV 201
+ +Y C V +S + V + P+ D S G +V
Sbjct: 91 SAVYYCANKLGWFPYWGQGTLVTVSAAKTTAPSVYPLA---PVCGDTS--------GSSV 139
Query: 202 YLYCYANG-FPAP-TISWRRDNSAALSTG 228
L C G FP P T++W NS +LS+G
Sbjct: 140 TLGCLVKGYFPEPVTLTW---NSGSLSSG 165
>pdb|2A77|L Chain L, Anti-cocaine Antibody 7.5.21, Crystal Form Ii
Length = 216
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 33/128 (25%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L+I + D G YYC + + G G K + + AP ++I P Q A
Sbjct: 78 LRISRVEAEDLGVYYCFQGSHIPWTFGGGTKLE-SKRADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|4AEH|H Chain H, Crystal Structure Of The Anti-Aahi Fab9c2 Antibody
Length = 231
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 36/147 (24%), Positives = 60/147 (40%), Gaps = 38/147 (25%)
Query: 106 WMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETDAGIYK 160
W+K + +E + IS GS H+ +F+ LT D +ST + + + D+ +Y
Sbjct: 36 WVKQRPGQGLEWIGNISPGGSNTNHNEKFKSKATLTADTSSSTAYMQLSSLTSDDSAVYY 95
Query: 161 CE-----------------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYL 203
C + +S + V + P+ D + G +V L
Sbjct: 96 CARYDGDYGSFDYWGQGTTLTVSSAKTTAPSVYPLA---PVCGDTT--------GSSVTL 144
Query: 204 YCYANG-FPAP-TISWRRDNSAALSTG 228
C G FP P T++W NS +LS+G
Sbjct: 145 GCLVKGYFPEPVTLTW---NSGSLSSG 168
>pdb|1N5Y|L Chain L, Hiv-1 Reverse Transcriptase Crosslinked To Post-
Translocation Aztmp-Terminated Dna (Complex P)
pdb|1N6Q|L Chain L, Hiv-1 Reverse Transcriptase Crosslinked To Pre-
Translocation Aztmp-Terminated Dna (Complex N)
pdb|1T03|L Chain L, Hiv-1 Reverse Transcriptase Crosslinked To Tenofovir
Terminated Template-Primer (Complex P)
pdb|1R0A|L Chain L, Crystal Structure Of Hiv-1 Reverse Transcriptase
Covalently Tethered To Dna Template-primer Solved To 2.8
Angstroms
pdb|3KLH|C Chain C, Crystal Structure Of Azt-Resistant Hiv-1 Reverse
Transcriptase Crosslinked To Post-Translocation
Aztmp-Terminated Dna (Complex P)
Length = 211
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I N+ D TYYC + G G K I + AP ++I P Q A
Sbjct: 73 LTISNLEPEDIATYYCQQYSKFPWTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 131
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 132 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 191
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 192 YTCEATHK 199
>pdb|1GGB|H Chain H, Major Antigen-Induced Domain Rearrangements In An Antibody
pdb|1GGC|H Chain H, Major Antigen-Induced Domain Rearrangements In An Antibody
Length = 215
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 29/69 (42%), Gaps = 2/69 (2%)
Query: 236 ILKIPNITKTDRGTYYCVAQNGV--GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAIL 293
LKI ++ D TYYCV + + G+G ++ AP + P G L
Sbjct: 81 FLKITSVDTADTATYYCVQEGYIYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTL 140
Query: 294 ECHVEAYPP 302
C V+ Y P
Sbjct: 141 GCLVKGYFP 149
>pdb|1C5B|H Chain H, Decarboxylase Catalytic Antibody 21d8 Unliganded Form
pdb|1C5C|H Chain H, Decarboxylase Catalytic Antibody 21d8-Hapten Complex
Length = 215
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 36/135 (26%), Positives = 56/135 (41%), Gaps = 11/135 (8%)
Query: 101 DYPVIWMKMDTAKKMEPLPI--SMSGSLIIHD---SRFQLTTDPETSTYILSIKEIQETD 155
Y + W+K + +E + + +G +D SR LT D +ST + + + D
Sbjct: 31 SYWMHWVKQRPGQGLEWIGLIDPSNGRTNFNDKFKSRATLTVDTSSSTAYMQLSSLTSED 90
Query: 156 AGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FPAP- 213
+ +Y C I V + P + + S S G T L C FP P
Sbjct: 91 SAVYYCVRIAYWGQGTLVTVSSASTKGPSVFPLAPSSKSTS-GGTAALGCLVKDYFPEPV 149
Query: 214 TISWRRDNSAALSTG 228
T+SW NS AL++G
Sbjct: 150 TVSW---NSGALTSG 161
>pdb|2AI0|L Chain L, Anti-Cocaine Antibody 7.5.21, Crystal Form Iii
pdb|2AI0|M Chain M, Anti-Cocaine Antibody 7.5.21, Crystal Form Iii
pdb|2AI0|N Chain N, Anti-Cocaine Antibody 7.5.21, Crystal Form Iii
pdb|2AI0|O Chain O, Anti-Cocaine Antibody 7.5.21, Crystal Form Iii
Length = 217
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 33/128 (25%), Positives = 53/128 (41%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L+I + D G YYC + + G G K + + AP ++I P Q A
Sbjct: 78 LRISRVEAEDLGVYYCFQGSHIPWTFGGGTKLE-SKRADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|2W9E|H Chain H, Structure Of Icsm 18 (Anti-Prp Therapeutic Antibody) Fab
Fragment Complexed With Human Prp Fragment 119-231
Length = 215
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 33/139 (23%), Positives = 61/139 (43%), Gaps = 16/139 (11%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K K +E + + + + ++ +F+ LT D +ST + + + D
Sbjct: 31 DYNLDWVKQSHGKTLEWIGNVYPNNGVTGYNQKFRGKATLTVDKSSSTAYMELHSLTSED 90
Query: 156 AGIYKCEV----IISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-F 210
+ +Y C + + V PP + + S ++ +V L C G F
Sbjct: 91 SAVYYCALYYYDVSYWGQGTLVTVSSAKTTPPSVYPLAPGS--AAQTNSVTLGCLVKGYF 148
Query: 211 PAP-TISWRRDNSAALSTG 228
P P T++W NS +LS+G
Sbjct: 149 PEPVTVTW---NSGSLSSG 164
>pdb|2DM2|A Chain A, Solution Structure Of The First Ig Domain Of Human
Palladin
Length = 110
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 25/67 (37%), Gaps = 5/67 (7%)
Query: 293 LECHVEAYPPPAIVWIKDGVQIM-NNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYAC 351
C V P P I W KDG QI + HY++ D SL G Y
Sbjct: 28 FTCRVAGNPKPKIYWFKDGKQISPKSDHYTIQR----DLDGTCSLHTTASTLDDDGNYTI 83
Query: 352 KAANKYG 358
AAN G
Sbjct: 84 MAANPQG 90
>pdb|3Q6F|A Chain A, Crystal Structure Of Fab Of Human Mab 2909 Specific For
Quaternary Neutralizing Epitope Of Hiv-1 Gp120
pdb|3Q6F|C Chain C, Crystal Structure Of Fab Of Human Mab 2909 Specific For
Quaternary Neutralizing Epitope Of Hiv-1 Gp120
pdb|3Q6F|E Chain E, Crystal Structure Of Fab Of Human Mab 2909 Specific For
Quaternary Neutralizing Epitope Of Hiv-1 Gp120
pdb|3Q6F|G Chain G, Crystal Structure Of Fab Of Human Mab 2909 Specific For
Quaternary Neutralizing Epitope Of Hiv-1 Gp120
pdb|3Q6F|I Chain I, Crystal Structure Of Fab Of Human Mab 2909 Specific For
Quaternary Neutralizing Epitope Of Hiv-1 Gp120
pdb|3Q6F|K Chain K, Crystal Structure Of Fab Of Human Mab 2909 Specific For
Quaternary Neutralizing Epitope Of Hiv-1 Gp120
Length = 213
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 36/200 (18%), Positives = 76/200 (38%), Gaps = 27/200 (13%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRR---------------DNSAALS---TGGSIYR 233
SV V+ G+T + C N + W + D + + +G +
Sbjct: 9 SVSVAPGKTARITCGGNNIANKNVHWYQQKPGQAPVLVIYYDDDRPSGIPDRFSGSNSGN 68
Query: 234 GNILKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQGQAL 287
L I + D YYC + G G + + + + AP +T+ P +
Sbjct: 69 TATLTISRVEAGDEADYYCQVWDSNSDHVVFGGGTQLTVLGQPKAAPSVTLFPPSSEELQ 128
Query: 288 QYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-R 344
A L C + + P A + W DG + + ++++++ +S +T E+ +
Sbjct: 129 ANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWK 188
Query: 345 QFGQYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 189 SHRSYSCQVTHEGSTVEKTV 208
>pdb|1XGY|L Chain L, Crystal Structure Of Anti-Meta I Rhodopsin Fab Fragment
K42- 41l
pdb|1XGY|M Chain M, Crystal Structure Of Anti-Meta I Rhodopsin Fab Fragment
K42- 41l
Length = 216
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 52/189 (27%), Positives = 81/189 (42%), Gaps = 22/189 (11%)
Query: 185 ISDNSTRSVIVSEGQTVYLYCYAN--GFPAPTISWRRDNSAA-----LSTGGSIYRGN-- 235
IS S++S++ S G T YLY Y G + +R N A+ S GS G
Sbjct: 21 ISCRSSKSLLHSNGIT-YLYWYLQRPGQSPQLLIYRMSNLASGVPDRFSGSGS---GTDF 76
Query: 236 ILKIPNITKTDRGTYYC--VAQNGV--GRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
L+I + D G YYC + ++ + G G K + + AP ++I P Q A
Sbjct: 77 ALRISRVEAEDVGVYYCGQMLEHPLTFGTGTKLELK-RADAAPTVSIFPPSSEQLTSGGA 135
Query: 292 ILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFG 347
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 136 SVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHN 195
Query: 348 QYACKAANK 356
Y C+A +K
Sbjct: 196 SYTCEATHK 204
>pdb|1CFS|B Chain B, Anti-P24 (Hiv-1) Fab Fragment Cb41 Complexed With An
Epitope-Unrelated Peptide
pdb|1CFT|B Chain B, Anti-P24 (Hiv-1) Fab Fragment Cb41 Complexed With An
Epitope-Unrelated D-Peptide
pdb|1CFN|B Chain B, Anti-P24 (Hiv-1) Fab Fragment Cb41 Complexed With An
Epitope-Related Peptide
pdb|1CFQ|B Chain B, Anti-P24 (Hiv-1) Fab Fragment Cb41
pdb|1BOG|B Chain B, Anti-P24 (Hiv-1) Fab Fragment Cb41 Complexed With An
Epitope-Homologous Peptide
pdb|1HH6|B Chain B, Anti-P24 (Hiv-1) Fab Fragment Cb41 Complexed With A
Peptide
pdb|1HH9|B Chain B, Anti-P24 (Hiv-1) Fab Fragment Cb41 Complexed With A
Peptide
pdb|1HI6|B Chain B, Anti-P24 (Hiv-1) Fab Fragment Cb41 Complexed With A
Peptide
Length = 213
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 35/145 (24%), Positives = 60/145 (41%), Gaps = 31/145 (21%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K +E + I S ++ +F+ LT D ++T + + + D
Sbjct: 31 DYEIHWVKQTPVHGLEWIGGIHPGSSGTAYNQKFKGKATLTADKSSTTAFMELSSLTSED 90
Query: 156 AGIYKCE----------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYC 205
+ +Y C V +S + V +V P+ + G +V L C
Sbjct: 91 SAVYYCTRKDYWGQGTLVTVSAAKTTAPSVYPLV---PVCGGTT--------GSSVTLGC 139
Query: 206 YANG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 140 LVKGYFPEPVTLTW---NSGSLSSG 161
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/84 (20%), Positives = 33/84 (39%)
Query: 236 ILKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILEC 295
+++ ++T D YYC ++ G+G ++ AP + P G L C
Sbjct: 80 FMELSSLTSEDSAVYYCTRKDYWGQGTLVTVSAAKTTAPSVYPLVPVCGGTTGSSVTLGC 139
Query: 296 HVEAYPPPAIVWIKDGVQIMNNQH 319
V+ Y P + + + + H
Sbjct: 140 LVKGYFPEPVTLTWNSGSLSSGVH 163
>pdb|1JNL|H Chain H, Crystal Structure Of Fab-Estradiol Complexes
Length = 216
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 40/149 (26%), Positives = 65/149 (43%), Gaps = 17/149 (11%)
Query: 92 LKCSV---QYADDYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETST 143
L CS D Y + W+K + ++ + I+ + + +D RFQ LT D ++T
Sbjct: 20 LSCSASGFNIKDTY-MFWVKQRPEQGLDWIGRINPANGISKYDPRFQGKATLTADTSSNT 78
Query: 144 YILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRR--PPIISDNSTRSVIVSEGQTV 201
L + + D +Y C + L V + V + PP + + S + V
Sbjct: 79 AYLQLDNLTSEDTAVYYCAIEKDLPWGQGTLVTVSVAKTTPPSVYPLAPGSAAQTNSM-V 137
Query: 202 YLYCYANG-FPAP-TISWRRDNSAALSTG 228
L C G FP P T++W NS +LS+G
Sbjct: 138 TLGCLVKGYFPEPVTVTW---NSGSLSSG 163
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 36/150 (24%), Positives = 58/150 (38%), Gaps = 34/150 (22%)
Query: 194 IVSEGQTVYLYCYANGF-------------PAPTISW--RRDNSAALSTGGSIYRGNI-- 236
+V G +V L C A+GF P + W R + + +S ++G
Sbjct: 11 LVKPGASVRLSCSASGFNIKDTYMFWVKQRPEQGLDWIGRINPANGISKYDPRFQGKATL 70
Query: 237 ----------LKIPNITKTDRGTYYCVAQNGV--GRGMKRNIAVEVEFAPVITINRPRQG 284
L++ N+T D YYC + + G+G ++V P + P G
Sbjct: 71 TADTSSNTAYLQLDNLTSEDTAVYYCAIEKDLPWGQGTLVTVSVAKTTPPSVYPLAP--G 128
Query: 285 QALQYDAI--LECHVEAY-PPPAIVWIKDG 311
A Q +++ L C V+ Y P P V G
Sbjct: 129 SAAQTNSMVTLGCLVKGYFPEPVTVTWNSG 158
>pdb|4DVB|B Chain B, The Crystal Structure Of The Fab Fragment Of Pro-upa
Antibody Mab-112
pdb|4DVB|L Chain L, The Crystal Structure Of The Fab Fragment Of Pro-upa
Antibody Mab-112
pdb|4DW2|L Chain L, The Crystal Structure Of Upa In Complex With The Fab
Fragment Of Mab- 112
Length = 215
Score = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 32/127 (25%), Positives = 52/127 (40%), Gaps = 7/127 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEV---EFAPVITINRPRQGQALQYDAIL 293
L I ++ D TYYC + R +E+ + AP ++I P Q A +
Sbjct: 74 LTISSVETEDAATYYCQHYSAYPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASV 133
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + P I W DG + N S + + D +S +S +T E + Y
Sbjct: 134 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 193
Query: 350 ACKAANK 356
C+A +K
Sbjct: 194 TCEATHK 200
>pdb|3VE0|A Chain A, Crystal Structure Of Sudan Ebolavirus Glycoprotein (Strain
Boniface) Bound To 16f6
Length = 220
Score = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 34/141 (24%), Positives = 57/141 (40%), Gaps = 18/141 (12%)
Query: 102 YPVIWMKMDTAKKMEPLPISMSGSLIIH-----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ +T K++E + SG + RF ++ D T L + ++ D
Sbjct: 32 YDMFWVRQNTEKRLEWVAYINSGGGNTYYPDTVKGRFTISRDNAKKTLFLQMSSLRSEDT 91
Query: 157 GIYKCEVIISLNN-------KVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG 209
+Y C + N+ S V PP + + + V L C G
Sbjct: 92 AMYYCARQLYGNSFFDYWGQGTSLTVSAAKTTPPSVYPLAP-GSAAAAASMVTLGCLVKG 150
Query: 210 -FPAP-TISWRRDNSAALSTG 228
FP P T++W NS +LS+G
Sbjct: 151 YFPEPVTVTW---NSGSLSSG 168
>pdb|3BIK|A Chain A, Crystal Structure Of The Pd-1PD-L1 Complex
pdb|3BIS|A Chain A, Crystal Structure Of The Pd-L1
pdb|3BIS|B Chain B, Crystal Structure Of The Pd-L1
Length = 222
Score = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 33/116 (28%), Positives = 51/116 (43%), Gaps = 13/116 (11%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI---- 292
L+I ++ D G Y C+ G G KR I V+V AP IN+ + L D +
Sbjct: 82 LQITDVKLQDAGVYRCMISYG-GADYKR-ITVKVN-APYNKINQ----RILVVDPVTSEH 134
Query: 293 -LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTS-LRVITIERRQF 346
L C E YP ++W Q+++ + + + F+ TS LR+ T F
Sbjct: 135 ELTCQAEGYPKAEVIWTSSDHQVLSGKTTTTNSKREEKLFNVTSTLRINTTTNEIF 190
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 27/120 (22%), Positives = 46/120 (38%), Gaps = 22/120 (18%)
Query: 146 LSIKEIQETDAGIYKCEVIIS------LNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQ 199
L I +++ DAG+Y+C + + KV+A I +R ++ + SE +
Sbjct: 82 LQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYNKINQRILVVDP------VTSEHE 135
Query: 200 TVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRG-------NILKIPNITKTDRGTYYC 252
L C A G+P + W + LS + N+ I T +YC
Sbjct: 136 ---LTCQAEGYPKAEVIWTSSDHQVLSGKTTTTNSKREEKLFNVTSTLRINTTTNEIFYC 192
>pdb|3T2N|L Chain L, Human Hepsin Protease In Complex With The Fab Fragment Of
An Inhibitory Antibody
pdb|3T2N|M Chain M, Human Hepsin Protease In Complex With The Fab Fragment Of
An Inhibitory Antibody
Length = 215
Score = 33.5 bits (75), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 28/144 (19%), Positives = 59/144 (40%), Gaps = 8/144 (5%)
Query: 229 GSIYRGNI-LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQ 283
GS+ G L + + D YYC G G K + + + AP +T+ P
Sbjct: 66 GSLLGGKAALTLSGVQPEDEAEYYCALWYSNHFIFGSGTKVTVLGQPKAAPSVTLFPPSS 125
Query: 284 GQALQYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITI 341
+ A L C + + P A + W D + + ++++++ +S +T
Sbjct: 126 EELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTP 185
Query: 342 ER-RQFGQYACKAANKYGSAQKEI 364
E+ + Y+C+ ++ + +K +
Sbjct: 186 EQWKSHRSYSCQVTHEGSTVEKTV 209
>pdb|3ZYJ|A Chain A, Netring1 In Complex With Ngl1
pdb|3ZYJ|C Chain C, Netring1 In Complex With Ngl1
Length = 440
Score = 33.5 bits (75), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGG-----SIYRGNILKIPNITKTDRGT 249
V+EG L C A+ ++SW N ++ G ++ L N+T D G
Sbjct: 353 VTEGMAAELKCRAST-SLTSVSWITPNGTVMTHGAYKVRIAVLSDGTLNFTNVTVQDTGM 411
Query: 250 YYCVAQNGVG 259
Y C+ N VG
Sbjct: 412 YTCMVSNSVG 421
>pdb|2WWK|O Chain O, Crystal Structure Of The Titin M10-Obscurin Like 1 Ig F17r
Mutant Complex
Length = 109
Score = 33.5 bits (75), Expect = 0.23, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 6/84 (7%)
Query: 273 APVITINRPRQGQALQ-YDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEF 331
+P + RPR + + +A L+C V PPP +VW K G Q+ ++ S +
Sbjct: 13 SPPCFLRRPRPVRVVSGAEAELKCVVLGEPPPVVVWEKGGQQLAASERLSFPA-----DG 67
Query: 332 SDTSLRVITIERRQFGQYACKAAN 355
++ L + G Y C+A N
Sbjct: 68 AEHGLLLTAALPTDAGVYVCRARN 91
>pdb|3S88|H Chain H, Crystal Structure Of Sudan Ebolavirus Glycoprotein (Strain
Gulu) Bound To 16f6
Length = 220
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 35/141 (24%), Positives = 58/141 (41%), Gaps = 18/141 (12%)
Query: 102 YPVIWMKMDTAKKMEPLPISMSGSLIIH-----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ +T K++E + SG + RF ++ D T L + ++ D
Sbjct: 32 YDMFWVRQNTEKRLEWVAYINSGGGNTYYPDTVKGRFTISRDNAKKTLFLQMSSLRSEDT 91
Query: 157 GIYKCEVIISLNN-------KVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG 209
+Y C + N+ S V PP + + S + V L C G
Sbjct: 92 AMYYCARQLYGNSFFDYWGQGTSLTVSAAKTTPPSVYPLAPGSAAAAA-SMVTLGCLVKG 150
Query: 210 -FPAP-TISWRRDNSAALSTG 228
FP P T++W NS +LS+G
Sbjct: 151 YFPEPVTVTW---NSGSLSSG 168
>pdb|3SBW|C Chain C, Crystal Structure Of The Complex Between The Extracellular
Domains Of Mouse Pd-1 Mutant And Human Pd-L1
Length = 222
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 33/116 (28%), Positives = 51/116 (43%), Gaps = 13/116 (11%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI---- 292
L+I ++ D G Y C+ G G KR I V+V AP IN+ + L D +
Sbjct: 82 LQITDVKLQDAGVYRCMISYG-GADYKR-ITVKVN-APYNKINQ----RILVVDPVTSEH 134
Query: 293 -LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTS-LRVITIERRQF 346
L C E YP ++W Q+++ + + + F+ TS LR+ T F
Sbjct: 135 ELTCQAEGYPKAEVIWTSSDHQVLSGKTTTTNSKREEKLFNVTSTLRINTTTNEIF 190
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 26/115 (22%), Positives = 46/115 (40%), Gaps = 12/115 (10%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVY-LY 204
L I +++ DAG+Y+C +IS + + V P + + R ++V + + L
Sbjct: 82 LQITDVKLQDAGVYRC--MISYGGADYKRITVKVNAP--YNKINQRILVVDPVTSEHELT 137
Query: 205 CYANGFPAPTISWRRDNSAALSTGGSIYRG-------NILKIPNITKTDRGTYYC 252
C A G+P + W + LS + N+ I T +YC
Sbjct: 138 CQAEGYPKAEVIWTSSDHQVLSGKTTTTNSKREEKLFNVTSTLRINTTTNEIFYC 192
>pdb|1GGI|H Chain H, Crystal Structure Of An Hiv-1 Neutralizing Antibody 50.1
In Complex With Its V3 Loop Peptide Antigen
pdb|1GGI|J Chain J, Crystal Structure Of An Hiv-1 Neutralizing Antibody 50.1
In Complex With Its V3 Loop Peptide Antigen
Length = 222
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 34/86 (39%), Gaps = 2/86 (2%)
Query: 236 ILKIPNITKTDRGTYYCVAQNGV--GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAIL 293
LKI ++ D TYYCV + + G+G ++ AP + P G L
Sbjct: 81 FLKITSVDTADTATYYCVQEGYIYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTL 140
Query: 294 ECHVEAYPPPAIVWIKDGVQIMNNQH 319
C V+ Y P + + + + H
Sbjct: 141 GCLVKGYFPEPVTLTWNSGSLSSGVH 166
>pdb|3FN3|A Chain A, Dimeric Structure Of Pd-L1
pdb|3FN3|B Chain B, Dimeric Structure Of Pd-L1
Length = 221
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 33/116 (28%), Positives = 51/116 (43%), Gaps = 13/116 (11%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI---- 292
L+I ++ D G Y C+ G G KR I V+V AP IN+ + L D +
Sbjct: 82 LQITDVKLQDAGVYRCMISYG-GADYKR-ITVKVN-APYNKINQ----RILVVDPVTSEH 134
Query: 293 -LECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTS-LRVITIERRQF 346
L C E YP ++W Q+++ + + + F+ TS LR+ T F
Sbjct: 135 ELTCQAEGYPKAEVIWTSSDHQVLSGKTTTTNSKREEKLFNVTSTLRINTTTNEIF 190
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 26/115 (22%), Positives = 46/115 (40%), Gaps = 12/115 (10%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVY-LY 204
L I +++ DAG+Y+C +IS + + V P + + R ++V + + L
Sbjct: 82 LQITDVKLQDAGVYRC--MISYGGADYKRITVKVNAP--YNKINQRILVVDPVTSEHELT 137
Query: 205 CYANGFPAPTISWRRDNSAALSTGGSIYRG-------NILKIPNITKTDRGTYYC 252
C A G+P + W + LS + N+ I T +YC
Sbjct: 138 CQAEGYPKAEVIWTSSDHQVLSGKTTTTNSKREEKLFNVTSTLRINTTTNEIFYC 192
>pdb|3KNB|A Chain A, Crystal Structure Of The Titin C-Terminus In Complex With
Obscurin- Like 1
pdb|3Q5O|A Chain A, Crystal Structure Of Human Titin Domain M10
pdb|3Q5O|B Chain B, Crystal Structure Of Human Titin Domain M10
Length = 100
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 295 CHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAA 354
C P P + W G +I ++Q H +D+ T+L ++ ++++ G Y
Sbjct: 27 CAFTGEPTPEVTWSCGGRKI-HSQEQGRFHIENTDDL--TTLIIMDVQKQDGGLYTLSLG 83
Query: 355 NKYGSAQKEIELFDR 369
N++GS + + R
Sbjct: 84 NEFGSDSATVNIHIR 98
>pdb|1OAK|L Chain L, Crystal Structure Of The Von Willebrand Factor (Vwf) A1
Domain In Complex With The Function Blocking Nmc-4 Fab
Length = 212
Score = 33.1 bits (74), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I N+ D TYYC + G G K + + AP ++I P Q A
Sbjct: 73 LTISNLEPEDIATYYCQQYEKLPWTFGGGTKLEVK-RADAAPTVSIFPPSSEQLTSGGAS 131
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 132 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 191
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 192 YTCEATHK 199
>pdb|2LQR|A Chain A, Nmr Structure Of Ig3 Domain Of Palladin
Length = 108
Score = 33.1 bits (74), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 25/67 (37%), Gaps = 5/67 (7%)
Query: 293 LECHVEAYPPPAIVWIKDGVQIM-NNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYAC 351
C V P P I W KDG QI + HY++ D SL G Y
Sbjct: 27 FTCRVAGNPKPKIYWFKDGKQISPKSDHYTIQR----DLDGTCSLHTTASTLDDDGNYTI 82
Query: 352 KAANKYG 358
AAN G
Sbjct: 83 MAANPQG 89
>pdb|1HYS|C Chain C, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With A Polypurine Tract Rna:dna
Length = 214
Score = 33.1 bits (74), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 50/128 (39%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I N+ D TYYC + G G K I + AP ++I P Q A
Sbjct: 73 LTISNLEPEDFATYYCQQYSKFPWTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGAS 131
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITIERRQFGQ- 348
+ C + + P I W DG N S + + D +S +S +T + +
Sbjct: 132 VVCFLNNFYPKDINVAWAIDGSAAANGVLNSWTDQDSKDSTYSMSSTLTLTADAYEAANS 191
Query: 349 YACKAANK 356
Y C A +K
Sbjct: 192 YTCAATHK 199
>pdb|3QOS|H Chain H, Crystal Structure Of Human Germline Antibody 3-23B3
pdb|3QOS|B Chain B, Crystal Structure Of Human Germline Antibody 3-23B3
Length = 228
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 39/144 (27%), Positives = 63/144 (43%), Gaps = 24/144 (16%)
Query: 102 YPVIWMKMDTAKKMEPL-PISMSG-SLIIHDS---RFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K +E + IS SG S DS RF ++ D +T L + ++ D
Sbjct: 32 YAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDT 91
Query: 157 GIYKCEVIISLNNKVSAEVELIVRRPPI-ISDNSTRSVIV---------SEGQTVYLYCY 206
+Y C + + E++ + + +S ST+ V + G T L C
Sbjct: 92 AVYYCAKY----DGIYGELDFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCL 147
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 148 VKDYFPEPVTVSW---NSGALTSG 168
>pdb|2G2R|L Chain L, Green-Fluorescent Antibody 11g10 In Complex With Its
Hapten (Nitro-Stilbene Derivative)
pdb|2G2R|A Chain A, Green-Fluorescent Antibody 11g10 In Complex With Its
Hapten (Nitro-Stilbene Derivative)
Length = 219
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 33/128 (25%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G Y+C+ G G K + + AP ++I P Q A
Sbjct: 78 LKISRVEAEDLGIYFCLQSTHFPLTFGAGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 136
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 137 VVCFLNNFYPRDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 196
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 197 YTCEATHK 204
>pdb|1MHP|H Chain H, Crystal Structure Of A Chimeric Alpha1 Integrin I-Domain
In Complex With The Fab Fragment Of A Humanized
Neutralizing Antibody
pdb|1MHP|X Chain X, Crystal Structure Of A Chimeric Alpha1 Integrin I-Domain
In Complex With The Fab Fragment Of A Humanized
Neutralizing Antibody
Length = 219
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 58/144 (40%), Gaps = 25/144 (17%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIHDS---RFQLTTDPETSTYILSIKEIQETDAG 157
Y + W++ K +E + IS G DS RF ++ D +T L + ++ D
Sbjct: 32 YTMSWVRQAPGKGLEWVATISGGGHTYYLDSVKGRFTISRDNSKNTLYLQMNSLRAEDTA 91
Query: 158 IYKCEVIISLNN--KVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYCY 206
+Y C V + L+ +S ST+ V + G T L C
Sbjct: 92 VYYCTRGFGDGGYFDVWGQGTLVT-----VSSASTKGPSVFPLAPSSKSTSGGTAALGCL 146
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 147 VKDYFPEPVTVSW---NSGALTSG 167
>pdb|1SM3|H Chain H, Crystal Structure Of The Tumor Specific Antibody Sm3
Complex With Its Peptide Epitope
Length = 218
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 44/102 (43%), Gaps = 9/102 (8%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISL---NNKVSAEVELIVRRPPIISDN 188
RF ++ D S+ L + ++ D GIY C + + V PP +
Sbjct: 69 RFTISRDDSKSSVYLQMNNLRAEDTGIYYCTGVGQFAYWGQGTTVTVSSAKTTPPTVYPL 128
Query: 189 STRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ S S+ V L C G FP P T++W NS +L++G
Sbjct: 129 APGSNAASQ-SMVTLGCLVKGYFPEPVTVTW---NSGSLASG 166
>pdb|3OPZ|H Chain H, Crystal Structure Of Trans-Sialidase In Complex With The
Fab Fragment Of A Neutralizing Monoclonal Igg Antibody
pdb|3OPZ|I Chain I, Crystal Structure Of Trans-Sialidase In Complex With The
Fab Fragment Of A Neutralizing Monoclonal Igg Antibody
pdb|3OPZ|J Chain J, Crystal Structure Of Trans-Sialidase In Complex With The
Fab Fragment Of A Neutralizing Monoclonal Igg Antibody
Length = 222
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 41/168 (24%), Positives = 67/168 (39%), Gaps = 40/168 (23%)
Query: 87 AQTADLKC-SVQYADDYPVI-WMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDP 139
+ + C +V Y Y I W+K +E + I + G I ++ +F+ LT D
Sbjct: 14 GTSVKMSCKAVGYTFTYDWIGWVKQRPGHGLEWIGDIYLGGGYINYNEKFKGKVILTADT 73
Query: 140 ETSTYILSIKEIQETDAGIYKCE-----------------VIISLNNKVSAEVELIVRRP 182
+ST + + + D+ IY C + +S + V +
Sbjct: 74 SSSTAYMQLSSLTSEDSAIYYCARGHYDGSYFDYWGQGTTLTVSSAKTTAPSVYPLA--- 130
Query: 183 PIISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
P+ D S G +V L C G FP P T++W NS +LS+G
Sbjct: 131 PVCGDTS--------GSSVTLGCLVKGYFPEPVTLTW---NSGSLSSG 167
>pdb|1FNS|L Chain L, Crystal Structure Of The Von Willebrand Factor (Vwf) A1
Domain I546v Mutant In Complex With The Function
Blocking Fab Nmc4
Length = 214
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I N+ D TYYC + G G K + + AP ++I P Q A
Sbjct: 73 LTISNLEPEDIATYYCQQYEKLPWTFGGGTKLEVK-RADAAPTVSIFPPSSEQLTSGGAS 131
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 132 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 191
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 192 YTCEATHK 199
>pdb|3NCM|A Chain A, Neural Cell Adhesion Molecule, Module 2, Nmr, 20
Structures
Length = 92
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 25/60 (41%), Gaps = 3/60 (5%)
Query: 196 SEGQTVYLYCYANGFPAPTISWR---RDNSAALSTGGSIYRGNILKIPNITKTDRGTYYC 252
EG+ + C PTI W+ RD + N L+I I KTD GTY C
Sbjct: 14 KEGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNNYLQIRGIKKTDEGTYRC 73
>pdb|1MCW|W Chain W, Three-Dimensional Structure Of A Hybrid Light Chain Dimer.
Protein Engineering Of A Binding Cavity
Length = 216
Score = 33.1 bits (74), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 26/136 (19%), Positives = 57/136 (41%), Gaps = 8/136 (5%)
Query: 237 LKIPNITKTDRGTYYCV-----AQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
L I + D Y+C+ A G G K + + + P +T+ P + A
Sbjct: 75 LTISGLLPDDEADYFCMSYLSDASFVFGSGTKVTVLRQPKANPTVTLFPPSSEELQANKA 134
Query: 292 ILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQFGQ 348
L C + + P A + W DG + + ++++++ +S +T E+ +
Sbjct: 135 TLVCLISDFYPGAVTVAWKADGSPVEAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRS 194
Query: 349 YACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 195 YSCQVTHEGSTVEKTV 210
>pdb|2YKL|H Chain H, Structure Of Human Anti-Nicotine Fab Fragment In Complex
With
Nicotine-11-Yl-Methyl-(4-Ethylamino-4-Oxo)-Butanoate
Length = 212
Score = 33.1 bits (74), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 33/133 (24%), Positives = 52/133 (39%), Gaps = 16/133 (12%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----------VGRGMKRNIAVEVEFAPVITINRPRQGQA 286
L++ ++T D YYCVA G G+G ++ P + P
Sbjct: 76 LRLSSVTAADTAVYYCVAWFGDLLSLKGVELWGQGTLVTVSSASTKGPSVFPLAPCSRST 135
Query: 287 LQYDAILECHVEAY-PPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQ 345
+ A L C V+ Y P P V G + + H + +S +S +S V+T+
Sbjct: 136 SESTAALGCLVKDYFPEPVTVSWNSGA-LTSGVHTFPAVLQSSGLYSLSS--VVTVPSSN 192
Query: 346 FG--QYACKAANK 356
FG Y C +K
Sbjct: 193 FGTQTYTCNVDHK 205
>pdb|1IGT|A Chain A, Structure Of Immunoglobulin
pdb|1IGT|C Chain C, Structure Of Immunoglobulin
Length = 214
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 48/201 (23%), Positives = 75/201 (37%), Gaps = 31/201 (15%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALS----------------- 226
I+ S S+ S G T+ + C+A+ +SW + +
Sbjct: 2 IVLTQSPSSLSASLGDTITITCHASQNINVWLSWYQQKPGNIPKLLIYKASNLHTGVPSR 61
Query: 227 -TGGSIYRGNILKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITIN 279
+G G L I ++ D TYYC Q G G G K I + AP ++I
Sbjct: 62 FSGSGSGTGFTLTISSLQPEDIATYYC--QQGQSYPLTFGGGTKLEIK-RADAAPTVSIF 118
Query: 280 RPRQGQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSL 336
P Q A + C + + P I W DG + N S + + D +S +S
Sbjct: 119 PPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSST 178
Query: 337 RVITI-ERRQFGQYACKAANK 356
+T E + Y C+A +K
Sbjct: 179 LTLTKDEYERHNSYTCEATHK 199
>pdb|2YK1|H Chain H, Structure Of Human Anti-Nicotine Fab Fragment In Complex
With Nicotine
Length = 211
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 33/133 (24%), Positives = 52/133 (39%), Gaps = 16/133 (12%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----------VGRGMKRNIAVEVEFAPVITINRPRQGQA 286
L++ ++T D YYCVA G G+G ++ P + P
Sbjct: 76 LRLSSVTAADTAVYYCVAWFGDLLSLKGVELWGQGTLVTVSSASTKGPSVFPLAPCSRST 135
Query: 287 LQYDAILECHVEAY-PPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQ 345
+ A L C V+ Y P P V G + + H + +S +S +S V+T+
Sbjct: 136 SESTAALGCLVKDYFPEPVTVSWNSGA-LTSGVHTFPAVLQSSGLYSLSS--VVTVPSSN 192
Query: 346 FG--QYACKAANK 356
FG Y C +K
Sbjct: 193 FGTQTYTCNVDHK 205
>pdb|2UV3|A Chain A, Structure Of The Signal-Regulatory Protein (Sirp) Alpha
Domain That Binds Cd47.
pdb|2UV3|B Chain B, Structure Of The Signal-Regulatory Protein (Sirp) Alpha
Domain That Binds Cd47.
pdb|2JJS|A Chain A, Structure Of Human Cd47 In Complex With Human Signal
Regulatory Protein (sirp) Alpha
pdb|2JJS|B Chain B, Structure Of Human Cd47 In Complex With Human Signal
Regulatory Protein (sirp) Alpha
pdb|2JJT|A Chain A, Structure Of Human Cd47 In Complex With Human Signal
Regulatory Protein (Sirp) Alpha
pdb|2JJT|B Chain B, Structure Of Human Cd47 In Complex With Human Signal
Regulatory Protein (Sirp) Alpha
Length = 126
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 33/82 (40%), Gaps = 19/82 (23%)
Query: 191 RSVIVSEGQTVYLYCYANGF-PAPTISWRRDNSAA---------------LSTGGSIYRG 234
+SV V+ G++ L+C P I W R A + S R
Sbjct: 11 KSVSVAAGESAILHCTVTSLIPVGPIQWFRGAGPARELIYNQKEGHFPRVTTVSESTKRE 70
Query: 235 NI---LKIPNITKTDRGTYYCV 253
N+ + I NIT D GTYYCV
Sbjct: 71 NMDFSISISNITPADAGTYYCV 92
>pdb|1XGU|B Chain B, Structure For Antibody Hyhel-63 Y33f Mutant Complexed With
Hen Egg Lysozyme
Length = 210
Score = 32.7 bits (73), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 2/85 (2%)
Query: 237 LKIPNITKTDRGTYYCVAQNG--VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
L++ ++T D TYYC + G G G ++ AP + P G L
Sbjct: 80 LQLNSVTTEDTATYYCASWGGDVWGAGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLG 139
Query: 295 CHVEAYPPPAIVWIKDGVQIMNNQH 319
C V+ Y P + + + + H
Sbjct: 140 CLVKGYFPEPVTLTWNSGSLSSGVH 164
>pdb|3ZYO|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
And Immunoglobulin Domain Of Netrin-G Ligand-3
Length = 411
Score = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 28/70 (40%), Gaps = 6/70 (8%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGG-----SIYRGNILKIPNITKTDRGT 249
V+EG L C G +++W N ++ G S+ L N+T D G
Sbjct: 324 VTEGMAAELKCRT-GTSMTSVNWLTPNGTLMTHGSYRVRISVLHDGTLNFTNVTVQDTGQ 382
Query: 250 YYCVAQNGVG 259
Y C+ N G
Sbjct: 383 YTCMVTNSAG 392
>pdb|1XGP|B Chain B, Structure For Antibody Hyhel-63 Y33a Mutant Complexed With
Hen Egg Lysozyme
Length = 210
Score = 32.7 bits (73), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 2/85 (2%)
Query: 237 LKIPNITKTDRGTYYCVAQNG--VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
L++ ++T D TYYC + G G G ++ AP + P G L
Sbjct: 80 LQLNSVTTEDTATYYCASWGGDVWGAGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLG 139
Query: 295 CHVEAYPPPAIVWIKDGVQIMNNQH 319
C V+ Y P + + + + H
Sbjct: 140 CLVKGYFPEPVTLTWNSGSLSSGVH 164
>pdb|1CIC|C Chain C, Idiotope-Anti-Idiotope Fab-Fab Complex; D1.3-E225
Length = 214
Score = 32.7 bits (73), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 48/194 (24%), Positives = 76/194 (39%), Gaps = 33/194 (17%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISW---RRDNSAAL------------------STGGS 230
S+ S G+TV + C A+G ++W ++ S L S G+
Sbjct: 10 SLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYYTTTLADGVPSRFSGSGSGT 69
Query: 231 IYRGNILKIPNITKTDRGTYYC----VAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQA 286
Y LKI ++ D G+YYC G G K + + AP ++I P Q
Sbjct: 70 QYS---LKINSLQPEDFGSYYCQHFWSTPRTFGGGTKLELK-RADAAPTVSIFPPSSEQL 125
Query: 287 LQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-E 342
A + C + + P I W DG + N S + + D +S +S +T E
Sbjct: 126 TSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLDSWTDQDSKDSTYSMSSTLTLTKDE 185
Query: 343 RRQFGQYACKAANK 356
+ Y C+A +K
Sbjct: 186 YERHNSYTCEATHK 199
>pdb|1XGR|B Chain B, Structure For Antibody Hyhel-63 Y33i Mutant Complexed With
Hen Egg Lysozyme
Length = 210
Score = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 2/85 (2%)
Query: 237 LKIPNITKTDRGTYYCVAQNG--VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
L++ ++T D TYYC + G G G ++ AP + P G L
Sbjct: 80 LQLNSVTTEDTATYYCASWGGDVWGAGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLG 139
Query: 295 CHVEAYPPPAIVWIKDGVQIMNNQH 319
C V+ Y P + + + + H
Sbjct: 140 CLVKGYFPEPVTLTWNSGSLSSGVH 164
>pdb|1XGT|B Chain B, Structure For Antibody Hyhel-63 Y33l Mutant Complexed With
Hen Egg Lysozyme
Length = 210
Score = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 2/85 (2%)
Query: 237 LKIPNITKTDRGTYYCVAQNG--VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
L++ ++T D TYYC + G G G ++ AP + P G L
Sbjct: 80 LQLNSVTTEDTATYYCASWGGDVWGAGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLG 139
Query: 295 CHVEAYPPPAIVWIKDGVQIMNNQH 319
C V+ Y P + + + + H
Sbjct: 140 CLVKGYFPEPVTLTWNSGSLSSGVH 164
>pdb|3MNV|B Chain B, Crystal Structure Of The Non-Neutralizing Hiv Antibody
13h11 Fab Fragment
pdb|3MNV|D Chain D, Crystal Structure Of The Non-Neutralizing Hiv Antibody
13h11 Fab Fragment
pdb|3MNW|B Chain B, Crystal Structure Of The Non-Neutralizing Hiv Antibody
13h11 Fab Fragment With A Gp41 Mper-Derived Peptide In A
Helical Conformation
pdb|3MNZ|B Chain B, Crystal Structure Of The Non-Neutralizing Hiv Antibody
13h11 Fab Fragment With A Gp41 Mper-Derived Peptide
Bearing Ala Substitutions In A Helical Conformation
pdb|3MO1|B Chain B, Crystal Structure Of The Non-Neutralizing Hiv Antibody
13h11 Fab Fragment
Length = 219
Score = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 41/160 (25%), Positives = 64/160 (40%), Gaps = 14/160 (8%)
Query: 79 SQEQIKDIAQTADLKC--SVQYADDYPVIWMKMDTAKKMEPLPI--SMSGSLIIHD---S 131
S ++K +T + C S DY V W+K K ++ + + +G D
Sbjct: 8 SGPELKKPGETVKISCKASGYTFTDYSVHWVKQVPGKGLKWMGWINTETGEPTYADDFKG 67
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEV-IISLNNKVSAEVELIVRRPPIISDNST 190
RF + + ST L I ++ D Y C + + + V + P + +
Sbjct: 68 RFAFSLESSASTAYLEIHNLKNEDTATYFCALGWLHWGLGTTLTVSSASTKGPSVFPLAP 127
Query: 191 RSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
S S G T L C FP P T+SW NS AL++G
Sbjct: 128 SSKSTS-GGTAALGCLVKDYFPEPVTVSW---NSGALTSG 163
>pdb|1DQJ|B Chain B, Crystal Structure Of The Anti-Lysozyme Antibody Hyhel-63
Complexed With Hen Egg White Lysozyme
pdb|1DQM|H Chain H, Crystal Structure Of Anti-Lysozyme Antibody
pdb|1DQQ|B Chain B, Crystal Structure Of Anti-Lysozyme Antibody Hyhel-63
pdb|1DQQ|D Chain D, Crystal Structure Of Anti-Lysozyme Antibody Hyhel-63
pdb|1NBY|B Chain B, Crystal Structure Of Hyhel-63 Complexed With Hel Mutant
K96a
pdb|1NBZ|B Chain B, Crystal Structure Of Hyhel-63 Complexed With Hel Mutant
K97a
Length = 210
Score = 32.7 bits (73), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 2/85 (2%)
Query: 237 LKIPNITKTDRGTYYCVAQNG--VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
L++ ++T D TYYC + G G G ++ AP + P G L
Sbjct: 80 LQLNSVTTEDTATYYCASWGGDVWGAGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLG 139
Query: 295 CHVEAYPPPAIVWIKDGVQIMNNQH 319
C V+ Y P + + + + H
Sbjct: 140 CLVKGYFPEPVTLTWNSGSLSSGVH 164
>pdb|3LEX|L Chain L, 2f5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal
Antibody 11f10 In Complex With Hiv-1 Gp41
pdb|3LEX|B Chain B, 2f5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal
Antibody 11f10 In Complex With Hiv-1 Gp41
Length = 219
Score = 32.7 bits (73), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 44/194 (22%), Positives = 75/194 (38%), Gaps = 12/194 (6%)
Query: 175 VELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPT-----ISWRRDNSAALSTGG 229
+ + + +P IS S++S++ S+G+T + +P +S TG
Sbjct: 11 LSVTIGQPASISCKSSQSLLDSDGKTYLNWLLQRPGQSPKRLIYLVSKLASGVPDRFTGS 70
Query: 230 SIYRGNILKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEV---EFAPVITINRPRQGQA 286
LKI + D G YYC +E+ + AP ++I P Q
Sbjct: 71 GSGTDFTLKISRVEAEDLGVYYCWQGTHFPWTFGGYTKLEIKRADAAPTVSIFPPSSEQL 130
Query: 287 LQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-E 342
A + C + + P I W DG + N S + + D +S +S +T E
Sbjct: 131 TSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDE 190
Query: 343 RRQFGQYACKAANK 356
+ Y C+A +K
Sbjct: 191 YERHNSYTCEATHK 204
>pdb|3KYK|H Chain H, Crystal Structure Of Li33 Igg1 Fab
Length = 227
Score = 32.7 bits (73), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 37/144 (25%), Positives = 59/144 (40%), Gaps = 24/144 (16%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETDA 156
YP+ W++ K +E + I SG + + RF ++ D +T L + ++ D
Sbjct: 32 YPMFWVRQAPGKGLEWVSWIGPSGGITKYADSVKGRFTISRDNSKNTLYLQMNSLRAEDT 91
Query: 157 GIYKCEVIISLNNKVSAEVELIVRRPPI-ISDNSTRSVIV---------SEGQTVYLYCY 206
Y C + +L R + +S ST+ V + G T L C
Sbjct: 92 ATYYC----AREGHNDWYFDLWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCL 147
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 148 VKDYFPEPVTVSW---NSGALTSG 168
>pdb|4GLR|I Chain I, Structure Of The Anti-ptau Fab (pt231/ps235_1) In Complex
With Phosphoepitope Pt231/ps235
pdb|4GLR|K Chain K, Structure Of The Anti-ptau Fab (pt231/ps235_1) In Complex
With Phosphoepitope Pt231/ps235
Length = 212
Score = 32.7 bits (73), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 25/133 (18%), Positives = 55/133 (41%), Gaps = 9/133 (6%)
Query: 241 NITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
+ D YYC A +G G G + + + AP +T+ P + A L
Sbjct: 74 GVQAEDEAVYYCGAYDGSAGGGIFGAGTTLTVLGQPKAAPSVTLFPPSSEELQANKATLV 133
Query: 295 CHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQFGQYAC 351
C + + P A + W D + + ++++++ +S +T E+ + Y+C
Sbjct: 134 CLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSC 193
Query: 352 KAANKYGSAQKEI 364
+ ++ + +K +
Sbjct: 194 QVTHEGSTVEKTV 206
>pdb|3G5Y|A Chain A, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
Length = 213
Score = 32.7 bits (73), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 47/202 (23%), Positives = 79/202 (39%), Gaps = 27/202 (13%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILK----- 238
I+ S S+ +S G TV + C+++ + I W + + S G IY G L+
Sbjct: 2 ILMTQSPVSMSLSLGDTVSITCHSSQDISSNIGWLQ-QAPGKSFKGLIYHGTNLEDGVPG 60
Query: 239 --------------IPNITKTDRGTYYCVAQNGVGRGMKRNIAVEV---EFAPVITINRP 281
I +++ D YYCV ++E+ + AP ++I P
Sbjct: 61 RFSGSGSGADYSLTISSLSSEDFVDYYCVQYGQFPWTFGGGTSLEIKRADAAPTVSIFPP 120
Query: 282 RQGQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRV 338
Q A + C + + P I W DG + N S + + D +S +S
Sbjct: 121 STEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT 180
Query: 339 ITI-ERRQFGQYACKAANKYGS 359
+T E + Y C+A +K S
Sbjct: 181 LTKDEYERHNSYTCEATHKTSS 202
>pdb|1JNL|L Chain L, Crystal Structure Of Fab-Estradiol Complexes
pdb|1JNN|L Chain L, Crystal Structure Of Fab-Estradiol Complexes
Length = 211
Score = 32.7 bits (73), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 50/202 (24%), Positives = 78/202 (38%), Gaps = 33/202 (16%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRD-----------NSAALSTG---- 228
I+ + S+ S G+TV + C A+G ++W + N+ L G
Sbjct: 2 IVMTQTPASLSASVGETVTITCRASGNIYNYLAWYQQKQGKSPQLLVYNAKTLVDGVPLR 61
Query: 229 ------GSIYRGNILKIPNITKTDRGTYYCV----AQNGVGRGMKRNIAVEVEFAPVITI 278
G+ Y LKI ++ D G YYC G G K I + AP ++I
Sbjct: 62 FSGSGSGTQYS---LKINSLQPEDFGNYYCHHFWNTPYTFGGGTKLEIK-RADAAPTVSI 117
Query: 279 NRPRQGQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTS 335
P Q A + C + + P I W DG + N S + + D +S +S
Sbjct: 118 FPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSS 177
Query: 336 LRVITI-ERRQFGQYACKAANK 356
+T E + Y C+A +K
Sbjct: 178 TLTLTKDEYERHNSYTCEATHK 199
>pdb|1XGQ|B Chain B, Structure For Antibody Hyhel-63 Y33v Mutant Complexed With
Hen Egg Lysozyme
Length = 210
Score = 32.7 bits (73), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 2/85 (2%)
Query: 237 LKIPNITKTDRGTYYCVAQNG--VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
L++ ++T D TYYC + G G G ++ AP + P G L
Sbjct: 80 LQLNSVTTEDTATYYCASWGGDVWGAGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLG 139
Query: 295 CHVEAYPPPAIVWIKDGVQIMNNQH 319
C V+ Y P + + + + H
Sbjct: 140 CLVKGYFPEPVTLTWNSGSLSSGVH 164
>pdb|3QVQ|A Chain A, The Structure Of An Oleispira Antarctica Phosphodiesterase
Olei02445 In Complex With The Product
Sn-Glycerol-3-Phosphate
pdb|3QVQ|B Chain B, The Structure Of An Oleispira Antarctica Phosphodiesterase
Olei02445 In Complex With The Product
Sn-Glycerol-3-Phosphate
pdb|3QVQ|C Chain C, The Structure Of An Oleispira Antarctica Phosphodiesterase
Olei02445 In Complex With The Product
Sn-Glycerol-3-Phosphate
pdb|3QVQ|D Chain D, The Structure Of An Oleispira Antarctica Phosphodiesterase
Olei02445 In Complex With The Product
Sn-Glycerol-3-Phosphate
Length = 252
Score = 32.7 bits (73), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 94 CSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYILSIKEIQE 153
S+ A + W+++D + +P+ I HD TTD + Y + E+++
Sbjct: 28 ASLHLAGQQGIKWVEIDVXLSGDGIPV------IFHDDYLSRTTDGDGLIYKTPLAELKQ 81
Query: 154 TDAGIYKCE 162
DAG +K +
Sbjct: 82 LDAGSWKGQ 90
>pdb|1F6A|A Chain A, Structure Of The Human Ige-Fc Bound To Its High Affinity
Receptor Fc(Epsilon)ri(Alpha)
Length = 176
Score = 32.7 bits (73), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 36/148 (24%), Positives = 59/148 (39%), Gaps = 23/148 (15%)
Query: 140 ETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDN---STRSVIVS 196
E + L+I + D+G YKC+ ++ AE E + + SD + +V
Sbjct: 47 EETNSSLNIVNAKFEDSGEYKCQ------HQQVAESEPVYLE--VFSDWLLLQASAEVVM 98
Query: 197 EGQTVYLYCYA-NGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQ 255
EGQ ++L C+ + + + +D A Y + + I N D GTYYC
Sbjct: 99 EGQPLFLRCHGWRNWDVYKVIYYKDGEAL----KYWYENHAISITNAAAEDSGTYYCT-- 152
Query: 256 NGVGRGMKRNIAVEVEFAPVITINRPRQ 283
G + E E + I PR+
Sbjct: 153 -----GKVWQLDYESEPLNITVIKAPRE 175
>pdb|3MCK|H Chain H, Crystal Structure Of Anti-Beta-Amyloid Antibody C705
pdb|3MCK|B Chain B, Crystal Structure Of Anti-Beta-Amyloid Antibody C705
Length = 228
Score = 32.7 bits (73), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 34/93 (36%), Gaps = 10/93 (10%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----------GRGMKRNIAVEVEFAPVITINRPRQGQA 286
LKI ++ TD TYYC +G G+G ++ AP + P G
Sbjct: 82 LKITSVDTTDTATYYCTRSSGSIVIATGFAYWGQGTLVTVSAAKTTAPSVYPLAPVCGDT 141
Query: 287 LQYDAILECHVEAYPPPAIVWIKDGVQIMNNQH 319
L C V+ Y P + + + + H
Sbjct: 142 TGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVH 174
>pdb|3PUC|A Chain A, Atomic Resolution Structure Of Titin Domain M7
Length = 99
Score = 32.7 bits (73), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 34/88 (38%), Gaps = 10/88 (11%)
Query: 178 IVRRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYR---- 233
I +P I++ + VS A G P PT W +D A T G Y+
Sbjct: 3 ISSKPVIVT--GLQDTTVSSDSVAKFAVKATGEPRPTAIWTKDGKAI--TQGGKYKLSED 58
Query: 234 --GNILKIPNITKTDRGTYYCVAQNGVG 259
G L+I +D G Y C +N G
Sbjct: 59 KGGFFLEIHKTDTSDSGLYTCTVKNSAG 86
Score = 32.0 bits (71), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 36/95 (37%), Gaps = 9/95 (9%)
Query: 274 PVITINRPRQGQALQYDAILECHVEAY--PPPAIVWIKDGVQIMNNQHYSVSHFATSDEF 331
PVI Q + D++ + V+A P P +W KDG I Y + S++
Sbjct: 7 PVIVTGL--QDTTVSSDSVAKFAVKATGEPRPTAIWTKDGKAITQGGKYKL-----SEDK 59
Query: 332 SDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
L + + G Y C N GS +L
Sbjct: 60 GGFFLEIHKTDTSDSGLYTCTVKNSAGSVSSSCKL 94
>pdb|4DTG|H Chain H, Hemostatic Effect Of A Monoclonal Antibody Mab 2021
Blocking The Interaction Between Fxa And Tfpi In A
Rabbit Hemophilia Model
Length = 222
Score = 32.3 bits (72), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 62/144 (43%), Gaps = 20/144 (13%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSL-IIHDS---RFQLTTDPETSTYILSIKEIQETD 155
+Y + W++ K++E + IS SGS DS RF ++ D ++ L + ++ D
Sbjct: 31 NYAMSWVRQTPEKRLEWVATISRSGSYSYFPDSVQGRFTISRDNAKNSLYLQMNSLRAED 90
Query: 156 AGIYKC---------EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCY 206
+Y C + + S + V + P + + S SE T L C
Sbjct: 91 TAVYYCARLGGYDEGDAMDSWGQGTTVTVSSASTKGPSVFPLAPCSRSTSE-STAALGCL 149
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 150 VKDYFPEPVTVSW---NSGALTSG 170
>pdb|2W9D|H Chain H, Structure Of Fab Fragment Of The Icsm 18 - Anti-Prp
Therapeutic Antibody At 1.57 A Resolution
Length = 215
Score = 32.3 bits (72), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 33/139 (23%), Positives = 60/139 (43%), Gaps = 16/139 (11%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K K +E + + + + ++ +F+ LT D +ST + + + D
Sbjct: 31 DYNLDWVKQSHGKTLEWIGNVYPNNGVTGYNQKFRGKATLTVDKSSSTAYMELHSLTSED 90
Query: 156 AGIYKCEV----IISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-F 210
+ +Y C + + V PP + + S ++ V L C G F
Sbjct: 91 SAVYYCALYYYDVSYWGQGTLVTVSSAKTTPPSVYPLAPGS--AAQTSMVTLGCLVKGYF 148
Query: 211 PAP-TISWRRDNSAALSTG 228
P P T++W NS +LS+G
Sbjct: 149 PEPVTVTW---NSGSLSSG 164
>pdb|2VXS|H Chain H, Structure Of Il-17a In Complex With A Potent, Fully Human
Neutralising Antibody
pdb|2VXS|I Chain I, Structure Of Il-17a In Complex With A Potent, Fully Human
Neutralising Antibody
pdb|2VXS|J Chain J, Structure Of Il-17a In Complex With A Potent, Fully Human
Neutralising Antibody
pdb|2VXS|K Chain K, Structure Of Il-17a In Complex With A Potent, Fully Human
Neutralising Antibody
Length = 225
Score = 32.3 bits (72), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 40/144 (27%), Positives = 62/144 (43%), Gaps = 25/144 (17%)
Query: 102 YPVIWMKMDTAKKMEPL-PISMSG-SLIIHDS---RFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K +E + IS SG S DS RF ++ D +T L + ++ D
Sbjct: 32 YAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDT 91
Query: 157 GIYKCEV-IISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYCY 206
+Y C +I + + L+ +S ST+ V + G T L C
Sbjct: 92 AVYYCARDLIHGVTRNWGQGTLVT-----VSSASTKGPSVFPLAPSSKSTSGGTAALGCL 146
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 147 VKDYFPQPVTVSW---NSGALTSG 167
>pdb|1F3D|H Chain H, Catalytic Antibody 4b2 In Complex With Its Amidinium
Hapten.
pdb|1F3D|K Chain K, Catalytic Antibody 4b2 In Complex With Its Amidinium
Hapten
Length = 217
Score = 32.3 bits (72), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 34/138 (24%), Positives = 56/138 (40%), Gaps = 14/138 (10%)
Query: 101 DYPVIWMKMDTAKKMEPLP--ISMSGSLIIHD---SRFQLTTDPETSTYILSIKEIQETD 155
DY + W+K K +E + + SG + + LT D +ST + + + D
Sbjct: 31 DYNIHWVKQSHGKSLEWIGYIVPYSGGTTFNQKFKGKATLTVDKSSSTAFMHLNSLTFED 90
Query: 156 AGIYKCEV---IISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FP 211
+ +Y C + + V PP + + S + V L C G FP
Sbjct: 91 SAVYYCANDYDGVYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVKGYFP 149
Query: 212 AP-TISWRRDNSAALSTG 228
P T++W NS +LS+G
Sbjct: 150 EPVTVTW---NSGSLSSG 164
>pdb|2Y7Q|A Chain A, The High-Affinity Complex Between Ige And Its Receptor Fc
Epsilon Ri
Length = 188
Score = 32.3 bits (72), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 36/148 (24%), Positives = 59/148 (39%), Gaps = 23/148 (15%)
Query: 140 ETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDN---STRSVIVS 196
E + L+I + D+G YKC+ ++ AE E + + SD + +V
Sbjct: 50 EETNSSLNIVNAKFEDSGEYKCQ------HQQVAESEPVYLE--VFSDWLLLQASAEVVM 101
Query: 197 EGQTVYLYCYA-NGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQ 255
EGQ ++L C+ + + + +D A Y + + I N D GTYYC
Sbjct: 102 EGQPLFLRCHGWRNWDVYKVIYYKDGEAL----KYWYENHAISITNAAAEDSGTYYCT-- 155
Query: 256 NGVGRGMKRNIAVEVEFAPVITINRPRQ 283
G + E E + I PR+
Sbjct: 156 -----GKVWQLDYESEPLNITVIKAPRE 178
>pdb|1LK3|H Chain H, Engineered Human Interleukin-10 Monomer Complexed To 9d7
Fab Fragment
pdb|1LK3|I Chain I, Engineered Human Interleukin-10 Monomer Complexed To 9d7
Fab Fragment
Length = 219
Score = 32.3 bits (72), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 37/146 (25%), Positives = 60/146 (41%), Gaps = 26/146 (17%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
D+ + W+K K +E + I+ + ++ +F+ LT D TST + + + D
Sbjct: 31 DFYIHWVKQSHGKSLEWIGYINPNSGYTNYNEKFKNKATLTVDKSTSTGYMELSRLTSED 90
Query: 156 AGIYKCEVIISLNN-----------KVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLY 204
+ Y C + NN VS+ P+ + +S V L
Sbjct: 91 SANYSCTRGVPGNNWFPYWGQGTLVTVSSAETTAPSVYPLAPGTALKS-----NSMVTLG 145
Query: 205 CYANG-FPAP-TISWRRDNSAALSTG 228
C G FP P T++W NS ALS+G
Sbjct: 146 CLVKGYFPEPVTVTW---NSGALSSG 168
>pdb|1F2X|K Chain K, Structure Of The Single-Domain Camelid Antibody Cab-Ca05
pdb|1F2X|L Chain L, Structure Of The Single-Domain Camelid Antibody Cab-Ca05
Length = 135
Score = 32.3 bits (72), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 102 YPVIWMKMDTAKKMEPLPISMSGSLIIHDS---RFQLTTDPETSTYILSIKEIQETDAGI 158
Y + W + K+ E + + GS DS RF ++ D +T L + ++ D I
Sbjct: 32 YCMGWFRQAPGKEREGVATILGGSTYYGDSVKGRFTISQDNAKNTVYLQMNSLKPEDTAI 91
Query: 159 YKC 161
Y C
Sbjct: 92 YYC 94
>pdb|3IDX|H Chain H, Crystal Structure Of Hiv-Gp120 Core In Complex With
Cd4-Binding Site Antibody B13, Space Group C222
pdb|3IDY|H Chain H, Crystal Structure Of Hiv-Gp120 Core In Complex With
Cd4-Binding Site Antibody B13, Space Group C2221
pdb|3IDY|B Chain B, Crystal Structure Of Hiv-Gp120 Core In Complex With
Cd4-Binding Site Antibody B13, Space Group C2221
Length = 231
Score = 32.3 bits (72), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 37/159 (23%), Positives = 62/159 (38%), Gaps = 43/159 (27%)
Query: 101 DYPVIWMKMDTAKKMEPLPISMSGSLIIHDSR-----------FQLTTDPETSTYILSIK 149
+Y + W++ K +E + +LI +D R F ++ D +T L +
Sbjct: 31 NYAMHWVRQAPGKGLEWV------ALIKYDGRNKYYADSVKGRFSISRDNSKNTLYLEMN 84
Query: 150 EIQETDAGIYKCEVIISLNNKVSAEVELIVRRPP---------IISDNSTRSVIV----- 195
++ D +Y C I L + +++ P +S ST+ V
Sbjct: 85 SLRAEDTAVYYCARDIGLKGE---HYDILTAYGPDYWGQGALVTVSSASTKGPSVFPLAP 141
Query: 196 ----SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ G T L C FP P T+SW NS AL++G
Sbjct: 142 SSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 177
>pdb|3QR2|A Chain A, Wild Type Cd147 Ig0 Domain
pdb|3QR2|B Chain B, Wild Type Cd147 Ig0 Domain
Length = 137
Score = 32.3 bits (72), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 31/76 (40%), Gaps = 17/76 (22%)
Query: 198 GQTVYLYCYANGFPAPTISWR------RDNSAALSTGGSIYRGNI-----------LKIP 240
G +V L+C A G P P I W D + L G + R +I + I
Sbjct: 36 GGSVELHCEAVGSPVPEIQWWFEGQGPNDICSQLWDGARLDRVHIHATYHQHAASTISID 95
Query: 241 NITKTDRGTYYCVAQN 256
+ + D GTY C A N
Sbjct: 96 TLVEEDTGTYECRASN 111
>pdb|1QKZ|H Chain H, 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
Length = 219
Score = 32.3 bits (72), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 35/152 (23%), Positives = 61/152 (40%), Gaps = 38/152 (25%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETD 155
DY + W++ +++E + IS G+ + RF ++ D + L + ++ D
Sbjct: 31 DYYMFWVRQTPEQRLEWVATISDGGAYTYYPDSVKGRFTISRDNAKNNLYLQMNSLKSED 90
Query: 156 AGIYKC-----------------EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEG 198
G+Y C V +S + V + P+ D + G
Sbjct: 91 TGMYYCARDPLEYYGMDYWGQGTSVAVSSAKTTAPSVYPLA---PVCGDTT--------G 139
Query: 199 QTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+V L C G FP P T++W NS +LS+G
Sbjct: 140 SSVTLGCLVKGYFPEPVTVTW---NSGSLSSG 168
>pdb|2M2D|A Chain A, Human Programmed Cell Death 1 Receptor
Length = 118
Score = 32.3 bits (72), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 23/99 (23%), Positives = 42/99 (42%), Gaps = 7/99 (7%)
Query: 90 ADLKCSV-QYADDYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQLTTDPETSTYILS 147
A CS ++ + + W +M + + + L S DSRF++T P + +S
Sbjct: 18 ATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDSRFRVTQLPNGRDFHMS 77
Query: 148 IKEIQETDAGIYKCEVI-----ISLNNKVSAEVELIVRR 181
+ + D+G Y C I + + AE+ + RR
Sbjct: 78 VVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERR 116
>pdb|3QQN|A Chain A, The Retinal Specific Cd147 Ig0 Domain: From Molecular
Structure To Biological Activity
pdb|3QQN|B Chain B, The Retinal Specific Cd147 Ig0 Domain: From Molecular
Structure To Biological Activity
Length = 137
Score = 32.3 bits (72), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 31/76 (40%), Gaps = 17/76 (22%)
Query: 198 GQTVYLYCYANGFPAPTISWR------RDNSAALSTGGSIYRGNI-----------LKIP 240
G +V L+C A G P P I W D + L G + R +I + I
Sbjct: 36 GGSVELHCEAVGSPVPEIQWWFEGQGPNDIXSQLWDGARLDRVHIHATYHQHAASTISID 95
Query: 241 NITKTDRGTYYCVAQN 256
+ + D GTY C A N
Sbjct: 96 TLVEEDTGTYECRASN 111
>pdb|2GCY|B Chain B, Humanized Antibody C25 Fab Fragment
Length = 218
Score = 32.3 bits (72), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 36/141 (25%), Positives = 57/141 (40%), Gaps = 17/141 (12%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETD 155
DY + W++ K +E + IS GS + RF ++ D +T L + ++ D
Sbjct: 31 DYYMYWVRQAPGKGLEWVATISDGGSYTYYPDSVKGRFTISRDNSKNTLYLQMNSLRAED 90
Query: 156 AGIYKC------EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG 209
+Y C + + V + P + + S S G T L C
Sbjct: 91 TAMYYCSRYRYDDAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGG-TAALGCLVKD 149
Query: 210 -FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 150 YFPEPVTVSW---NSGALTSG 167
>pdb|1RMF|H Chain H, Structures Of A Monoclonal Anti-Icam-1 Antibody R6.5
Fragment At 2.8 Angstroms Resolution
Length = 216
Score = 32.3 bits (72), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 36/148 (24%), Positives = 63/148 (42%), Gaps = 30/148 (20%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K AK +E + IS ++ +F+ +T D ++T L + + D
Sbjct: 31 DYAIHWVKESHAKSLEWIGVISAYSGDTNYNQKFKGKATMTVDKSSNTAYLELARLTSED 90
Query: 156 AGIYKCE----VIISLN----------NKVSAEVELIVRRPPIISDNSTRSVIVSEGQTV 201
+ IY C +++S + + + P+ D + SV + G V
Sbjct: 91 SAIYYCARGGWLLLSFDYWGQGTTLTVSSAKTTAPSVTPLAPVCGDTTGSSVTL--GVLV 148
Query: 202 YLYCYANGFPAP-TISWRRDNSAALSTG 228
Y FP P T++W NS +LS+G
Sbjct: 149 KGY-----FPEPVTLTW---NSGSLSSG 168
>pdb|2ENS|A Chain A, Solution Structure Of The Third Ig-Like Domain From Human
Advanced Glycosylation End Product-Specific Receptor
Length = 96
Score = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 27/60 (45%), Gaps = 5/60 (8%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVA 254
V+ G TV L C P+P I W +D +L +P I D+GTY CVA
Sbjct: 22 VAPGGTVTLTCEVPAQPSPQIHWMKDGVPLPLP-----PSPVLILPEIGPQDQGTYSCVA 76
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 293 LECHVEAYPPPAIVWIKDGV 312
L C V A P P I W+KDGV
Sbjct: 30 LTCEVPAQPSPQIHWMKDGV 49
>pdb|2E9W|A Chain A, Crystal Structure Of The Extracellular Domain Of Kit In
Complex With Stem Cell Factor (Scf)
pdb|2E9W|B Chain B, Crystal Structure Of The Extracellular Domain Of Kit In
Complex With Stem Cell Factor (Scf)
Length = 489
Score = 32.3 bits (72), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 36/174 (20%), Positives = 73/174 (41%), Gaps = 20/174 (11%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNN-KVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLY 204
L+I + D+G++ C + + V+ +E++ + I +V V++G+ V L
Sbjct: 250 LTISSARVNDSGVFMCYANNTFGSANVTTTLEVVDKGFINIFPMINTTVFVNDGENVDLI 309
Query: 205 CYANGFPAP----------TISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTY-YCV 253
FP P T + + ++ +I + L + + T+ GTY + V
Sbjct: 310 VEYEAFPKPEHQQWIYMNRTFTDKWEDYPKSENESNIRYVSELHLTRLKGTEGGTYTFLV 369
Query: 254 AQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAIVW 307
+ + V + N+ V + ++T +R G +L+C +P P I W
Sbjct: 370 SNSDVNAAIAFNVYVNTK-PEILTYDRLVNG-------MLQCVAAGFPEPTIDW 415
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 31/115 (26%), Positives = 46/115 (40%), Gaps = 25/115 (21%)
Query: 105 IWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYILSIKEIQETDAGIYKCEVI 164
I+M K E P S + S I + S LT ++ T+ G Y
Sbjct: 324 IYMNRTFTDKWEDYPKSENESNIRYVSELHLT-------------RLKGTEGGTY---TF 367
Query: 165 ISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTV--YLYCYANGFPAPTISW 217
+ N+ V+A + V +T+ I++ + V L C A GFP PTI W
Sbjct: 368 LVSNSDVNAAIAFNVYV-------NTKPEILTYDRLVNGMLQCVAAGFPEPTIDW 415
>pdb|4HKB|N Chain N, Ch67 Fab (unbound) From The Ch65-67 Lineage
pdb|4HKB|B Chain B, Ch67 Fab (unbound) From The Ch65-67 Lineage
pdb|4HKB|D Chain D, Ch67 Fab (unbound) From The Ch65-67 Lineage
pdb|4HKB|F Chain F, Ch67 Fab (unbound) From The Ch65-67 Lineage
pdb|4HKB|H Chain H, Ch67 Fab (unbound) From The Ch65-67 Lineage
pdb|4HKB|K Chain K, Ch67 Fab (unbound) From The Ch65-67 Lineage
Length = 213
Score = 32.3 bits (72), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 38/203 (18%), Positives = 75/203 (36%), Gaps = 33/203 (16%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISW--RRDNSAAL-------------------STGGS 230
SV V+ GQT + C N + W ++ A + S G+
Sbjct: 8 SVSVAPGQTATITCGGNNIGRKRVDWFQQKPGQAPVLVVYEDSDRPSGIPERFSDSNSGT 67
Query: 231 IYRGNILKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQG 284
L I + D YYC + G G K + + + AP +T+ P
Sbjct: 68 TA---TLTISRVEAGDEADYYCQVWDSDSDHVVFGGGTKLTVLGQPKAAPSVTLFPPSSE 124
Query: 285 QALQYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIE 342
+ A L C + + P A + W D + + ++++++ +S +T E
Sbjct: 125 ELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPE 184
Query: 343 R-RQFGQYACKAANKYGSAQKEI 364
+ + Y+C+ ++ + +K +
Sbjct: 185 QWKSHRSYSCQVTHEGSTVEKTV 207
>pdb|1KNO|B Chain B, Crystal Structure Of The Complex Of A Catalytic Antibody
Fab With A Transition State Analog: Structural
Similarities In Esterase-Like Abzymes
pdb|1KNO|D Chain D, Crystal Structure Of The Complex Of A Catalytic Antibody
Fab With A Transition State Analog: Structural
Similarities In Esterase-Like Abzymes
pdb|1KNO|F Chain F, Crystal Structure Of The Complex Of A Catalytic Antibody
Fab With A Transition State Analog: Structural
Similarities In Esterase-Like Abzymes
Length = 220
Score = 32.3 bits (72), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 35/147 (23%), Positives = 57/147 (38%), Gaps = 38/147 (25%)
Query: 106 WMKMDTAKKMEPLPISMSGSLIIH-----DSRFQLTTDPETSTYILSIKEIQETDAGIYK 160
W++ K +E + SGS I+ RF ++ D +T L + ++ D +Y
Sbjct: 36 WVRQAPEKGLEWVAYISSGSSTIYYADTVKGRFTISRDNPKNTLFLQMTSLRSEDTAMYY 95
Query: 161 CE-----------------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYL 203
C V +S + V + P+ D + G +V L
Sbjct: 96 CARGDYYGSRGAYWGQGTLVTVSAAKTTAPSVYPLA---PVCGDTT--------GSSVTL 144
Query: 204 YCYANG-FPAP-TISWRRDNSAALSTG 228
C G FP P T++W NS +LS+G
Sbjct: 145 GCLVKGYFPEPVTLTW---NSGSLSSG 168
>pdb|4DGV|H Chain H, Structure Of The Hepatitis C Virus Envelope Glycoprotein
E2 Antigenic Region 412-423 Bound To The Broadly
Neutralizing Antibody Hcv1, P2(1) Form
pdb|4DGY|H Chain H, Structure Of The Hepatitis C Virus Envelope Glycoprotein
E2 Antigenic Region 412-423 Bound To The Broadly
Neutralizing Antibody Hcv1, C2 Form
Length = 226
Score = 32.3 bits (72), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 37/146 (25%), Positives = 60/146 (41%), Gaps = 20/146 (13%)
Query: 100 DDYPVIWMKMDTAKKMEPLPISM--SGSLIIHDS---RFQLTTDPETSTYILSIKEIQET 154
++Y + W++ K +E L + + DS RF ++ D +T L + ++
Sbjct: 30 NNYGMHWVRQTPGKGLEWLAVIWFDENNKYYADSVRGRFTISRDNSKNTLFLQMNSLKTE 89
Query: 155 DAGIYKCEVIISLNNKVSAEVELIVRRPPI-ISDNSTRSVIV---------SEGQTVYLY 204
D +Y C ISL + + +S ST+ V + G T L
Sbjct: 90 DTAMYYCARDISLVRDAFIYFDFWGLGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALG 149
Query: 205 CYANG-FPAP-TISWRRDNSAALSTG 228
C FP P T+SW NS AL++G
Sbjct: 150 CLVKDYFPEPVTVSW---NSGALTSG 172
>pdb|2ADF|H Chain H, Crystal Structure And Paratope Determination Of 82d6a3, An
Antithrombotic Antibody Directed Against The Von
Willebrand Factor A3-Domain
Length = 218
Score = 32.0 bits (71), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 31/138 (22%), Positives = 49/138 (35%), Gaps = 33/138 (23%)
Query: 198 GQTVYLYCYANGF-------------PAPTISWR--RDNSAALSTGGSIYRGNI------ 236
G+TV + C A+G+ P + W ++ + +T G +RG
Sbjct: 15 GETVKISCKASGYTFINYGMNWVKQAPGKGLKWMGWKNTNTGETTYGEEFRGRFAFSLET 74
Query: 237 ------LKIPNITKTDRGTYYCVAQNGV------GRGMKRNIAVEVEFAPVITINRPRQG 284
L+I N+ D TY+C N G+G ++ AP + P G
Sbjct: 75 SVSTAYLQINNLKNEDTATYFCARDNPYYALDYWGQGTTVTVSSAKTTAPSVYPLAPVCG 134
Query: 285 QALQYDAILECHVEAYPP 302
L C V+ Y P
Sbjct: 135 DTTGSSVTLGCLVKGYFP 152
>pdb|3T2N|H Chain H, Human Hepsin Protease In Complex With The Fab Fragment Of
An Inhibitory Antibody
pdb|3T2N|I Chain I, Human Hepsin Protease In Complex With The Fab Fragment Of
An Inhibitory Antibody
Length = 225
Score = 32.0 bits (71), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 38/140 (27%), Positives = 56/140 (40%), Gaps = 20/140 (14%)
Query: 101 DYPVIWMKMDTAKKMEPLPI--SMSGSLIIHD---SRFQLTTDPETSTYILSIKEIQETD 155
DY + W++ + +E + + +GS D RF + D ST L I ++ D
Sbjct: 31 DYSMRWVRQAPGQGLEWMGWINTETGSPTYADDFKGRFVFSLDTSVSTAYLQISSLKAED 90
Query: 156 AGIYKCEVII------SLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG 209
+Y C +L SA + P S ST + G V Y
Sbjct: 91 TAVYYCARGFAYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDY----- 145
Query: 210 FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 146 FPEPVTVSW---NSGALTSG 162
>pdb|1KCR|L Chain L, Crystal Structure Of Antibody Pc283 In Complex With Ps1
Peptide
Length = 213
Score = 32.0 bits (71), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 46/198 (23%), Positives = 74/198 (37%), Gaps = 26/198 (13%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISW---RRDNSAALS-------------- 226
I+ S +S+ +S G+ V L C A+ +SW + + S L
Sbjct: 2 IVLTQSPKSMSMSVGERVTLSCKASENVGTYVSWYQQKPEQSPKLLIYGASNRYTGVPDR 61
Query: 227 -TGGSIYRGNILKIPNITKTDRGTYYC---VAQNGVGRGMKRNIAVEVEFAPVITINRPR 282
TG LKI ++ D Y+C + G G K I + AP ++I P
Sbjct: 62 FTGSGSATDFTLKISSVQAEDLADYHCGQTYSYPTFGGGTKLAIK-RADAAPTVSIFPPS 120
Query: 283 QGQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNN--QHYSVSHFATSDEFSDTSLRV 338
Q A + C + + P I W DG + N ++ A S ++L +
Sbjct: 121 SEQLTAGGASVVCFLNNFYPKDINVKWKIDGSERQNGVANSWTAQDSADSTYSMSSTLTL 180
Query: 339 ITIERRQFGQYACKAANK 356
E + Y C+A +K
Sbjct: 181 TKDEYERHNSYTCEATHK 198
>pdb|1NSN|H Chain H, The Crystal Structure Of Antibody N10-Staphylococcal
Nuclease Complex At 2.9 Angstroms Resolution
Length = 210
Score = 32.0 bits (71), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 6/80 (7%)
Query: 236 ILKIPNITKTDRGTYYCVAQNG-VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI-- 292
+++ ++T D GT+YC NG G+G ++ P + P G A Q +++
Sbjct: 80 FMQLNSVTTEDTGTFYCTRGNGDWGQGTTLTVSSAKTTPPSVYPLAP--GSAAQTNSMVT 137
Query: 293 LECHVEAY-PPPAIVWIKDG 311
L C V+ Y P P V G
Sbjct: 138 LGCLVKGYFPEPVTVTWNSG 157
>pdb|4HKX|B Chain B, Influenza Hemagglutinin In Complex With Ch67 Fab
Length = 214
Score = 32.0 bits (71), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 38/203 (18%), Positives = 75/203 (36%), Gaps = 33/203 (16%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISW--RRDNSAAL-------------------STGGS 230
SV V+ GQT + C N + W ++ A + S G+
Sbjct: 9 SVSVAPGQTATITCGGNNIGRKRVDWFQQKPGQAPVLVVYDSDRPSGIPEERFSDSNSGT 68
Query: 231 IYRGNILKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQG 284
L I + D YYC + G G K + + + AP +T+ P
Sbjct: 69 TA---TLTISRVEAGDEADYYCQVWDSDSDHVVFGGGTKLTVLGQPKAAPSVTLFPPSSE 125
Query: 285 QALQYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIE 342
+ A L C + + P A + W D + + ++++++ +S +T E
Sbjct: 126 ELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPE 185
Query: 343 R-RQFGQYACKAANKYGSAQKEI 364
+ + Y+C+ ++ + +K +
Sbjct: 186 QWKSHRSYSCQVTHEGSTVEKTV 208
>pdb|1R24|B Chain B, Fab From Murine Igg3 Kappa
pdb|1R24|D Chain D, Fab From Murine Igg3 Kappa
Length = 217
Score = 32.0 bits (71), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 40/156 (25%), Positives = 61/156 (39%), Gaps = 41/156 (26%)
Query: 100 DDYPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQET 154
++ + W++ K +E + IS GS I + RF ++ D +T L + ++
Sbjct: 30 SNFGMHWVRQAPEKGLEWVAYISSGGSSINYADTVKGRFTISRDNPKNTLFLQMTSLRSE 89
Query: 155 DAGIYKC--------------------EVIISLNNKVSAEVELIVRRPPIISDNSTRSVI 194
D IY C +I+S + V +V P SD S
Sbjct: 90 DTAIYYCTRGGTGTRSLYYFDYWGQGATLIVSSATTTAPSVYPLV---PGCSDTS----- 141
Query: 195 VSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
G +V L C G FP P T+ W N ALS+G
Sbjct: 142 ---GSSVTLGCLVKGYFPGPVTVKW---NYGALSSG 171
>pdb|1KTR|H Chain H, Crystal Structure Of The Anti-His Tag Antibody 3d5 Single-
Chain Fragment (Scfv) In Complex With A Oligohistidine
Peptide
Length = 114
Score = 32.0 bits (71), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 22/94 (23%), Positives = 45/94 (47%), Gaps = 9/94 (9%)
Query: 78 ISQEQIKDIAQTADLKCSVQYAD----DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSR 132
+ Q +D+ A +K S + + DY + W+K K +E + I+ + ++ +
Sbjct: 4 LQQSGPEDVKPGASVKISCKASGYTFTDYYMNWVKQSPGKGLEWIGDINPNNGGTSYNQK 63
Query: 133 FQ----LTTDPETSTYILSIKEIQETDAGIYKCE 162
F+ LT D +ST + ++ + D+ +Y CE
Sbjct: 64 FKGRATLTVDKSSSTAYMELRSLTSEDSSVYYCE 97
>pdb|3CXD|H Chain H, Crystal Structure Of Anti-Osteopontin Antibody 23c3 In
Complex With Its Epitope Peptide
pdb|3DSF|H Chain H, Crystal Structure Of Anti-Osteopontin Antibody 23c3 In
Complex With W43a Mutated Epitope Peptide
Length = 216
Score = 32.0 bits (71), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 30/73 (41%), Gaps = 3/73 (4%)
Query: 237 LKIPNITKTDRGTYYCVAQNG--VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
L++ N+ D YYCV Q G G+G ++ V+ P + P G L
Sbjct: 83 LQMNNLKTEDTAMYYCVRQMGDYWGQGTTLTVSSAVKTPPSVYPLAPGGGAISNSMVTLG 142
Query: 295 CHVEAY-PPPAIV 306
C V Y P P V
Sbjct: 143 CLVNGYFPEPVTV 155
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 44/101 (43%), Gaps = 8/101 (7%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKC--EVIISLNNKVSAEVELIVRRPPIISDNS 189
RF ++ D S L + ++ D +Y C ++ + V V+ PP + +
Sbjct: 69 RFTISRDDSQSMLYLQMNNLKTEDTAMYYCVRQMGDYWGQGTTLTVSSAVKTPPSVYPLA 128
Query: 190 TRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+S V L C NG FP P T++W N+ +L +G
Sbjct: 129 PGGGAISN-SMVTLGCLVNGYFPEPVTVTW---NAGSLGSG 165
>pdb|1F4W|H Chain H, Crystal Structure Of An Anti-Carbohydrate Antibody
Directed Against Vibrio Cholerae O1 In Complex With
Antigen
pdb|1F4X|H Chain H, Crystal Structure Of An Anti-Carbohydrate Antibody
Directed Against Vibrio Cholerae O1 In Complex With
Antigen
pdb|1F4Y|H Chain H, Crystal Structure Of An Anti-Carbohydrate Antibody
Directed Against Vibrio Cholerae O1 In Complex With
Antigen
Length = 216
Score = 32.0 bits (71), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 35/139 (25%), Positives = 57/139 (41%), Gaps = 16/139 (11%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K++E + IS G + RF ++ D +T L + +Q D
Sbjct: 32 YDMSWVRQTPEKRLEWVAFISSGGGRTSYPDTVKGRFTISRDDAKNTLYLQMSSLQSEDT 91
Query: 157 GIYKC-----EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-F 210
+Y C V+ + V PP + + S + V L C G F
Sbjct: 92 AMYYCTRHFYAVLDYWGRGTTLTVSSAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVKGYF 150
Query: 211 PAP-TISWRRDNSAALSTG 228
P P T++W NS +LS+G
Sbjct: 151 PEPVTVTW---NSGSLSSG 166
>pdb|2ARJ|L Chain L, Cd8alpha-Alpha In Complex With Yts 105.18 Fab
pdb|2ARJ|A Chain A, Cd8alpha-Alpha In Complex With Yts 105.18 Fab
Length = 211
Score = 32.0 bits (71), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 48/212 (22%), Positives = 78/212 (36%), Gaps = 28/212 (13%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISW------------------RRDNSAAL 225
I+ S S+ VS G+ V L C A+ I+W R
Sbjct: 2 IVMTQSPSSLAVSAGERVTLNCKASQNVRNNIAWYQQKPGQSPKLLIYYASYRYTGVPDR 61
Query: 226 STGGSIYRGNILKIPNITKTDRGTYYCV----AQNGVGRGMKRNIAVEVEFAPVITINRP 281
TG L I ++ D YYC + G G K + + + AP ++I P
Sbjct: 62 FTGDGFGTDFTLAINSVQADDAAFYYCQRIYNSPYTFGAGTKLEL-IRADAAPTVSIFPP 120
Query: 282 RQGQALQYDAILECHVEAYPPP--AIVWIKDGVQIMNNQHYSVSHFATSDEFSDTS--LR 337
Q A + C V + P ++ W DG + + SV+ + D S L
Sbjct: 121 SMEQLTSGGASVVCFVNNFYPRDISVKWKIDGSEQRDGVLDSVTDQDSKDSTYSMSSTLS 180
Query: 338 VITIERRQFGQYACKAANKYGSAQKEIELFDR 369
+ +E + Y C+ +K S+ ++ F+R
Sbjct: 181 LTKVEYERHNLYTCEVVHK-TSSSPVVKSFNR 211
>pdb|1XGY|H Chain H, Crystal Structure Of Anti-Meta I Rhodopsin Fab Fragment
K42- 41l
pdb|1XGY|I Chain I, Crystal Structure Of Anti-Meta I Rhodopsin Fab Fragment
K42- 41l
Length = 219
Score = 32.0 bits (71), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 58/140 (41%), Gaps = 16/140 (11%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K + +E + I ++ +F+ LT D +ST + + + D
Sbjct: 31 DYYINWVKQRPGQGLEWIGWIFPRNGNTKYNEKFKGKATLTVDKSSSTAFMQLSSLTSED 90
Query: 156 AGIYKCEVIIS-----LNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG- 209
+ +Y C +S + V PP + + S + V L C G
Sbjct: 91 SAVYFCATTVSYVMDYWGQGTTVTVSSAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVKGY 149
Query: 210 FPAP-TISWRRDNSAALSTG 228
FP P T++W NS +LS+G
Sbjct: 150 FPEPVTVTW---NSGSLSSG 166
>pdb|1SEQ|H Chain H, Fab Mnac13
Length = 225
Score = 32.0 bits (71), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 39/163 (23%), Positives = 61/163 (37%), Gaps = 29/163 (17%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y + W + KK+E + IS G + RF ++ D +T L + ++ D
Sbjct: 32 YTMSWARQTPEKKLEWVAYISKGGGSTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDT 91
Query: 157 GIYKCEVIISLNN-----------KVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYC 205
+Y C N S V PP + + S + V L C
Sbjct: 92 ALYYCARGAMFGNDFKYPMDRWGQGTSVTVSSAATTPPSVYPLAPGSAAQTN-SMVTLGC 150
Query: 206 YANG-FPAP-TISWRRDNSAALSTGGSIYRGNILKIPNITKTD 246
G FP P T++W NS +LS+G + P + K+D
Sbjct: 151 LVKGYFPEPVTVTW---NSGSLSSG-------VHTFPAVLKSD 183
>pdb|1OPG|H Chain H, Opg2 Fab Fragment
pdb|1BM3|H Chain H, Immunoglobulin Opg2 Fab-Peptide Complex
Length = 227
Score = 32.0 bits (71), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 33/147 (22%), Positives = 54/147 (36%), Gaps = 24/147 (16%)
Query: 102 YPVIWMKMDTAKKMEPLPISMSGSLIIH-----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K++E + G IH RF ++ D + L + ++ D
Sbjct: 32 YGMSWVRQTPEKRLEWVAAISGGGTYIHYPDSVKGRFTISRDNAKNNLYLQMSSLRSEDT 91
Query: 157 GIYKCE-------------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYL 203
+Y C + S V PP + + S + V L
Sbjct: 92 ALYYCTRHPFYRYDGGNYYAMDHWGQGTSVTVSAAKTTPPSVYPLAPGSAAQTN-SMVTL 150
Query: 204 YCYANG-FPAP-TISWRRDNSAALSTG 228
C G FP P T++W NS +LS+G
Sbjct: 151 GCLVKGYFPEPVTVTW---NSGSLSSG 174
>pdb|1IGI|H Chain H, 26-10 Fab:digoxin Complex-Affinity And Specificity Due To
Surface Complementarity
pdb|1IGJ|B Chain B, 26-10 Fab:digoxin Complex-Affinity And Specificity Due To
Surface Complementarity
pdb|1IGJ|D Chain D, 26-10 Fab:digoxin Complex-Affinity And Specificity Due To
Surface Complementarity
Length = 218
Score = 32.0 bits (71), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 34/143 (23%), Positives = 64/143 (44%), Gaps = 20/143 (13%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
D+ + W++ K ++ + IS + ++ +F+ LT D +ST + ++ + D
Sbjct: 31 DFYMNWVRQSHGKSLDYIGYISPYSGVTGYNQKFKGKATLTVDKSSSTAYMELRSLTSED 90
Query: 156 AGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV--------SEGQTVYLYCYA 207
+ +Y C S NK + + + S +T + + G +V L C
Sbjct: 91 SAVYYCAG--SSGNKWAMDYWGHGASVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLV 148
Query: 208 NG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 149 KGYFPEPVTLTW---NSGSLSSG 168
>pdb|3P0V|H Chain H, Anti-EgfrHER3 FAB DL11 ALONE
pdb|3P0V|I Chain I, Anti-EgfrHER3 FAB DL11 ALONE
pdb|3P0Y|H Chain H, Anti-EgfrHER3 FAB DL11 IN COMPLEX WITH DOMAIN III OF EGFR
Extracellular Region
pdb|3P11|H Chain H, Anti-EgfrHER3 FAB DL11 IN COMPLEX WITH DOMAINS I-Iii Of
The Her3 Extracellular Region
Length = 228
Score = 32.0 bits (71), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 37/144 (25%), Positives = 60/144 (41%), Gaps = 26/144 (18%)
Query: 104 VIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETDAGI 158
+ W++ K +E L IS +G + RF ++ D +T L + ++ D +
Sbjct: 34 IHWVRQAPGKGLEWLGEISAAGGYTDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAV 93
Query: 159 YKCEVIISLNNKVSAEVELIVRRPP---IISDNSTRSVIV---------SEGQTVYLYCY 206
Y C + ++VS E + +S ST+ V + G T L C
Sbjct: 94 YYC----ARESRVSFEAAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCL 149
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 150 VKDYFPEPVTVSW---NSGALTSG 170
>pdb|1CK0|H Chain H, Anti-Anti-Idiotypic Antibody Against Human Angiotensin Ii,
Unliganded Form
pdb|2CK0|H Chain H, Anti-Anti-Idiotypic Antibody Against Human Angiotensin Ii,
Complex With A Synthetic Cyclic Peptide
pdb|3CK0|H Chain H, Anti-Anti-Idiotypic Antibody Against Human Angiotensin Ii,
Complex With Human Angiotensin Ii
Length = 219
Score = 32.0 bits (71), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 29/105 (27%), Positives = 43/105 (40%), Gaps = 12/105 (11%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKC------EVIISLNNKVSAEVELIVRRPPII 185
RF ++ D S L + ++ D GIY C E + + V PP +
Sbjct: 69 RFTISRDDSQSMLYLQMNNLKTEDTGIYYCVRGRDGEAMDYWGQGTTLTVSSAKTTPPSV 128
Query: 186 SDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ S + V L C G FP P T++W NS +LS+G
Sbjct: 129 YPLAPGSAAQTN-SMVTLGCLVKGYFPEPVTVTW---NSGSLSSG 169
>pdb|3OJD|A Chain A, Anti-Indolicidin Monoclonal Antibody V2d2 (Fab Fragment)
Length = 214
Score = 32.0 bits (71), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 46/206 (22%), Positives = 84/206 (40%), Gaps = 41/206 (19%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRD-----------NSAALSTG---- 228
I+ + S+ S G++V + C A+G ++W + N++ L+ G
Sbjct: 2 IVMTQTPASLSASVGESVTITCKASGNIHNYLAWYQQKGGKSPQLLVFNASTLADGVPSR 61
Query: 229 ------GSIYRGNILKIPNITKTDRGTYYC--VAQNGVGRGMKRNIAVE-VEFAPVITIN 279
G+ Y LKI ++ D G+YYC G N+ ++ + AP ++I
Sbjct: 62 FSGSGSGTQYS---LKINSLQPEDFGSYYCQHFWSTPFTFGTGTNLEIKRADAAPTVSIF 118
Query: 280 RPRQGQALQYDAILECHVEAYPPPAI--VWIKDGVQ----IMN---NQHYSVSHFATSDE 330
P Q A + C + + P I W DG + ++N +Q S ++ S
Sbjct: 119 PPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQGGVLNSWTDQDSKDSTYSMS-- 176
Query: 331 FSDTSLRVITIERRQFGQYACKAANK 356
++L + E + Y C+A +K
Sbjct: 177 ---STLTLTKDEYERHNSYTCEATHK 199
>pdb|1I8L|A Chain A, Human B7-1CTLA-4 Co-Stimulatory Complex
pdb|1I8L|B Chain B, Human B7-1CTLA-4 Co-Stimulatory Complex
Length = 208
Score = 32.0 bits (71), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 41/150 (27%), Positives = 63/150 (42%), Gaps = 30/150 (20%)
Query: 84 KDIAQTADLKC----SVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDP 139
K++ + A L C SV+ + W K KKM + MSG + I T
Sbjct: 6 KEVKEVATLSCGHNVSVEELAQTRIYWQK---EKKM--VLTMMSGDMNIWPEYKNRTIFD 60
Query: 140 ETSTYILSIKEIQETDAGIYKCEVII----SLNNKVSAEVELIVRR---PPIISD----- 187
T+ + I ++ +D G Y+C V+ + + AEV L V+ P ISD
Sbjct: 61 ITNNLSIVILALRPSDEGTYECVVLKYEKDAFKREHLAEVTLSVKADFPTPSISDFEIPT 120
Query: 188 NSTRSVIVSEGQTVYLYCYANGFPAPTISW 217
++ R +I S + GFP P +SW
Sbjct: 121 SNIRRIICST---------SGGFPEPHLSW 141
>pdb|3RRQ|A Chain A, Crystal Structure Of The Extracellular Domain Of Human
Pd-1
Length = 129
Score = 31.6 bits (70), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 22/99 (22%), Positives = 42/99 (42%), Gaps = 7/99 (7%)
Query: 90 ADLKCSV-QYADDYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQLTTDPETSTYILS 147
A CS ++ + + W +M + + + L S D RF++T P + +S
Sbjct: 19 ATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDCRFRVTQLPNGRDFHMS 78
Query: 148 IKEIQETDAGIYKCEVI-----ISLNNKVSAEVELIVRR 181
+ + D+G Y C I + + + AE+ + RR
Sbjct: 79 VVRARRNDSGTYLCGAISLAPKLQIKESLRAELRVTERR 117
>pdb|1DR9|A Chain A, Crystal Structure Of A Soluble Form Of B7-1 (Cd80)
Length = 201
Score = 31.6 bits (70), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 41/150 (27%), Positives = 63/150 (42%), Gaps = 30/150 (20%)
Query: 84 KDIAQTADLKC----SVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDP 139
K++ + A L C SV+ + W K KKM + MSG + I T
Sbjct: 6 KEVKEVATLSCGHNVSVEELAQTRIYWQK---EKKM--VLTMMSGDMNIWPEYKNRTIFD 60
Query: 140 ETSTYILSIKEIQETDAGIYKCEVII----SLNNKVSAEVELIVRR---PPIISD----- 187
T+ + I ++ +D G Y+C V+ + + AEV L V+ P ISD
Sbjct: 61 ITNNLSIVILALRPSDEGTYECVVLKYEKDAFKREHLAEVTLSVKADFPTPSISDFEIPT 120
Query: 188 NSTRSVIVSEGQTVYLYCYANGFPAPTISW 217
++ R +I S + GFP P +SW
Sbjct: 121 SNIRRIICST---------SGGFPEPHLSW 141
>pdb|2EC8|A Chain A, Crystal Structure Of The Exctracellular Domain Of The
Receptor Tyrosine Kinase, Kit
Length = 524
Score = 31.6 bits (70), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 36/174 (20%), Positives = 73/174 (41%), Gaps = 20/174 (11%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNN-KVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLY 204
L+I + D+G++ C + + V+ +E++ + I +V V++G+ V L
Sbjct: 275 LTISSARVNDSGVFMCYANNTFGSANVTTTLEVVDKGFINIFPMINTTVFVNDGENVDLI 334
Query: 205 CYANGFPAP----------TISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTY-YCV 253
FP P T + + ++ +I + L + + T+ GTY + V
Sbjct: 335 VEYEAFPKPEHQQWIYMNRTFTDKWEDYPKSENESNIRYVSELHLTRLKGTEGGTYTFLV 394
Query: 254 AQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAIVW 307
+ + V + N+ V + ++T +R G +L+C +P P I W
Sbjct: 395 SNSDVNAAIAFNVYVNTK-PEILTYDRLVNG-------MLQCVAAGFPEPTIDW 440
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 30/116 (25%), Positives = 46/116 (39%), Gaps = 27/116 (23%)
Query: 105 IWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYILSIKEIQETDAGIYKCEVI 164
I+M K E P S + S I + S LT ++ T+ G Y
Sbjct: 349 IYMNRTFTDKWEDYPKSENESNIRYVSELHLT-------------RLKGTEGGTY---TF 392
Query: 165 ISLNNKVSAEVELIV---RRPPIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISW 217
+ N+ V+A + V +P I++ + + + L C A GFP PTI W
Sbjct: 393 LVSNSDVNAAIAFNVYVNTKPEILTYDRLVNGM--------LQCVAAGFPEPTIDW 440
>pdb|1AE6|H Chain H, Igg-Fab Fragment Of Mouse Monoclonal Antibody Ctm01
Length = 218
Score = 31.6 bits (70), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 36/143 (25%), Positives = 57/143 (39%), Gaps = 19/143 (13%)
Query: 101 DYPVIWMKMDTAKKMEPLPISMSGSL-IIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + WMK + +E + GS ++ +F+ LT D +ST + + + D
Sbjct: 31 DYYINWMKQKPGQGLEWIGWIDPGSGNTKYNEKFKGKATLTVDTSSSTAYMQLSSLTSED 90
Query: 156 AGIYKCE--------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYA 207
+Y C + S V PP + + S + V L C
Sbjct: 91 TAVYFCAREKTTYYYAMDYWGQGTSVTVSAAKTTPPSVYPLAPGSAAQTNSM-VTLGCLV 149
Query: 208 NG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 150 KGYFPEPVTVTW---NSGSLSSG 169
>pdb|3PIQ|L Chain L, Crystal Structure Of Human 2909 Fab, A Quaternary
Structure-Specific Antibody Against Hiv-1
pdb|3PIQ|B Chain B, Crystal Structure Of Human 2909 Fab, A Quaternary
Structure-Specific Antibody Against Hiv-1
pdb|3PIQ|D Chain D, Crystal Structure Of Human 2909 Fab, A Quaternary
Structure-Specific Antibody Against Hiv-1
pdb|3PIQ|F Chain F, Crystal Structure Of Human 2909 Fab, A Quaternary
Structure-Specific Antibody Against Hiv-1
pdb|3PIQ|I Chain I, Crystal Structure Of Human 2909 Fab, A Quaternary
Structure-Specific Antibody Against Hiv-1
pdb|3PIQ|K Chain K, Crystal Structure Of Human 2909 Fab, A Quaternary
Structure-Specific Antibody Against Hiv-1
Length = 211
Score = 31.6 bits (70), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 35/200 (17%), Positives = 75/200 (37%), Gaps = 27/200 (13%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRR---------------DNSAALS---TGGSIYR 233
SV V+ G+T + C N + W + D + + +G +
Sbjct: 9 SVSVAPGKTARITCGGNNIANKNVHWYQQKPGQAPVLVIYYDDDRPSGIPDRFSGSNSGN 68
Query: 234 GNILKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQGQAL 287
L I + D YYC + G G + + + + AP +T+ P +
Sbjct: 69 TATLTISRVEAGDEADYYCQVWDSNSDHVVFGGGTQLTVLGQPKAAPSVTLFPPSSEELQ 128
Query: 288 QYDAILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-R 344
A L C + + P A + W D + + ++++++ +S +T E+ +
Sbjct: 129 ANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWK 188
Query: 345 QFGQYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 189 SHRSYSCQVTHEGSTVEKTV 208
>pdb|2FJF|H Chain H, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|B Chain B, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|D Chain D, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|F Chain F, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|I Chain I, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|K Chain K, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|N Chain N, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|P Chain P, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|R Chain R, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|T Chain T, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|V Chain V, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|X Chain X, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJG|H Chain H, Structure Of The G6 Fab, A Phage Derived Fab Fragment, In
Complex With Vegf
pdb|2FJG|B Chain B, Structure Of The G6 Fab, A Phage Derived Fab Fragment, In
Complex With Vegf
Length = 227
Score = 31.6 bits (70), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 36/147 (24%), Positives = 58/147 (39%), Gaps = 27/147 (18%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETD 155
DY + W++ K +E + I+ +G + RF ++ D +T L + ++ D
Sbjct: 31 DYWIHWVRQAPGKGLEWVAGITPAGGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAED 90
Query: 156 AGIYKCEVII-------------SLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVY 202
+Y C + +L SA + P S ST + G V
Sbjct: 91 TAVYYCARFVFFLPYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVK 150
Query: 203 LYCYANGFPAP-TISWRRDNSAALSTG 228
Y FP P T+SW NS AL++G
Sbjct: 151 DY-----FPEPVTVSW---NSGALTSG 169
>pdb|1IGT|B Chain B, Structure Of Immunoglobulin
pdb|1IGT|D Chain D, Structure Of Immunoglobulin
Length = 444
Score = 31.6 bits (70), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 36/151 (23%), Positives = 60/151 (39%), Gaps = 37/151 (24%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETD 155
DY + W++ K++E + IS G + RF ++ D +T L + ++ D
Sbjct: 31 DYYMYWVRQTPEKRLEWVAYISNGGGSTYYPDTVKGRFTISRDNAKNTLYLQMSRLKSED 90
Query: 156 AGIYKCE----------------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQ 199
+Y C V +S + V + P+ D + G
Sbjct: 91 TAMYYCARHGGYYAMDYWGQGTTVTVSSAKTTAPSVYPLA---PVCGDTT--------GS 139
Query: 200 TVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+V L C G FP P T++W NS +LS+G
Sbjct: 140 SVTLGCLVKGYFPEPVTLTW---NSGSLSSG 167
>pdb|1J89|A Chain A, Human High Affinity Fc Receptor Fc(Epsilon)ri(Alpha),
Tetragonal Crystal Form 2
pdb|1J89|B Chain B, Human High Affinity Fc Receptor Fc(Epsilon)ri(Alpha),
Tetragonal Crystal Form 2
pdb|1J89|C Chain C, Human High Affinity Fc Receptor Fc(Epsilon)ri(Alpha),
Tetragonal Crystal Form 2
pdb|1J89|D Chain D, Human High Affinity Fc Receptor Fc(Epsilon)ri(Alpha),
Tetragonal Crystal Form 2
pdb|1J89|E Chain E, Human High Affinity Fc Receptor Fc(Epsilon)ri(Alpha),
Tetragonal Crystal Form 2
pdb|1J88|A Chain A, Human High Affinity Fc Receptor Fc(epsilon)ri(alpha),
Tetragonal Crystal Form 1
pdb|1J88|B Chain B, Human High Affinity Fc Receptor Fc(epsilon)ri(alpha),
Tetragonal Crystal Form 1
pdb|1J88|C Chain C, Human High Affinity Fc Receptor Fc(epsilon)ri(alpha),
Tetragonal Crystal Form 1
pdb|1J88|D Chain D, Human High Affinity Fc Receptor Fc(epsilon)ri(alpha),
Tetragonal Crystal Form 1
pdb|1J88|E Chain E, Human High Affinity Fc Receptor Fc(epsilon)ri(alpha),
Tetragonal Crystal Form 1
Length = 172
Score = 31.6 bits (70), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 30/111 (27%), Positives = 47/111 (42%), Gaps = 10/111 (9%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYC 205
L+I + D+G YKC+ S V L V ++ S +V EGQ ++L C
Sbjct: 53 LNIVNAKFEDSGEYKCQ---HQQVNESEPVYLEVFSDWLLLQASAE--VVMEGQPLFLRC 107
Query: 206 YA-NGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQ 255
+ + + + +D A Y + + I N T D GTYYC +
Sbjct: 108 HGWRNWDVYKVIYYKDGEAL----KYWYENHNISITNATVEDSGTYYCTGK 154
>pdb|2Q8A|H Chain H, Structure Of The Malaria Antigen Ama1 In Complex With A
Growth- Inhibitory Antibody
Length = 210
Score = 31.6 bits (70), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 28/70 (40%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECH 296
L++ ++T D YYC + G+G ++ P + P G L C
Sbjct: 81 LQLSSLTSEDTAVYYCTLSHFWGQGTTLTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCL 140
Query: 297 VEAYPPPAIV 306
V+ Y P ++
Sbjct: 141 VKGYFPESVT 150
>pdb|3QOT|H Chain H, Crystal Structure Of Human Germline Antibody 1-69B3
Length = 228
Score = 31.6 bits (70), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 37/169 (21%), Positives = 68/169 (40%), Gaps = 26/169 (15%)
Query: 79 SQEQIKDIAQTADLKCSVQYA--DDYPVIWMKMDTAKKMEPL----PISMSGSLIIH-DS 131
S ++K + + C Y + W++ + +E + PI + +
Sbjct: 7 SGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQG 66
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPI-ISDNST 190
R +T D TST + + ++ D +Y C + + + E++ + + +S ST
Sbjct: 67 RVTITADESTSTAYMELSSLRSEDTAVYYC----ARYDGIYGELDFWGQGTLVTVSSAST 122
Query: 191 RSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ V + G T L C FP P T+SW NS AL++G
Sbjct: 123 KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 168
>pdb|3U7W|L Chain L, Crystal Structure Of Nih45-46 Fab
pdb|3U7Y|L Chain L, Structure Of Nih45-46 Fab In Complex With Gp120 Of 93th057
Hiv
Length = 210
Score = 31.6 bits (70), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 30/126 (23%), Positives = 50/126 (39%), Gaps = 7/126 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEF-APVITINRPRQGQALQYDAILEC 295
L I N+ D G YYC G+G K + ++ AP + I P Q A + C
Sbjct: 71 LSISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKSGTASVVC 130
Query: 296 HVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ---YA 350
+ + P + W D N SV+ + D S +T+ + + + YA
Sbjct: 131 LLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHKVYA 189
Query: 351 CKAANK 356
C+ ++
Sbjct: 190 CEVTHQ 195
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 39/95 (41%), Gaps = 16/95 (16%)
Query: 144 YILSIKEIQETDAGIYKCEV--IISLNNKVSAEVELIVRRPPII----SDNSTRSVIVSE 197
Y LSI ++ D G+Y C+ KV +++ V P + SD +S S
Sbjct: 69 YNLSISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKSGTAS- 127
Query: 198 GQTVYLYCYANGF--PAPTISWRRDNSAALSTGGS 230
+ C N F + W+ DN AL +G S
Sbjct: 128 -----VVCLLNNFYPREAKVQWKVDN--ALQSGNS 155
>pdb|3FZU|H Chain H, Igg1 Fab Characterized By HD EXCHANGE
pdb|3FZU|C Chain C, Igg1 Fab Characterized By HD EXCHANGE
Length = 223
Score = 31.6 bits (70), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 35/145 (24%), Positives = 62/145 (42%), Gaps = 25/145 (17%)
Query: 100 DDYPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQET 154
++Y + W++ + +E + IS SG + RF ++ + +T L + ++
Sbjct: 32 NNYYMDWVRQAPGQGLEWVSRISSSGDPTWYADSVKGRFTISRENAKNTLFLQMNSLRAE 91
Query: 155 DAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYC 205
D +Y C + + ++ V + V S ST+ V + G T L C
Sbjct: 92 DTAVYYCASLTTGSDSWGQGVLVTV------SSASTKGPSVFPLAPSSKSTSGGTAALGC 145
Query: 206 YANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 146 LVKDYFPEPVTVSW---NSGALTSG 167
>pdb|2Q8B|H Chain H, Structure Of The Malaria Antigen Ama1 In Complex With A
Growth- Inhibitory Antibody
Length = 210
Score = 31.6 bits (70), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 28/70 (40%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECH 296
L++ ++T D YYC + G+G ++ P + P G L C
Sbjct: 81 LQLSSLTSEDTAVYYCTLSHFWGQGTTLTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCL 140
Query: 297 VEAYPPPAIV 306
V+ Y P ++
Sbjct: 141 VKGYFPESVT 150
>pdb|3QEG|H Chain H, Crystal Structure Of Human N12-I2 Fab, An Adcc And
Neutralizing Anti- Hiv-1 Env Antibody
Length = 239
Score = 31.6 bits (70), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 15/94 (15%)
Query: 79 SQEQIKDIAQTADLKCSVQYA--DDYPVIWMKMDTAKKMEPLPISMSGSLIIHD------ 130
S ++K + + C Y + W++ + +E M G + I D
Sbjct: 7 SGAEVKKPGSSVKVSCRASRGTFSSYGITWVRQAPGQGLE----WMGGIIPIFDVTNYAQ 62
Query: 131 ---SRFQLTTDPETSTYILSIKEIQETDAGIYKC 161
R +TTD E ST + ++ ++ D+ +Y C
Sbjct: 63 NFQGRVAITTDAEMSTAYMELRSLKSEDSAVYYC 96
>pdb|4DKE|H Chain H, Crystal Structure Of Human Interleukin-34 Bound To Fab1.1
pdb|4DKE|I Chain I, Crystal Structure Of Human Interleukin-34 Bound To Fab1.1
Length = 230
Score = 31.6 bits (70), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 44/108 (40%), Gaps = 14/108 (12%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTR 191
RF ++ D +T L + ++ D +Y C + +K A +S ST+
Sbjct: 67 RFTISADTSKNTAYLQMNSLRAEDTAVYYCARGLGKGSKRGAMDYWGQGTLVTVSSASTK 126
Query: 192 SVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
V + G T L C FP P T+SW NS AL++G
Sbjct: 127 GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 171
>pdb|1A6T|A Chain A, Fab Fragment Of Mab1-Ia Monoclonal Antibody To Human
Rhinovirus 14 Nim-Ia Site
pdb|1A6T|C Chain C, Fab Fragment Of Mab1-Ia Monoclonal Antibody To Human
Rhinovirus 14 Nim-Ia Site
Length = 210
Score = 31.6 bits (70), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 33/128 (25%), Positives = 51/128 (39%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I + D TYYC + G G K + + AP ++I P Q A
Sbjct: 72 LTISGVEAEDAATYYCQQYSSHPLTFGGGTKLELK-RADAAPTVSIFPPSSEQLTSGGAS 130
Query: 293 LECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQ 348
+ C + + P I W DG + N S + + D +S +S +T E +
Sbjct: 131 VVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 190
Query: 349 YACKAANK 356
Y C+A +K
Sbjct: 191 YTCEATHK 198
>pdb|3MJ6|A Chain A, Crystal Structure Of The Gammadelta T Cell Costimulatory
Receptor Junctional Adhesion Molecule-Like Protein, Jaml
pdb|3MJ7|A Chain A, Crystal Structure Of The Complex Of Jaml And Coxsackie And
Adenovirus Receptor, Car
pdb|3MJ9|A Chain A, Crystal Structure Of Jaml In Complex With The Stimulatory
Antibody Hl4e10
Length = 268
Score = 31.6 bits (70), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 11/91 (12%)
Query: 86 IAQTADLKCSVQYADDYPVI---WMKMDTAKKMEPLPIS-----MSG---SLIIHDSRFQ 134
+ T ++CS+Q ++ V WM + E +S SG SL +R
Sbjct: 132 VGDTTQMRCSIQSTEEKRVTKVNWMFSSGSHTEEETVLSYDSNMRSGKFQSLGRFRNRVD 191
Query: 135 LTTDPETSTYILSIKEIQETDAGIYKCEVII 165
LT D + + ++ ++E+D GIY C + +
Sbjct: 192 LTGDISRNDGSIKLQTVKESDQGIYTCSIYV 222
Score = 28.5 bits (62), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 34/147 (23%), Positives = 59/147 (40%), Gaps = 18/147 (12%)
Query: 69 SQRTPTISYISQEQIKDIAQTADLKCSVQYADDYPVI---WMKMDTAKKMEPLPISMSGS 125
SQ P ++ S + + ++ + C VQ ++ V W+ + +
Sbjct: 2 SQGLPGLTVSSPQLRVHVGESVLMGCVVQRTEEKHVDRVDWLFSKDKDDASEYVLFYYSN 61
Query: 126 LIIHDSRFQ----LTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRR 181
L + RFQ L D + L ++++Q+ D GIY CE I L N E +V +
Sbjct: 62 LSVPTGRFQNRSHLVGDTFHNDGSLLLQDVQKADEGIYTCE--IRLKN------ESMVMK 113
Query: 182 PPI---ISDNSTRSVIVSEGQTVYLYC 205
P+ + R + V G T + C
Sbjct: 114 KPVELWVLPEEPRDLRVRVGDTTQMRC 140
>pdb|4DVB|A Chain A, The Crystal Structure Of The Fab Fragment Of Pro-upa
Antibody Mab-112
pdb|4DVB|H Chain H, The Crystal Structure Of The Fab Fragment Of Pro-upa
Antibody Mab-112
Length = 213
Score = 31.6 bits (70), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 40/165 (24%), Positives = 68/165 (41%), Gaps = 24/165 (14%)
Query: 80 QEQIKDIAQ---TADLKCSVQ--YADDYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDS-- 131
QE D+ + + L CS Y + W++ K++E + I+ GS DS
Sbjct: 5 QESGGDLVKPGGSLKLSCSASGFTFSRYAMSWVRQTPEKRLEWVASITNGGSTYYSDSVK 64
Query: 132 -RFQLTTDPETSTYILSIKEIQETDAGIYKCE------VIISLNNKVSAEVELIVRRPPI 184
RF ++ D + L + ++ D +Y CE + + V PP
Sbjct: 65 GRFIISRDNARNILSLQMSSLRSEDTAMYYCERGELTYAMDYWGQGTTVTVSSAKTTPPS 124
Query: 185 ISDNSTRSVIVSEGQTVYLYCYANGFPAP-TISWRRDNSAALSTG 228
+ + + +V+ G V Y FP P T++W NS +LS+G
Sbjct: 125 VYPLAPGNSMVTLGCLVKGY-----FPEPVTVTW---NSGSLSSG 161
>pdb|1UWE|H Chain H, Molecular Mechanism Of Enantioselective Proton Transfer To
Carbon In Catalytic Antibody 14d9
pdb|1UWE|V Chain V, Molecular Mechanism Of Enantioselective Proton Transfer To
Carbon In Catalytic Antibody 14d9
pdb|1UWE|Y Chain Y, Molecular Mechanism Of Enantioselective Proton Transfer To
Carbon In Catalytic Antibody 14d9
Length = 218
Score = 31.6 bits (70), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 34/143 (23%), Positives = 59/143 (41%), Gaps = 22/143 (15%)
Query: 101 DYPVIWMKMDTAKKMEPL----PISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQ 152
D+ + W+K +E + P + G+ ++ +F+ LT D +ST + + +
Sbjct: 29 DFTIYWVKQSHGDSLEWIGGIDPHNGGGA---YNQKFRVKATLTVDTSSSTAYIHLNSLT 85
Query: 153 ETDAGIYKCEVIIS-----LNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYA 207
D+ +Y C + + V + P + + S S G T L C
Sbjct: 86 SEDSAVYYCAIFYGNFFDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTS-GGTAALGCLV 144
Query: 208 NG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 145 KDYFPEPVTVSW---NSGALTSG 164
>pdb|1WWC|A Chain A, Nt3 Binding Domain Of Human Trkc Receptor
Length = 118
Score = 31.6 bits (70), Expect = 0.77, Method: Composition-based stats.
Identities = 29/116 (25%), Positives = 50/116 (43%), Gaps = 7/116 (6%)
Query: 266 IAVEVEFAP-VITINRPRQGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSH 324
+A+ V + P V+++ P L+ + +E V PPP + W+ +G + ++ V +
Sbjct: 1 VALTVYYPPRVVSLEEPE----LRLEHCIEFVVRGNPPPTLHWLHNGQPLRESKIIHVEY 56
Query: 325 FATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIE-LFDRETQTGDETFP 379
+ E S+ L G Y A N G+A + I F +E DE P
Sbjct: 57 YQEG-EISEGCLLFNKPTHYNNGNYTLIAKNPLGTANQTINGHFLKEPFPVDEVSP 111
>pdb|1F2Q|A Chain A, Crystal Structure Of The Human High-Affinity Ige Receptor
pdb|1J86|A Chain A, Human High Affinity Fc Receptor Fc(Epsilon)ri(Alpha),
Monoclinic Crystal Form 2
pdb|1J86|B Chain B, Human High Affinity Fc Receptor Fc(Epsilon)ri(Alpha),
Monoclinic Crystal Form 2
pdb|1RPQ|A Chain A, High Affinity Ige Receptor (Alpha Chain) Complexed With
Tight-Binding E131 'zeta' Peptide From Phage Display
pdb|1RPQ|B Chain B, High Affinity Ige Receptor (Alpha Chain) Complexed With
Tight-Binding E131 'zeta' Peptide From Phage Display
pdb|1RPQ|C Chain C, High Affinity Ige Receptor (Alpha Chain) Complexed With
Tight-Binding E131 'zeta' Peptide From Phage Display
pdb|1RPQ|D Chain D, High Affinity Ige Receptor (Alpha Chain) Complexed With
Tight-Binding E131 'zeta' Peptide From Phage Display
Length = 176
Score = 31.6 bits (70), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 30/111 (27%), Positives = 47/111 (42%), Gaps = 10/111 (9%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYC 205
L+I + D+G YKC+ S V L V ++ S +V EGQ ++L C
Sbjct: 53 LNIVNAKFEDSGEYKCQ---HQQVNESEPVYLEVFSDWLLLQASAE--VVMEGQPLFLRC 107
Query: 206 YA-NGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQ 255
+ + + + +D A Y + + I N T D GTYYC +
Sbjct: 108 HGWRNWDVYKVIYYKDGEAL----KYWYENHNISITNATVEDSGTYYCTGK 154
>pdb|3ZYI|A Chain A, Netring2 In Complex With Ngl2
Length = 452
Score = 31.6 bits (70), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 8/82 (9%)
Query: 183 PIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGG-----SIYRGNIL 237
P I D + R + +SEG+ L C P ++ W N LS S+ L
Sbjct: 353 PFIMD-APRDLNISEGRMAELKCRTP--PMSSVKWLLPNGTVLSHASRHPRISVLNDGTL 409
Query: 238 KIPNITKTDRGTYYCVAQNGVG 259
++ +D G Y C+ N G
Sbjct: 410 NFSHVLLSDTGVYTCMVTNVAG 431
>pdb|3AAZ|B Chain B, Crystal Structure Of The Humanized Recombinant Fab
Fragment Of A Murine; Antibody
pdb|3AAZ|L Chain L, Crystal Structure Of The Humanized Recombinant Fab
Fragment Of A Murine; Antibody
Length = 229
Score = 31.6 bits (70), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 45/190 (23%), Positives = 71/190 (37%), Gaps = 16/190 (8%)
Query: 181 RPPIISDNSTRSVIVSEGQTVYLYCYANGFPAP-----TISWRRDNSAALSTGGSIYRGN 235
P IS S++S++ S G T + +P +S R +G
Sbjct: 17 EPASISCRSSQSIVHSNGHTYLEWYLQKPGQSPRLLIYQVSTRFSGVPDRFSGSGSGTDF 76
Query: 236 ILKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
LKI + D G YYC + V G+G K I V AP + I P Q A
Sbjct: 77 TLKISRVEAEDVGVYYCFQASLVPLTFGQGTKLEIKRTVA-APSVFIFPPSDEQLKSGTA 135
Query: 292 ILECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 136 SVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKH 194
Query: 349 --YACKAANK 356
YAC+ ++
Sbjct: 195 KVYACEVTHQ 204
>pdb|2G2R|H Chain H, Green-Fluorescent Antibody 11g10 In Complex With Its
Hapten (Nitro-Stilbene Derivative)
pdb|2G2R|B Chain B, Green-Fluorescent Antibody 11g10 In Complex With Its
Hapten (Nitro-Stilbene Derivative)
Length = 219
Score = 31.6 bits (70), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 35/143 (24%), Positives = 62/143 (43%), Gaps = 23/143 (16%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETDA 156
Y + WMK K++E + I+ ++ +F+ LT D ++T + + + D+
Sbjct: 32 YYMNWMKQSHGKRLEWIAVINPYNGFTTYNQKFKGKATLTVDKSSNTAYMDLNSLTSEDS 91
Query: 157 GIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYCYA 207
+Y C ++V +V +S T + V + G +V L C
Sbjct: 92 AVYYCVPYDYAADRVYWGHGTLV----TVSTAKTTAPSVYPLAPVCGGTTGSSVTLGCLV 147
Query: 208 NG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 148 KGYFPEPVTLTW---NSGSLSSG 167
>pdb|3SKU|E Chain E, Herpes Simplex Virus Glycoprotein D Bound To The Human
Receptor Nectin-1
pdb|3SKU|D Chain D, Herpes Simplex Virus Glycoprotein D Bound To The Human
Receptor Nectin-1
pdb|3SKU|F Chain F, Herpes Simplex Virus Glycoprotein D Bound To The Human
Receptor Nectin-1
Length = 319
Score = 31.6 bits (70), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 50/240 (20%), Positives = 90/240 (37%), Gaps = 36/240 (15%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVI-VSEGQ----T 200
+ + ++ D G+Y CE +++ L V P T++V+ +GQ
Sbjct: 79 IRLSRLELEDEGVYICEFATFPTGNRESQLNLTVMAKPTNWIEGTQAVLRAKKGQDDKVL 138
Query: 201 VYLYCYANGFPAPTISW--RRDNSAAL----STGGSIYRGNILKIPNITKTDRGTYYCVA 254
V ANG P +SW R A + G++ + ++ + + + C+
Sbjct: 139 VATCTSANGKPPSVVSWETRLKGEAEYQEIRNPNGTVTVISRYRLVPSREAHQQSLACIV 198
Query: 255 QNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQ-YDAILECHVEAYPPPA-IVW----- 307
+ R K ++ + V++ P +TI LQ D L C +A PP W
Sbjct: 199 NYHMDR-FKESLTLNVQYEPEVTIEGFDGNWYLQRMDVKLTCKADANPPATEYHWTTLNG 257
Query: 308 -IKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
+ GV+ N + F +S G Y C+A N G+ ++E+
Sbjct: 258 SLPKGVEAQNRTLF----FKGPINYSLA------------GTYICEATNPIGTRSGQVEV 301
>pdb|3TNN|H Chain H, Crystal Structure Of N5-I5 Fab, An Adcc Mediating And
Non-Neutralizing Cd4i Anti-Hiv- 1 Antibody.
pdb|3TNN|A Chain A, Crystal Structure Of N5-I5 Fab, An Adcc Mediating And
Non-Neutralizing Cd4i Anti-Hiv- 1 Antibody.
pdb|3TNN|C Chain C, Crystal Structure Of N5-I5 Fab, An Adcc Mediating And
Non-Neutralizing Cd4i Anti-Hiv- 1 Antibody.
pdb|3TNN|E Chain E, Crystal Structure Of N5-I5 Fab, An Adcc Mediating And
Non-Neutralizing Cd4i Anti-Hiv- 1 Antibody
Length = 226
Score = 31.6 bits (70), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 38/145 (26%), Positives = 61/145 (42%), Gaps = 26/145 (17%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSG-SLIIHDS---RFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K +E + I+ SG + DS RF ++ D +T L + ++ D
Sbjct: 32 YAMSWVRQAPGKGLEWVSSINNSGRNTFSADSVKGRFTISRDNSKNTLFLVMNSLRAEDT 91
Query: 157 GIYKCEVIISLNNKVS--AEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYC 205
+Y C + L + L+ +S ST+ V + G T L C
Sbjct: 92 AVYYCAKDLRLGGGSDYWGQGTLVT-----VSSASTKGPSVFPLAPSSKSTSGGTAALGC 146
Query: 206 YANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 147 LVKDYFPEPVTVSW---NSGALTSG 168
>pdb|1O7V|A Chain A, High Resolution Structure Of Siglec-7
pdb|2HRL|A Chain A, Siglec-7 In Complex With Gt1b
pdb|2DF3|A Chain A, The Structure Of Siglec-7 In Complex With
Alpha(2,3)ALPHA(2,6) Disialyl Lactotetraosyl
2-(Trimethylsilyl)ethyl
pdb|1O7S|A Chain A, High Resolution Structure Of Siglec-7
pdb|2G5R|A Chain A, Crystal Structure Of Siglec-7 In Complex With
Methyl-9-(Aminooxalyl- Amino)-9-Deoxyneu5ac
(Oxamido-Neu5ac)
Length = 127
Score = 31.6 bits (70), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIY 159
RF L DP+T LSI++ + +DAG Y
Sbjct: 77 RFHLLGDPQTKNCTLSIRDARMSDAGRY 104
>pdb|1J87|A Chain A, Human High Affinity Fc Receptor Fc(Epsilon)ri(Alpha),
Hexagonal Crystal Form 1
Length = 172
Score = 31.6 bits (70), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 30/111 (27%), Positives = 47/111 (42%), Gaps = 10/111 (9%)
Query: 146 LSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYC 205
L+I + D+G YKC+ S V L V ++ S +V EGQ ++L C
Sbjct: 53 LNIVNAKFEDSGEYKCQ---HQQVNESEPVYLEVFSDWLLLQASAE--VVMEGQPLFLRC 107
Query: 206 YA-NGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQ 255
+ + + + +D A Y + + I N T D GTYYC +
Sbjct: 108 HGWRNWDVYKVIYYKDGEAL----KYWYENHNISITNATVEDSGTYYCTGK 154
>pdb|1NKO|A Chain A, Energetic And Structural Basis Of Sialylated
Oligosaccharide Recognition By The Natural Killer Cell
Inhibitory Receptor P75AIRM1 OR SIGLEC-7
Length = 132
Score = 31.6 bits (70), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIY 159
RF L DP+T LSI++ + +DAG Y
Sbjct: 76 RFHLLGDPQTKNCTLSIRDARMSDAGRY 103
>pdb|4DN4|H Chain H, Crystal Structure Of The Complex Between Cnto888 Fab And
Mcp-1 Mutant P8a
Length = 228
Score = 31.6 bits (70), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 37/169 (21%), Positives = 68/169 (40%), Gaps = 26/169 (15%)
Query: 79 SQEQIKDIAQTADLKCSVQYA--DDYPVIWMKMDTAKKMEPL----PISMSGSLIIH-DS 131
S ++K + + C Y + W++ + +E + PI + +
Sbjct: 7 SGAEVKKPGSSVKVSCKASGGTFSSYGISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQG 66
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPI-ISDNST 190
R +T D TST + + ++ D +Y C + + + E++ + + +S ST
Sbjct: 67 RVTITADESTSTAYMELSSLRSEDTAVYYC----ARYDGIYGELDFWGQGTLVTVSSAST 122
Query: 191 RSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ V + G T L C FP P T+SW NS AL++G
Sbjct: 123 KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 168
>pdb|4FMF|A Chain A, Crystal Structure Of Human Nectin-1 Full Ectodomain
(D1-D3)
pdb|4FMF|B Chain B, Crystal Structure Of Human Nectin-1 Full Ectodomain
(D1-D3)
pdb|4FMF|C Chain C, Crystal Structure Of Human Nectin-1 Full Ectodomain
(D1-D3)
pdb|4FMF|D Chain D, Crystal Structure Of Human Nectin-1 Full Ectodomain
(D1-D3)
Length = 313
Score = 31.6 bits (70), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 51/247 (20%), Positives = 92/247 (37%), Gaps = 36/247 (14%)
Query: 139 PETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVI-VSE 197
P + + + ++ D G+Y CE +++ L V P T++V+ +
Sbjct: 72 PSFTDGTIRLSRLELEDEGVYICEFATFPTGNRESQLNLTVMAKPTNWIEGTQAVLRAKK 131
Query: 198 GQ----TVYLYCYANGFPAPTISW--RRDNSAAL----STGGSIYRGNILKIPNITKTDR 247
GQ V ANG P +SW R A + G++ + ++ + +
Sbjct: 132 GQDDKVLVATCTSANGKPPSVVSWETRLKGEAEYQEIRNPNGTVTVISRYRLVPSREAHQ 191
Query: 248 GTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQ-YDAILECHVEAYPPPA-I 305
+ C+ + R K ++ + V++ P +TI LQ D L C +A PP
Sbjct: 192 QSLACIVNYHMDR-FKESLTLNVQYEPEVTIEGFDGNWYLQRMDVKLTCKADANPPATEY 250
Query: 306 VW------IKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKAANKYGS 359
W + GV+ N + F +S G Y C+A N G+
Sbjct: 251 HWTTLNGSLPKGVEAQNRTLF----FKGPINYSLA------------GTYICEATNPIGT 294
Query: 360 AQKEIEL 366
++E+
Sbjct: 295 RSGQVEV 301
>pdb|2XKN|B Chain B, Crystal Structure Of The Fab Fragment Of The Anti-Egfr
Antibody 7a7
pdb|2XKN|D Chain D, Crystal Structure Of The Fab Fragment Of The Anti-Egfr
Antibody 7a7
Length = 216
Score = 31.6 bits (70), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 36/148 (24%), Positives = 59/148 (39%), Gaps = 35/148 (23%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K++E + IS GS + RF ++ D +T L + ++ D
Sbjct: 32 YAMSWVRQTPEKRLEWVATISSGGSYSYYPDSVKGRFTISRDNVKNTLYLQMSSLRSEDT 91
Query: 157 GIYKCE--------------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVY 202
+Y C V +S V + P+ D + G +V
Sbjct: 92 AMYYCARDSGGFAYWGQGTLVTVSAAKTTPPSVYPLA---PVCGDTT--------GSSVT 140
Query: 203 LYCYANG-FPAP-TISWRRDNSAALSTG 228
L C G FP P T++W NS +LS+G
Sbjct: 141 LGCLVKGYFPEPVTVTW---NSGSLSSG 165
>pdb|1NLD|H Chain H, Fab Fragment Of A Neutralizing Antibody Directed Against
An Epitope Of Gp41 From Hiv-1
Length = 215
Score = 31.2 bits (69), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 27/69 (39%), Gaps = 2/69 (2%)
Query: 236 ILKIPNITKTDRGTYYCVAQNG--VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAIL 293
K+ ++ DR YYC + G G+G ++ AP + P G L
Sbjct: 79 FFKMNSLQPNDRAIYYCARRGGDFWGQGTTVTVSSASTTAPSVYPLAPVSGDQTNSSVTL 138
Query: 294 ECHVEAYPP 302
C V+ Y P
Sbjct: 139 GCLVKGYFP 147
>pdb|1PLG|H Chain H, Evidence For The Extended Helical Nature Of Polysaccharide
Epitopes. The 2.8 Angstroms Resolution Structure And
Thermodynamics Of Ligand Binding Of An Antigen Binding
Fragment Specific For Alpha-(2->8)- Polysialic Acid
Length = 215
Score = 31.2 bits (69), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 36/150 (24%), Positives = 61/150 (40%), Gaps = 36/150 (24%)
Query: 101 DYPVIWMKMDTAKKMEPLPISMSGSL-IIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K + +E + GS ++ +F+ LT D +ST + + + D
Sbjct: 31 DYYIHWVKQRPGEGLEWIGWIYPGSGNTKYNEKFKGKATLTVDTSSSTAYMQLSSLTSED 90
Query: 156 AGIYKC---------------EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQT 200
+ +Y C V +S + V + P+ D + G +
Sbjct: 91 SAVYFCARGGKFAMDYWGQGTSVTVSSAKTTAPSVYPLA---PVCGDTT--------GSS 139
Query: 201 VYLYCYANG-FPAP-TISWRRDNSAALSTG 228
V L C G FP P T++W NS +LS+G
Sbjct: 140 VTLGCLVKGYFPEPVTLTW---NSGSLSSG 166
>pdb|1RSF|A Chain A, Nmr Structure Of Monomeric Car D1 Domain
Length = 126
Score = 31.2 bits (69), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 324 HFATSD-EFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
HF ++D + D S+ V ++ G Y CK G A K+I L
Sbjct: 74 HFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHL 117
>pdb|1V7M|H Chain H, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|1V7M|I Chain I, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|1V7N|H Chain H, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|1V7N|I Chain I, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|1V7N|J Chain J, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|1V7N|K Chain K, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|2ZKH|H Chain H, Human Thrombopoietin Neutralizing Antibody Tn1 Fab
Length = 217
Score = 31.2 bits (69), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 28/101 (27%), Positives = 42/101 (41%), Gaps = 8/101 (7%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCE--VIISLNNKVSAEVELIVRRPPIISDNS 189
RF ++ D S+ L + ++ D GIY C + V PP + +
Sbjct: 69 RFTVSRDDSKSSVYLQMNSLRAEDTGIYYCSGWSFLYWGQGTLVTVSAAKTTPPSVYPLA 128
Query: 190 TRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
S + V L C G FP P T++W NS +LS+G
Sbjct: 129 PGSAAQTN-SMVTLGCLVKGYFPEPVTVTW---NSGSLSSG 165
>pdb|4DN3|H Chain H, Crystal Structure Of Anti-Mcp-1 Antibody Cnto888
Length = 225
Score = 31.2 bits (69), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 37/169 (21%), Positives = 68/169 (40%), Gaps = 26/169 (15%)
Query: 79 SQEQIKDIAQTADLKCSVQYA--DDYPVIWMKMDTAKKMEPL----PISMSGSLIIH-DS 131
S ++K + + C Y + W++ + +E + PI + +
Sbjct: 7 SGAEVKKPGSSVKVSCKASGGTFSSYGISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQG 66
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPI-ISDNST 190
R +T D TST + + ++ D +Y C + + + E++ + + +S ST
Sbjct: 67 RVTITADESTSTAYMELSSLRSEDTAVYYC----ARYDGIYGELDFWGQGTLVTVSSAST 122
Query: 191 RSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ V + G T L C FP P T+SW NS AL++G
Sbjct: 123 KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 168
>pdb|4D9L|L Chain L, Fab Structure Of Anti-Hiv-1 Gp120 V2 Mab 697
pdb|4D9L|M Chain M, Fab Structure Of Anti-Hiv-1 Gp120 V2 Mab 697
pdb|4D9L|N Chain N, Fab Structure Of Anti-Hiv-1 Gp120 V2 Mab 697
pdb|4D9L|O Chain O, Fab Structure Of Anti-Hiv-1 Gp120 V2 Mab 697
Length = 215
Score = 31.2 bits (69), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 25/137 (18%), Positives = 56/137 (40%), Gaps = 9/137 (6%)
Query: 237 LKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITINRPRQGQALQYD 290
L I + D YYC + + G G K + + + P +T+ P +
Sbjct: 75 LAITGLQAEDEADYYCQSYDSSLSGYVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANK 134
Query: 291 AILECHVEAYPPPA--IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER-RQFG 347
A L C + + P A + W D + + ++++++ +S +T E+ +
Sbjct: 135 ATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHR 194
Query: 348 QYACKAANKYGSAQKEI 364
Y+C+ ++ + +K +
Sbjct: 195 SYSCQVTHEGSTVEKTV 211
>pdb|4AMK|H Chain H, Fab Fragment Of Antiporphrin Antibody 13g10
Length = 217
Score = 31.2 bits (69), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 33/140 (23%), Positives = 58/140 (41%), Gaps = 16/140 (11%)
Query: 101 DYPVIWMKMDTAKKMEPLPISMSGSL-IIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
Y + W+K + +E + + G+ + +F+ LT D +ST + + + D
Sbjct: 31 SYNMHWVKQTPGQGLEWIGVIYPGNGDTSYSQKFKGKATLTADKSSSTAYMQLSSLTSED 90
Query: 156 AGIYKCE-----VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG- 209
+ +Y C ++ S V PP + + S + V L C G
Sbjct: 91 SAVYYCSRGGAGIMAYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTN-SMVTLGCLVKGY 149
Query: 210 FPAP-TISWRRDNSAALSTG 228
FP P T++W NS +LS+G
Sbjct: 150 FPEPVTVTW---NSGSLSSG 166
>pdb|2NZ9|D Chain D, Crystal Structure Of Botulinum Neurotoxin Type A Complexed
With Monoclonal Antibody Ar2
pdb|2NZ9|F Chain F, Crystal Structure Of Botulinum Neurotoxin Type A Complexed
With Monoclonal Antibody Ar2
Length = 224
Score = 31.2 bits (69), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 36/141 (25%), Positives = 57/141 (40%), Gaps = 17/141 (12%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETD 155
D+ + W++ K +E + IS GS + + RF + D +T L + ++ D
Sbjct: 31 DHYMYWVRQAPGKGLEWVATISDGGSYTYYSDSVEGRFTTSRDNSKNTLYLQMNSLRAED 90
Query: 156 AGIYKC------EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG 209
IY C + + V + P + + S S G T L C
Sbjct: 91 TAIYYCSRYRYDDAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTS-GGTAALGCLVKD 149
Query: 210 -FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 150 YFPEPVTVSW---NSGALTSG 167
>pdb|1MF2|H Chain H, Anti Hiv1 Protease Fab Complex
pdb|1MF2|N Chain N, Anti Hiv1 Protease Fab Complex
pdb|2HRP|H Chain H, Antigen-Antibody Complex
pdb|2HRP|N Chain N, Antigen-Antibody Complex
Length = 226
Score = 31.2 bits (69), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 35/143 (24%), Positives = 55/143 (38%), Gaps = 24/143 (16%)
Query: 106 WMKMDTAKKMEPLPISMSGSLIIH-----DSRFQLTTDPETSTYILSIKEIQETDAGIYK 160
W++ K +E + SGS I+ RF ++ D +T L + ++ D +Y
Sbjct: 36 WVRQAPEKGLEWVAYISSGSSTIYYADTVKGRFTISRDNPKNTLFLQMTSLRSEDTALYY 95
Query: 161 CE-------------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYA 207
C V+ S V PP + + S + V L C
Sbjct: 96 CARSGGIERYDGTYYVMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTN-SMVTLGCLV 154
Query: 208 NG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 155 KGYFPEPVTVTW---NSGSLSSG 174
>pdb|1QYG|H Chain H, Anti-Cocaine Antibody M82g2 Complexed With Benzoylecgonine
pdb|1RFD|H Chain H, Anti-Cocaine Antibody M82g2
pdb|1RIU|H Chain H, Anti-Cocaine Antibody M82g2 Complexed With
Norbenzoylecgonine
pdb|1RIV|H Chain H, Anti-Cocaine Antibody M82g2 Complexed With Meta-
Oxybenzoylecgonine
Length = 223
Score = 31.2 bits (69), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 30/107 (28%), Positives = 44/107 (41%), Gaps = 13/107 (12%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVS-------AEVELIVRRPPI 184
RF ++ D S+ L + ++ D GIY C + L + V PP
Sbjct: 69 RFTISRDDSKSSVYLQMNSLRAEDTGIYYCTSVPQLGRGFAYWGQGTLVTVSAASTTPPS 128
Query: 185 ISDNS-TRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ + + G V L C G FP P T++W NS ALS+G
Sbjct: 129 VYPLAPGSGGASTSGSMVTLGCLVKGYFPEPVTVTW---NSGALSSG 172
>pdb|1M71|B Chain B, Crystal Structure Of A Monoclonal Fab Specific For
Shigella Flexneri Y Lipopolysaccharide
pdb|1M7D|B Chain B, Crystal Structure Of A Monoclonal Fab Specific For
Shigella Flexneri Y Lipopolysaccharide Complexed With A
Trisaccharide
pdb|1M7I|B Chain B, Crystal Structure Of A Monoclonal Fab Specific For
Shigella Flexneri Y Lipopolysaccharide Complexed With A
Pentasaccharide
Length = 220
Score = 31.2 bits (69), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 33/115 (28%), Positives = 45/115 (39%), Gaps = 32/115 (27%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKC----------------EVIISLNNKVSAEV 175
RF ++ D S+ L + ++ D GIY C V +S + V
Sbjct: 69 RFTISRDDSKSSVYLQMNNLRAEDTGIYYCTRGGAVGAMDYWGQGTSVTVSSATTTAPSV 128
Query: 176 ELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+V P SD S G +V L C G FP P T+ W N ALS+G
Sbjct: 129 YPLV---PGCSDTS--------GSSVTLGCLVKGYFPEPVTVKW---NYGALSSG 169
>pdb|1Q72|H Chain H, Anti-Cocaine Antibody M82g2 Complexed With Cocaine
Length = 223
Score = 31.2 bits (69), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 30/108 (27%), Positives = 44/108 (40%), Gaps = 13/108 (12%)
Query: 131 SRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVS-------AEVELIVRRPP 183
RF ++ D S+ L + ++ D GIY C + L + V PP
Sbjct: 68 GRFTISRDDSKSSVYLQMNSLRAEDTGIYYCTSVPQLGRGFAYWGQGTLVTVSAASTTPP 127
Query: 184 IISDNS-TRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ + + G V L C G FP P T++W NS ALS+G
Sbjct: 128 SVYPLAPGSGGASTSGSMVTLGCLVKGYFPEPVTVTW---NSGALSSG 172
>pdb|1L7I|H Chain H, Crystal Structure Of The Anti-Erbb2 Fab2c4
Length = 222
Score = 31.2 bits (69), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 38/146 (26%), Positives = 59/146 (40%), Gaps = 26/146 (17%)
Query: 101 DYPVIWMKMDTAKKMEPLP--ISMSGSLIIHD---SRFQLTTDPETSTYILSIKEIQETD 155
DY + W++ K +E + SG I + RF L+ D +T L + ++ D
Sbjct: 31 DYTMDWVRQAPGKGLEWVADVNPNSGGSIYNQRFKGRFTLSVDRSKNTLYLQMNSLRAED 90
Query: 156 AGIYKCEVII--SLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLY 204
+Y C + S + L+ +S ST+ V + G T L
Sbjct: 91 TAVYYCARNLGPSFYFDYWGQGTLVT-----VSSASTKGPSVFPLAPSSKSTSGGTAALG 145
Query: 205 CYANG-FPAP-TISWRRDNSAALSTG 228
C FP P T+SW NS AL++G
Sbjct: 146 CLVKDYFPEPVTVSW---NSGALTSG 168
>pdb|3O11|H Chain H, Anti-Beta-Amyloid Antibody C706 Fab In Space Group C2
pdb|3O11|B Chain B, Anti-Beta-Amyloid Antibody C706 Fab In Space Group C2
pdb|3MCL|H Chain H, Anti-Beta-Amyloid Antibody C706 Fab In Space Group P21
Length = 228
Score = 31.2 bits (69), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 36/141 (25%), Positives = 60/141 (42%), Gaps = 26/141 (18%)
Query: 106 WMKMDTAKKMEPLPISMSGSLII-HDSRFQ----LTTDPETSTYILSIKEIQETDAGIYK 160
W+K +E + + GS H++ F+ T D ++T + + + D+ +Y
Sbjct: 36 WIKQRPGHGLEWIGEVLPGSGKSNHNANFKGRATFTADTASNTAYMQLSSLTSEDSAVYY 95
Query: 161 CEVIISLNNKVS--AEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYCYANG 209
C S NN ++ + L+ +S ST+ V + G T L C
Sbjct: 96 CAREGSNNNALAYWGQGTLVT-----VSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKD 150
Query: 210 -FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 151 YFPEPVTVSW---NSGALTSG 168
>pdb|1WWB|X Chain X, Ligand Binding Domain Of Human Trkb Receptor
Length = 103
Score = 31.2 bits (69), Expect = 1.0, Method: Composition-based stats.
Identities = 26/97 (26%), Positives = 40/97 (41%), Gaps = 7/97 (7%)
Query: 270 VEFAPVITINRPRQGQALQYDAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVS--HFAT 327
V FAP IT + + + V+ P PA+ W +G I+N Y + H
Sbjct: 1 VHFAPTITF---LESPTSDHHWCIPFTVKGNPKPALQWFYNGA-ILNESKYICTKIHVTN 56
Query: 328 SDEFSDTSLRVITIERRQFGQYACKAANKYGSAQKEI 364
E+ L++ G Y A N+YG +K+I
Sbjct: 57 HTEYHGC-LQLDNPTHMNNGDYTLIAKNEYGKDEKQI 92
>pdb|1S78|D Chain D, Insights Into Erbb Signaling From The Structure Of The
Erbb2- Pertuzumab Complex
pdb|1S78|F Chain F, Insights Into Erbb Signaling From The Structure Of The
Erbb2- Pertuzumab Complex
Length = 226
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 38/146 (26%), Positives = 59/146 (40%), Gaps = 26/146 (17%)
Query: 101 DYPVIWMKMDTAKKMEPLPI--SMSGSLIIHD---SRFQLTTDPETSTYILSIKEIQETD 155
DY + W++ K +E + SG I + RF L+ D +T L + ++ D
Sbjct: 31 DYTMDWVRQAPGKGLEWVADVNPNSGGSIYNQRFKGRFTLSVDRSKNTLYLQMNSLRAED 90
Query: 156 AGIYKCEVII--SLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLY 204
+Y C + S + L+ +S ST+ V + G T L
Sbjct: 91 TAVYYCARNLGPSFYFDYWGQGTLVT-----VSSASTKGPSVFPLAPSSKSTSGGTAALG 145
Query: 205 CYANG-FPAP-TISWRRDNSAALSTG 228
C FP P T+SW NS AL++G
Sbjct: 146 CLVKDYFPEPVTVSW---NSGALTSG 168
>pdb|3NGB|L Chain L, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
pdb|3NGB|C Chain C, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
pdb|3NGB|F Chain F, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
pdb|3NGB|K Chain K, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
Length = 210
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 30/126 (23%), Positives = 50/126 (39%), Gaps = 7/126 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEF-APVITINRPRQGQALQYDAILEC 295
L I N+ D G YYC G+G K + ++ AP + I P Q A + C
Sbjct: 71 LTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKSGTASVVC 130
Query: 296 HVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ---YA 350
+ + P + W D N SV+ + D S +T+ + + + YA
Sbjct: 131 LLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHKVYA 189
Query: 351 CKAANK 356
C+ ++
Sbjct: 190 CEVTHQ 195
>pdb|2VXT|H Chain H, Crystal Structure Of Human Il-18 Complexed To Murine
Reference Antibody 125-2h Fab
pdb|2VXU|H Chain H, Crystal Structure Of Murine Reference Antibody 125-2h Fab
Fragment
pdb|2VXU|I Chain I, Crystal Structure Of Murine Reference Antibody 125-2h Fab
Fragment
Length = 216
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 33/136 (24%), Positives = 58/136 (42%), Gaps = 12/136 (8%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K K +E + I ++ +F+ LT D ++T + + + D
Sbjct: 31 DYFIYWVKQSHGKSLEWIGDIDPYNGDTSYNQKFRDKATLTVDQSSTTAFMHLNSLTSED 90
Query: 156 AGIYKCEVIISLNNKVS-AEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FPAP 213
+ +Y C + + + V PP + + S + V L C G FP P
Sbjct: 91 SAVYFCARGLRFWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVKGYFPEP 149
Query: 214 -TISWRRDNSAALSTG 228
T++W NS +LS+G
Sbjct: 150 VTVTW---NSGSLSSG 162
>pdb|3UTZ|A Chain A, Endogenous-Like Inhibitory Antibodies Targeting Activated
Metalloproteinase Motifs Show Therapeutic Potential
pdb|3UTZ|D Chain D, Endogenous-Like Inhibitory Antibodies Targeting Activated
Metalloproteinase Motifs Show Therapeutic Potential
pdb|3UTZ|E Chain E, Endogenous-Like Inhibitory Antibodies Targeting Activated
Metalloproteinase Motifs Show Therapeutic Potential
Length = 219
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 33/129 (25%), Positives = 50/129 (38%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K I V AP + I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQASHVPPTFGSGTKLEIKRTVA-APSVFIFPPSDEQLKSGTAS 136
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 137 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 195
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 196 VYACEVTHQ 204
>pdb|3U82|B Chain B, Binding Of Herpes Simplex Virus Glycoprotein D To Nectin-1
Exploits Host Cell Adhesion
Length = 317
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 38/176 (21%), Positives = 70/176 (39%), Gaps = 13/176 (7%)
Query: 139 PETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVI-VSE 197
P + + + ++ D G+Y CE +++ L V P T++V+ +
Sbjct: 73 PSFTDGTIRLSRLELEDEGVYICEFATFPTGNRESQLNLTVMAKPTNWIEGTQAVLRAKK 132
Query: 198 GQ----TVYLYCYANGFPAPTISW--RRDNSAAL----STGGSIYRGNILKIPNITKTDR 247
GQ V ANG P +SW R A + G++ + ++ + +
Sbjct: 133 GQDDKVLVATCTSANGKPPSVVSWETRLKGEAEYQEIRNPNGTVTVISRYRLVPSREAHQ 192
Query: 248 GTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQ-YDAILECHVEAYPP 302
+ C+ + R K ++ + V++ P +TI LQ D L C +A PP
Sbjct: 193 QSLACIVNYHMDR-FKESLTLNVQYEPEVTIEGFDGNWYLQRMDVKLTCKADANPP 247
>pdb|2R0K|H Chain H, Protease Domain Of Hgfa With Inhibitor Fab58
Length = 225
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 35/141 (24%), Positives = 56/141 (39%), Gaps = 24/141 (17%)
Query: 104 VIWMKMDTAKKMEPLPI--SMSGSLIIHDS---RFQLTTDPETSTYILSIKEIQETDAGI 158
+ W++ K +E + I G DS RF ++ D +T L + ++ D +
Sbjct: 34 IHWVRQAPGKGLEWVAIINPNGGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAV 93
Query: 159 YKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYCYANG 209
Y C + + L+ +S ST+ V + G T L C
Sbjct: 94 YYCARSARFSFDYWGQGTLVT-----VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKD 148
Query: 210 -FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 149 YFPEPVTVSW---NSGALTSG 166
>pdb|3ALP|A Chain A, Cell Adhesion Protein
pdb|3ALP|B Chain B, Cell Adhesion Protein
pdb|3U83|A Chain A, Crystal Structure Of Nectin-1
Length = 331
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 38/176 (21%), Positives = 70/176 (39%), Gaps = 13/176 (7%)
Query: 139 PETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVI-VSE 197
P + + + ++ D G+Y CE +++ L V P T++V+ +
Sbjct: 87 PSFTDGTIRLSRLELEDEGVYICEFATFPTGNRESQLNLTVMAKPTNWIEGTQAVLRAKK 146
Query: 198 GQ----TVYLYCYANGFPAPTISW--RRDNSAAL----STGGSIYRGNILKIPNITKTDR 247
GQ V ANG P +SW R A + G++ + ++ + +
Sbjct: 147 GQDDKVLVATCTSANGKPPSVVSWETRLKGEAEYQEIRNPNGTVTVISRYRLVPSREAHQ 206
Query: 248 GTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQ-YDAILECHVEAYPP 302
+ C+ + R K ++ + V++ P +TI LQ D L C +A PP
Sbjct: 207 QSLACIVNYHMDR-FKESLTLNVQYEPEVTIEGFDGNWYLQRMDVKLTCKADANPP 261
>pdb|1F5W|A Chain A, Dimeric Structure Of The Coxsackie Virus And Adenovirus
Receptor D1 Domain
pdb|1F5W|B Chain B, Dimeric Structure Of The Coxsackie Virus And Adenovirus
Receptor D1 Domain
pdb|1EAJ|A Chain A, Dimeric Structure Of The Coxsackie Virus And Adenovirus
Receptor D1 Domain At 1.35 Angstrom Resolution
pdb|1EAJ|B Chain B, Dimeric Structure Of The Coxsackie Virus And Adenovirus
Receptor D1 Domain At 1.35 Angstrom Resolution
Length = 126
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 324 HFATSD-EFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
HF ++D + D S+ V ++ G Y CK G A K+I L
Sbjct: 78 HFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHL 121
>pdb|2W9L|A Chain A, Canine Adenovirus Type 2 Fibre Head In Complex With Car
Domain D1 And Sialic Acid
pdb|2W9L|B Chain B, Canine Adenovirus Type 2 Fibre Head In Complex With Car
Domain D1 And Sialic Acid
pdb|2W9L|G Chain G, Canine Adenovirus Type 2 Fibre Head In Complex With Car
Domain D1 And Sialic Acid
pdb|2W9L|J Chain J, Canine Adenovirus Type 2 Fibre Head In Complex With Car
Domain D1 And Sialic Acid
pdb|2W9L|K Chain K, Canine Adenovirus Type 2 Fibre Head In Complex With Car
Domain D1 And Sialic Acid
pdb|2W9L|O Chain O, Canine Adenovirus Type 2 Fibre Head In Complex With Car
Domain D1 And Sialic Acid
pdb|2W9L|P Chain P, Canine Adenovirus Type 2 Fibre Head In Complex With Car
Domain D1 And Sialic Acid
pdb|2W9L|T Chain T, Canine Adenovirus Type 2 Fibre Head In Complex With Car
Domain D1 And Sialic Acid
pdb|2W9L|V Chain V, Canine Adenovirus Type 2 Fibre Head In Complex With Car
Domain D1 And Sialic Acid
pdb|2W9L|X Chain X, Canine Adenovirus Type 2 Fibre Head In Complex With Car
Domain D1 And Sialic Acid
pdb|2W9L|Y Chain Y, Canine Adenovirus Type 2 Fibre Head In Complex With Car
Domain D1 And Sialic Acid
pdb|2W9L|Z Chain Z, Canine Adenovirus Type 2 Fibre Head In Complex With Car
Domain D1 And Sialic Acid
Length = 124
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 324 HFATSD-EFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
HF ++D + D S+ V ++ G Y CK G A K+I L
Sbjct: 77 HFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHL 120
>pdb|2J12|B Chain B, Ad37 Fibre Head In Complex With Car D1
pdb|2J1K|A Chain A, Cav-2 Fibre Head In Complex With Car D1
pdb|2J1K|B Chain B, Cav-2 Fibre Head In Complex With Car D1
pdb|2J1K|G Chain G, Cav-2 Fibre Head In Complex With Car D1
pdb|2J1K|J Chain J, Cav-2 Fibre Head In Complex With Car D1
pdb|2J1K|K Chain K, Cav-2 Fibre Head In Complex With Car D1
pdb|2J1K|O Chain O, Cav-2 Fibre Head In Complex With Car D1
pdb|2J1K|P Chain P, Cav-2 Fibre Head In Complex With Car D1
pdb|2J1K|T Chain T, Cav-2 Fibre Head In Complex With Car D1
pdb|2J1K|V Chain V, Cav-2 Fibre Head In Complex With Car D1
pdb|2J1K|X Chain X, Cav-2 Fibre Head In Complex With Car D1
pdb|2J1K|Y Chain Y, Cav-2 Fibre Head In Complex With Car D1
pdb|2J1K|Z Chain Z, Cav-2 Fibre Head In Complex With Car D1
Length = 128
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 324 HFATSD-EFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
HF ++D + D S+ V ++ G Y CK G A K+I L
Sbjct: 80 HFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHL 123
>pdb|1PZ5|B Chain B, Structural Basis Of Peptide-Carbohydrate Mimicry In An
Antibody Combining Site
Length = 220
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 33/115 (28%), Positives = 45/115 (39%), Gaps = 32/115 (27%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKC----------------EVIISLNNKVSAEV 175
RF ++ D S+ L + ++ D GIY C V +S + V
Sbjct: 69 RFTISRDDSKSSVYLQMNNLRAEDTGIYYCTRGGAVGAMDYWGQGTSVTVSSATTTAPSV 128
Query: 176 ELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+V P SD S G +V L C G FP P T+ W N ALS+G
Sbjct: 129 YPLV---PGCSDTS--------GSSVTLGCLVKGYFPEPVTVKW---NYGALSSG 169
>pdb|2BK8|A Chain A, M1 Domain From Titin
Length = 97
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 30/74 (40%), Gaps = 6/74 (8%)
Query: 295 CHVEAYPPPA-IVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQYACKA 353
C +E Y + W Q+ N++ Y +++ E L V I + G Y CK
Sbjct: 23 CKIENYDQSTQVTWYFGVRQLENSEKYEITY-----EDGVAILYVKDITKLDDGTYRCKV 77
Query: 354 ANKYGSAQKEIELF 367
N YG ELF
Sbjct: 78 VNDYGEDSSYAELF 91
>pdb|3PP3|L Chain L, Epitope Characterization And Crystal Structure Of Ga101
Provide Insights Into The Molecular Basis For The Type I
TYPE II Distinction Of Anti- Cd20 Antibodies
pdb|3PP3|K Chain K, Epitope Characterization And Crystal Structure Of Ga101
Provide Insights Into The Molecular Basis For The Type I
TYPE II Distinction Of Anti- Cd20 Antibodies
pdb|3PP4|L Chain L, Epitope Characterization And Crystal Structure Of Ga101
Provide Insights Into The Molecular Basis For The Type I
TYPE II Distinction Of Anti- Cd20 Antibodies
Length = 219
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 53/195 (27%), Positives = 77/195 (39%), Gaps = 26/195 (13%)
Query: 181 RPPIISDNSTRSVIVSEGQTVYLYCYAN--GFPAPTISWRRDNSAA-----LSTGGSIYR 233
P IS S++S++ S G T YLY Y G + ++ N + S GS
Sbjct: 17 EPASISCRSSKSLLHSNGIT-YLYWYLQKPGQSPQLLIYQMSNLVSGVPDRFSGSGS--- 72
Query: 234 GN--ILKIPNITKTDRGTYYCVAQN-----GVGRGMKRNIAVEVEFAPVITINRPRQGQA 286
G LKI + D G YYC AQN G G K I V AP + I P Q
Sbjct: 73 GTDFTLKISRVEAEDVGVYYC-AQNLELPYTFGGGTKVEIKRTVA-APSVFIFPPSDEQL 130
Query: 287 LQYDAILECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERR 344
A + C + + P + W D N SV+ + D S +T+ +
Sbjct: 131 KSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKA 189
Query: 345 QFGQ---YACKAANK 356
+ + YAC+ ++
Sbjct: 190 DYEKHKVYACEVTHQ 204
>pdb|1KB5|H Chain H, Murine T-Cell Receptor Variable DomainFAB COMPLEX
Length = 219
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 36/151 (23%), Positives = 61/151 (40%), Gaps = 38/151 (25%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETDA 156
Y + W+K K +E + I I ++ +F+ LT D +ST + +K + D+
Sbjct: 32 YNMNWVKQSNGKSLEWIGNIDPYYGGISYNQKFKGRATLTVDKSSSTAYMQLKSLTSEDS 91
Query: 157 GIYKCE-----------------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQ 199
+Y C + +S + V + P+ D + G
Sbjct: 92 AVYYCARSRTDLYYFDYWGQGTTLTVSSAKTTAPSVYPLA---PVCGDTT--------GS 140
Query: 200 TVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+V L C G FP P T++W NS +LS+G
Sbjct: 141 SVTLGCLVKGYFPEPVTLTW---NSGSLSSG 168
>pdb|1FL6|L Chain L, The Hapten Complexed Germline Precursor To Sulfide Oxidase
Catalytic Antibody 28b4
pdb|1FL6|A Chain A, The Hapten Complexed Germline Precursor To Sulfide Oxidase
Catalytic Antibody 28b4
pdb|1FL5|L Chain L, The Unliganded Germline Precursor To The Sulfide Oxidase
Catalytic Antibody 28b4.
pdb|1FL5|A Chain A, The Unliganded Germline Precursor To The Sulfide Oxidase
Catalytic Antibody 28b4
Length = 217
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 30/128 (23%), Positives = 50/128 (39%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVE---FAPVITINRPRQGQALQYDAIL 293
LKI + D G YYC + V R +E++ AP + I P Q A +
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASV 137
Query: 294 ECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ--- 348
C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 138 VCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHKV 196
Query: 349 YACKAANK 356
YAC+ ++
Sbjct: 197 YACEVTHQ 204
>pdb|1I9R|H Chain H, Structure Of Cd40l In Complex With The Fab Fragment Of
Humanized 5c8 Antibody
pdb|1I9R|K Chain K, Structure Of Cd40l In Complex With The Fab Fragment Of
Humanized 5c8 Antibody
pdb|1I9R|X Chain X, Structure Of Cd40l In Complex With The Fab Fragment Of
Humanized 5c8 Antibody
Length = 219
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 31/109 (28%), Positives = 45/109 (41%), Gaps = 18/109 (16%)
Query: 131 SRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNST 190
S+ LT D ST + + ++ D +Y C N+ S +V +S ST
Sbjct: 66 SKATLTVDKSASTAYMELSSLRSEDTAVYYCTRSDGRNDMDSWGQGTLV----TVSSAST 121
Query: 191 RSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ V + G T L C FP P T+SW NS AL++G
Sbjct: 122 KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 167
>pdb|3CVH|H Chain H, How Tcr-Like Antibody Recognizes Mhc-Bound Peptide
pdb|3CVH|Q Chain Q, How Tcr-Like Antibody Recognizes Mhc-Bound Peptide
pdb|3CVI|H Chain H, How Tcr-Like Antibody Recognizes Mhc-Bound Peptide
Length = 219
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 58/144 (40%), Gaps = 20/144 (13%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K K +E + I+ + I++ +F+ LT D +S + ++ + D
Sbjct: 30 DYNMDWVKQSHGKSLEWIGDINPNNGGTIYNQKFKGKATLTVDKSSSAAYMEVRSLTSED 89
Query: 156 AGIYKCEVIISLNN---------KVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCY 206
+Y C N V PP + + S + V L C
Sbjct: 90 TAVYYCARKPYYGNFAWFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSM-VTLGCL 148
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 149 VKGYFPEPVTVTW---NSGSLSSG 169
>pdb|2WBW|B Chain B, Ad37 Fibre Head In Complex With Car D1 And Sialic Acid
Length = 128
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 324 HFATSD-EFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
HF ++D + D S+ V ++ G Y CK G A K+I L
Sbjct: 80 HFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHL 123
>pdb|1H3P|H Chain H, Structural Characterisation Of A Monoclonal Antibody
Specific For The Pres1 Region Of The Hepatitis B Virus
Length = 219
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 36/142 (25%), Positives = 59/142 (41%), Gaps = 21/142 (14%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K++E + +S GS + RF ++ D +T L + ++ D
Sbjct: 32 YAMSWVRQSPEKRLEWVAEVSSDGSYAYYPDTLTGRFTISRDNAKNTLYLEMTSLRSEDT 91
Query: 157 GIYKCEVIISLNNKVS-------AEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG 209
+Y C S N V+ V PP + + S + V L C G
Sbjct: 92 AMYYCA---SFNWDVAYWGQGTLVTVSAAKTTPPSVYPLAPGS-LAQTNSMVTLGCLVKG 147
Query: 210 -FPAP-TISWRRDNSAALSTGG 229
FP P T++W NS +LS+ G
Sbjct: 148 YFPEPVTVTW---NSGSLSSSG 166
>pdb|2W65|A Chain A, Anti Citrullinated Collagen Type 2 Antibody Acc4 In
Complex With A Citrullinated Peptide
pdb|2W65|C Chain C, Anti Citrullinated Collagen Type 2 Antibody Acc4 In
Complex With A Citrullinated Peptide
Length = 218
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 39/165 (23%), Positives = 61/165 (36%), Gaps = 19/165 (11%)
Query: 79 SQEQIKDIAQTADLKC--SVQYADDYPVIWMKMDTAKKMEPLPI--SMSGSLIIHD---S 131
S ++K +T + C S DY + W+K K ++ + + +G D
Sbjct: 7 SGPELKKPGETVKISCKASGYTFTDYSIHWVKQAPGKGLKWMGWINTETGEPTYTDDFKG 66
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIIS------LNNKVSAEVELIVRRPPII 185
RF + + ST L I ++ D Y C + V PP +
Sbjct: 67 RFAFSLESSASTAFLQINNLKNEDTATYFCARATTATELAYWGQGTLVTVSAAKTTPPSV 126
Query: 186 SDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ S V L C G FP P T++W NS +LS+G
Sbjct: 127 YPLAPGSA-AQRNSMVTLGCLVKGYFPEPVTVTW---NSGSLSSG 167
>pdb|2DL9|A Chain A, Solution Structure Of The Ig-Like Domain Of Human Leucine-
Rich Repeat-Containing Protein 4
Length = 103
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 8/82 (9%)
Query: 183 PIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGG-----SIYRGNIL 237
P I D + R + +SEG+ L C P ++ W N LS S+ L
Sbjct: 8 PFIMD-APRDLNISEGRMAELKCRTP--PMSSVKWLLPNGTVLSHASRHPRISVLNDGTL 64
Query: 238 KIPNITKTDRGTYYCVAQNGVG 259
++ +D G Y C+ N G
Sbjct: 65 NFSHVLLSDTGVYTCMVTNVAG 86
>pdb|3HR5|H Chain H, M1prime Peptide From Ige Bound By Humanized Antibody 47h4
Fab
pdb|3HR5|B Chain B, M1prime Peptide From Ige Bound By Humanized Antibody 47h4
Fab
pdb|3HR5|I Chain I, M1prime Peptide From Ige Bound By Humanized Antibody 47h4
Fab
pdb|3HR5|J Chain J, M1prime Peptide From Ige Bound By Humanized Antibody 47h4
Fab
Length = 226
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 33/140 (23%), Positives = 55/140 (39%), Gaps = 16/140 (11%)
Query: 101 DYPVIWMKMDTAKKMEPLPISMSGSLIIH-----DSRFQLTTDPETSTYILSIKEIQETD 155
DY + W++ K +E + + I+ RF ++ D +T L + ++ D
Sbjct: 31 DYGIAWVRQAPGKGLEWVAFISDLAYTIYYADTVTGRFTISRDNSKNTLYLQMNSLRAED 90
Query: 156 AGIYKC-----EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG- 209
+Y C + + V + P + + S S G T L C
Sbjct: 91 TAVYYCARDNWDAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTS-GGTAALGCLVKDY 149
Query: 210 FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 150 FPEPVTVSW---NSGALTSG 166
>pdb|1LO4|H Chain H, Retro-Diels-Alderase Catalytic Antibody 9d9
Length = 220
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 37/150 (24%), Positives = 59/150 (39%), Gaps = 37/150 (24%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIHDS---RFQLTTDPETSTYILSIKEIQETDAG 157
Y + W++ ++E + IS G L DS RF ++ D + L + ++ D
Sbjct: 32 YGMSWVRQTPQMRLEWVASISYGGLLYFSDSVKGRFTISRDIVRNILTLQMSRLRSEDTA 91
Query: 158 IYKCE-----------------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQT 200
IY C V +S + V + P+ D + G +
Sbjct: 92 IYYCARGTSFVRYFDVWGAGTTVTVSSAKTTAPSVYPLA---PVCGDTT--------GSS 140
Query: 201 VYLYCYANG-FPAP-TISWRRDNSAALSTG 228
V L C G FP P T++W NS +LS+G
Sbjct: 141 VTLGCLVKGYFPEPVTLTW---NSGSLSSG 167
>pdb|3KS0|H Chain H, Crystal Structure Of The Heme Domain Of Flavocytochrome B2
In Complex With Fab B2b4
pdb|3KS0|K Chain K, Crystal Structure Of The Heme Domain Of Flavocytochrome B2
In Complex With Fab B2b4
Length = 225
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 41/157 (26%), Positives = 61/157 (38%), Gaps = 20/157 (12%)
Query: 87 AQTADLKCSV---QYADDYPVIWMKMDTAKKMEPLP-ISMSGSLIIH---DSRFQLTTDP 139
+QT L CSV Y W++ K+E + IS GS + +SR +T D
Sbjct: 15 SQTLSLTCSVTGDSITSGY-WNWIRKFPGNKLEYMGYISYGGSTYYNPSLESRISITRDT 73
Query: 140 ETSTYILSIKEIQETDAGIYKCEVIIS------LNNKVSAEVELIVRRPPIISDNSTRSV 193
+ Y L + + D Y C + + V PP + + S
Sbjct: 74 SKNQYYLQLNSVTTEDTATYFCARLFGSYYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSA 133
Query: 194 IVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ V L C G FP P T++W NS +LS+G
Sbjct: 134 AQTNSM-VTLGCLVKGYFPEPVTVTW---NSGSLSSG 166
>pdb|1AXT|H Chain H, Immune Versus Natural Selection: Antibody Aldolases With
The Rates Of Natural Enzymes
pdb|3FO9|H Chain H, Crystal Structure Of Aldolase Antibody 33f12 Fab' In
Complex With Hapten 1,3-Diketone
pdb|3FO9|B Chain B, Crystal Structure Of Aldolase Antibody 33f12 Fab' In
Complex With Hapten 1,3-Diketone
Length = 218
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 29/110 (26%), Positives = 47/110 (42%), Gaps = 24/110 (21%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVII---------SLNNKVSAEVELIVRRP 182
+F ++ D S L + ++ D GIY C++ +L +A+ P
Sbjct: 69 KFTISRDDSKSRLYLQMNSLRTEDTGIYYCKIYFYSFSYWGQGTLVTVSAAKTTAPSVYP 128
Query: 183 --PIISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
P+ D + G +V L C G FP P T++W NS +LS+G
Sbjct: 129 LAPVCGDTT--------GSSVTLGCLVKGYFPEPVTLTW---NSGSLSSG 167
>pdb|1BBJ|H Chain H, Crystal Structure Of A Chimeric Fab' Fragment Of An
Antibody Binding Tumour Cells
pdb|1BBJ|B Chain B, Crystal Structure Of A Chimeric Fab' Fragment Of An
Antibody Binding Tumour Cells
Length = 212
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 35/137 (25%), Positives = 58/137 (42%), Gaps = 13/137 (9%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
D+ + W K + +E + IS I ++ +F+ LT D +ST + + + D
Sbjct: 31 DHAIHWAKQKPEQGLEWIGYISPGNDDIKYNEKFKGKATLTADKSSSTAYMQLNSLTSED 90
Query: 156 AGIYKCE--VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FPA 212
+ +Y C+ + V + P + + S SE T L C FP
Sbjct: 91 SAVYFCKRSYYGHWGQGTTLTVSSASTKGPSVFPLAPCSRSTSE-STAALGCLVKDYFPE 149
Query: 213 P-TISWRRDNSAALSTG 228
P T+SW NS AL++G
Sbjct: 150 PVTVSW---NSGALTSG 163
>pdb|2Q6W|B Chain B, The Structure Of Hla-Dra, Drb30101 (Dr52a) With Bound
Platelet Integrin Peptide Associated With Fetal And
Neonatal Alloimmune Thrombocytopenia
pdb|2Q6W|E Chain E, The Structure Of Hla-Dra, Drb30101 (Dr52a) With Bound
Platelet Integrin Peptide Associated With Fetal And
Neonatal Alloimmune Thrombocytopenia
Length = 190
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 244 KTDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPP 303
K R YC GVG + V+ P +T+ P + Q LQ+ +L C V + P
Sbjct: 71 KRGRVDNYCRHNYGVGE----SFTVQRRVHPQVTVY-PAKTQPLQHHNLLVCSVSGFYPG 125
Query: 304 AI--VWIKDG 311
+I W ++G
Sbjct: 126 SIEVRWFRNG 135
>pdb|1CLY|L Chain L, Igg Fab (Human Igg1, Kappa) Chimeric Fragment (Cbr96)
Complexed With Lewis Y Nonoate Methyl Ester
pdb|1UCB|L Chain L, Structure Of Uncomplexed Fab Compared To Complex (1cly,
1clz)
Length = 219
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 33/129 (25%), Positives = 50/129 (38%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + V G G K I V AP + I P Q A
Sbjct: 78 LKISRVEAEDLGVYYCFQGSHVPFTFGSGTKLEIKRTVA-APSVFIFPPSDEQLKSGTAS 136
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 137 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 195
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 196 VYACEVTHQ 204
>pdb|3KNB|B Chain B, Crystal Structure Of The Titin C-Terminus In Complex With
Obscurin- Like 1
Length = 107
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 290 DAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQY 349
+A L+C V PPP +VW K G Q+ ++ S + ++ L + G Y
Sbjct: 30 EAELKCVVLGEPPPVVVWEKGGQQLAASERLSFPA-----DGAEHGLLLTAALPTDAGVY 84
Query: 350 ACKAAN 355
C+A N
Sbjct: 85 VCRARN 90
>pdb|2WP3|O Chain O, Crystal Structure Of The Titin M10-Obscurin Like 1 Ig
Complex
pdb|2WWM|C Chain C, Crystal Structure Of The Titin M10-Obscurin Like 1 Ig
Complex In Space Group P1
pdb|2WWM|O Chain O, Crystal Structure Of The Titin M10-Obscurin Like 1 Ig
Complex In Space Group P1
Length = 109
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 290 DAILECHVEAYPPPAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQY 349
+A L+C V PPP +VW K G Q+ ++ S + ++ L + G Y
Sbjct: 31 EAELKCVVLGEPPPVVVWEKGGQQLAASERLSFPA-----DGAEHGLLLTAALPTDAGVY 85
Query: 350 ACKAAN 355
C+A N
Sbjct: 86 VCRARN 91
>pdb|3BKY|H Chain H, Crystal Structure Of Chimeric Antibody C2h7 Fab In Complex
With A Cd20 Peptide
Length = 226
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 39/173 (22%), Positives = 71/173 (41%), Gaps = 23/173 (13%)
Query: 76 SYISQEQIKDIAQTADLKCSVQYAD----DYPVIWMKMDTAKKMEPLPISMSGSL-IIHD 130
+Y+ Q + + A +K S + + Y + W+K + +E + G+ ++
Sbjct: 2 AYLQQSGAELVRPGASVKMSCKASGYTFTSYNMHWVKQTPRQGLEWIGAIYPGNGDTSYN 61
Query: 131 SRFQ----LTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIIS 186
+F+ LT D +ST + + + D+ +Y C ++ +N +S
Sbjct: 62 QKFKGKATLTVDKSSSTAYMQLSSLTSEDSAVYFCARVVYYSNSYWYFDVWGTGTTVTVS 121
Query: 187 DNSTRSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
ST+ V + G T L C FP P T+SW NS AL++G
Sbjct: 122 AASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 171
>pdb|3MA9|H Chain H, Crystal Structure Of Gp41 Derived Protein Complexed With
Fab 8066
Length = 245
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 40/177 (22%), Positives = 67/177 (37%), Gaps = 40/177 (22%)
Query: 79 SQEQIKDIAQTADLKCSVQYA--DDYPVIWMKMDTAKKMEPLPISMSGSLI------IHD 130
S ++K + + C + Y W++ + +E + GS+I +
Sbjct: 7 SGAEVKKPGSSVKVSCKASGGTFNSYAFSWVRQAPGQGLEWM-----GSIIPIFGTTNYA 61
Query: 131 SRFQ----LTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVS----AEVELIVRRP 182
+FQ +T D TST + + ++ D +Y C N + L+
Sbjct: 62 QKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARYFDTYNNYGFANWGQGTLVT--- 118
Query: 183 PIISDNSTRSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+S ST+ V + G T L C FP P T+SW NS AL++G
Sbjct: 119 --VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 170
>pdb|3LEY|H Chain H, 2f5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal
Antibody 6a7 In Complex With Hiv-1 Gp41
Length = 221
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 4/88 (4%)
Query: 236 ILKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
L++ ++T D TYYC N + G+G ++ AP + P G
Sbjct: 80 FLQLNSVTTEDTATYYCAFGNYLPAYWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSV 139
Query: 292 ILECHVEAYPPPAIVWIKDGVQIMNNQH 319
L C V+ Y P + + + + H
Sbjct: 140 TLGCLVKGYFPEPVTLTWNSGSLSSGVH 167
>pdb|1AHW|B Chain B, A Complex Of Extracellular Domain Of Tissue Factor With An
Inhibitory Fab (5g9)
pdb|1AHW|E Chain E, A Complex Of Extracellular Domain Of Tissue Factor With An
Inhibitory Fab (5g9)
pdb|1FGN|H Chain H, Monoclonal Murine Antibody 5g9-Anti-Human Tissue Factor
Length = 214
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 36/140 (25%), Positives = 57/140 (40%), Gaps = 16/140 (11%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K + +E + I I+D +FQ +T D ++T L + + D
Sbjct: 31 DYYMHWVKQRPEQGLEWIGLIDPENGNTIYDPKFQGKASITADTSSNTAYLQLSSLTSED 90
Query: 156 AGIYKCEVIIS-----LNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG- 209
+Y C S + V PP + + S + V L C G
Sbjct: 91 TAVYYCARDNSYYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVKGY 149
Query: 210 FPAP-TISWRRDNSAALSTG 228
FP P T++W NS +LS+G
Sbjct: 150 FPEPVTVTW---NSGSLSSG 166
>pdb|1CLY|H Chain H, Igg Fab (Human Igg1, Kappa) Chimeric Fragment (Cbr96)
Complexed With Lewis Y Nonoate Methyl Ester
pdb|1UCB|H Chain H, Structure Of Uncomplexed Fab Compared To Complex (1cly,
1clz)
Length = 219
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 34/142 (23%), Positives = 58/142 (40%), Gaps = 18/142 (12%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETD 155
DY + W++ K++E + IS G + + RF ++ D ++ L + ++ D
Sbjct: 31 DYYMYWVRQTPEKRLEWVAYISQGGDITDYPDTVKGRFTISRDNAKNSLYLQMSRLKSED 90
Query: 156 AGIYKCEVIIS-------LNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYAN 208
+Y C + V + + P + + S S G T L C
Sbjct: 91 TAMYYCARGLDDGAWFAYWGQGTLVTVSVASTKGPSVFPLAPSSKSTS-GGTAALGCLVK 149
Query: 209 G-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 150 DYFPQPVTVSW---NSGALTSG 168
>pdb|3NH7|H Chain H, Crystal Structure Of The Neutralizing Fab Fragment Abd1556
Bound To The Bmp Type I Receptor Ia
pdb|3NH7|I Chain I, Crystal Structure Of The Neutralizing Fab Fragment Abd1556
Bound To The Bmp Type I Receptor Ia
pdb|3NH7|J Chain J, Crystal Structure Of The Neutralizing Fab Fragment Abd1556
Bound To The Bmp Type I Receptor Ia
pdb|3NH7|K Chain K, Crystal Structure Of The Neutralizing Fab Fragment Abd1556
Bound To The Bmp Type I Receptor Ia
Length = 234
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 36/144 (25%), Positives = 56/144 (38%), Gaps = 19/144 (13%)
Query: 100 DDYPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQET 154
+Y + W++ K +E + S SGSL + RF ++ D +T L + ++
Sbjct: 30 SNYTLNWVRQAPGKGLEWVSYTSSSGSLTGYADSVKGRFTISRDNSKNTLYLQMNSLRAE 89
Query: 155 DAGIYKCE--------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCY 206
D +Y C V + P + + S S G T L C
Sbjct: 90 DTAVYYCARERWHVRGYFDHWGQGTLVTVSSASTKGPSVFPLAPSSKSTS-GGTAALGCL 148
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 149 VKDYFPEPVTVSW---NSGALTSG 169
>pdb|2VQ1|B Chain B, Anti Trimeric Lewis X Fab54-5c10-A
pdb|2VQ1|F Chain F, Anti Trimeric Lewis X Fab54-5c10-A
Length = 218
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 15/106 (14%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV-----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
LKI ++ D TYYC G G+G ++ AP + P
Sbjct: 82 LKIASVVTADTATYYCARIPGFGFDYWGQGTTLTVSSATTTAPSVYPLVPGCSDTSGSSV 141
Query: 292 ILECHVEAY-PPPAIV-W----IKDGVQ----IMNNQHYSVSHFAT 327
L C V+ Y P P V W + GV+ ++ + YS+S T
Sbjct: 142 TLGCLVKGYFPEPVTVKWNYGALSSGVRTVSSVLQSGFYSLSSLVT 187
>pdb|2JJU|A Chain A, Structure Of Human Signal Regulatory Protein (Sirp) Beta
pdb|2JJU|B Chain B, Structure Of Human Signal Regulatory Protein (Sirp) Beta
Length = 127
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 33/82 (40%), Gaps = 19/82 (23%)
Query: 191 RSVIVSEGQTVYLYCYANGF-PAPTISWRRDNSAA--------------LSTGGSIYRGN 235
+SV V+ G++ L C P I W R A ++T + + N
Sbjct: 11 KSVSVAAGESATLRCAMTSLIPVGPIMWFRGAGAGRELIYNQKEGHFPRVTTVSELTKRN 70
Query: 236 IL----KIPNITKTDRGTYYCV 253
L I NIT D GTYYCV
Sbjct: 71 NLDFSISISNITPADAGTYYCV 92
>pdb|1CT8|B Chain B, Catalytic Antibody 7c8 Complex
pdb|1CT8|D Chain D, Catalytic Antibody 7c8 Complex
Length = 220
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 34/136 (25%), Positives = 54/136 (39%), Gaps = 17/136 (12%)
Query: 106 WMKMDTAKKMEPLPISMSGSL-IIHDSRF----QLTTDPETSTYILSIKEIQETDAGIYK 160
W+K + +E + +GS +++ F +LT D +ST + + D+ IY
Sbjct: 36 WLKQKPGQSLEWIAWIYAGSGGTVYNQHFTDKARLTVDTSSSTAYMQFSSLTTEDSAIYY 95
Query: 161 C------EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FPAP 213
C E V PP + + S + V L C G FP P
Sbjct: 96 CARYRYDEGFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVKGYFPEP 154
Query: 214 -TISWRRDNSAALSTG 228
T++W NS +LS+G
Sbjct: 155 VTVTW---NSGSLSSG 167
>pdb|2PET|A Chain A, Lutheran Glycoprotein, N-Terminal Domains 1 And 2.
pdb|2PF6|A Chain A, Lutheran Glycoprotein, N-Terminal Domains 1 And 2
pdb|2PF6|B Chain B, Lutheran Glycoprotein, N-Terminal Domains 1 And 2
Length = 231
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 35/130 (26%), Positives = 48/130 (36%), Gaps = 8/130 (6%)
Query: 100 DDYPVIWMKMDTAKKMEPLP-ISMSGS---LIIHDSRFQLTTDPETSTYILSIKEIQETD 155
D Y + W D + L M GS + +HD+R + S L + E Q D
Sbjct: 29 DHYMLEWFLTDRSGARPRLASAEMQGSELQVTMHDTRGRSPPYQLDSQGRLVLAEAQVGD 88
Query: 156 AGIYKCEVIISLNNKVSAEVELIVRRPP----IISDNSTRSVIVSEGQTVYLYCYANGFP 211
Y C V A L V P + + T SV+ Q + NG P
Sbjct: 89 ERDYVCVVRAGAAGTAEATARLNVFAKPEATEVSPNKGTLSVMEDSAQEIATCNSRNGNP 148
Query: 212 APTISWRRDN 221
AP I+W R+
Sbjct: 149 APKITWYRNG 158
>pdb|4HWU|A Chain A, Crystal Structure Of The Ig-C2 Type 1 Domain From Mouse
Fibroblast Growth Factor Receptor 2 (Fgfr2)
[nysgrc-005912]
pdb|4HWU|B Chain B, Crystal Structure Of The Ig-C2 Type 1 Domain From Mouse
Fibroblast Growth Factor Receptor 2 (Fgfr2)
[nysgrc-005912]
Length = 95
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 194 IVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCV 253
+V+ G+++ L C A ISW +D ++ G L+I T D G Y C
Sbjct: 12 VVAPGESLELQCMLK--DAAVISWTKDGVHLGPNNRTVLIGEYLQIKGATPRDSGLYACT 69
Query: 254 A 254
A
Sbjct: 70 A 70
>pdb|1UJ3|B Chain B, Crystal Structure Of A Humanized Fab Fragment Of Anti-
Tissue-Factor Antibody In Complex With Tissue Factor
Length = 217
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 59/144 (40%), Gaps = 24/144 (16%)
Query: 101 DYPVIWMKMDTAKKMEPLPIS-MSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K + +E + + + ++D +FQ +T D TST + + ++ D
Sbjct: 31 DYYMHWVKQRPGQGLEWIGGNDPANGHSMYDPKFQGRVTITADTSTSTVFMELSSLRSED 90
Query: 156 AGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYCY 206
+Y C + L+ +S ST+ V + T L C
Sbjct: 91 TAVYYCARDSGYAMDYWGQGTLVT-----VSSASTKGPSVFPLAPCSRSTSESTAALGCL 145
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 146 VKDYFPEPVTVSW---NSGALTSG 166
>pdb|4AH2|B Chain B, Hla-Dr1 With Covalently Linked Clip106-120 In Canonical
Orientation
Length = 229
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 251 YCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAI--VWI 308
YC GVG + V+ P +T+ P + Q LQ+ +L C V + P +I W
Sbjct: 109 YCRHNYGVGE----SFTVQRRVEPKVTVY-PSKTQPLQHHNLLVCSVSGFYPGSIEVRWF 163
Query: 309 KDG 311
++G
Sbjct: 164 RNG 166
>pdb|3HC4|H Chain H, Bha10 Igg1 Fab Quadruple Mutant Variant - Antibody
Directed At Human Ltbr
Length = 213
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 41/104 (39%), Gaps = 14/104 (13%)
Query: 131 SRFQLTTDPETSTYILSIKEIQETDAGIYKC----EVIISLNNKVSAEVELIVRRPPIIS 186
R +T D TST + + ++ D +Y C E + V + P
Sbjct: 66 GRVTITADKSTSTAYMELSSLRSEDTAVYYCARSWEGFDYWGQGTTVTVSSASTKGP--- 122
Query: 187 DNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
S + S G T L C FP P T+SW NS AL++G
Sbjct: 123 --SVFPLAPSSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 161
>pdb|1FLR|H Chain H, 4-4-20 Fab Fragment
Length = 219
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 30/113 (26%), Positives = 46/113 (40%), Gaps = 30/113 (26%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKC--------------EVIISLNNKVSAEVEL 177
RF ++ D S+ L + ++ D GIY C V +S + V
Sbjct: 69 RFTISRDDSKSSVYLQMNNLRVEDMGIYYCTGSYYGMDYWGQGTSVTVSSAKTTAPSVYP 128
Query: 178 IVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ P+ D + G +V L C G FP P T++W NS +LS+G
Sbjct: 129 LA---PVCGDTT--------GSSVTLGCLVKGYFPEPVTLTW---NSGSLSSG 167
>pdb|1IKF|H Chain H, A Conformation Of Cyclosporin A In Aqueous Environment
Revealed By The X-Ray Structure Of A Cyclosporin-Fab
Complex
Length = 228
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 5/66 (7%)
Query: 101 DYPVIWMKMDTAKKMEPLPI--SMSGSLIIHD---SRFQLTTDPETSTYILSIKEIQETD 155
DY + W++ ++ K++E + + GS D RF ++ D +T L + ++ D
Sbjct: 31 DYYMYWVRQNSEKRLEWVAFISNGGGSAFYADIVKGRFTISRDNAKNTLYLQMSRLKSED 90
Query: 156 AGIYKC 161
+Y C
Sbjct: 91 TAMYYC 96
>pdb|3M8O|L Chain L, Human Iga1 Fab Fragment
pdb|3QNX|A Chain A, Orthorhombic Form Of Human Iga1 Fab Fragment, Sharing Same
Fv As Igg
pdb|3QNY|A Chain A, Monoclinic Form Of Human Iga1 Fab Fragment, Sharing Same
Fv As Igg
pdb|3QNY|C Chain C, Monoclinic Form Of Human Iga1 Fab Fragment, Sharing Same
Fv As Igg
pdb|3QNZ|A Chain A, Orthorhombic Form Of Igg1 Fab Fragment (in Complex With
Antigenic Tubulin Peptide) Sharing Same Fv As Iga
pdb|3QO0|A Chain A, Monoclinic Form Of Igg1 Fab Fragment (In Complex With
Antigenic Peptide) Sharing Same Fv As Iga
pdb|3QO1|A Chain A, Monoclinic Form Of Igg1 Fab Fragment (apo Form) Sharing
Same Fv As Iga
Length = 219
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 51/129 (39%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D GTYYC+ G+G + I V AP + I P Q A
Sbjct: 78 LKIIRVEAEDAGTYYCMQNKQTPLTFGQGTRLEIKRTVA-APSVFIFPPSDEQLKSGTAS 136
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 137 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 195
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 196 VYACEVTHQ 204
>pdb|1GSA|A Chain A, Structure Of Glutathione Synthetase Complexed With Adp And
Glutathione
pdb|1GSH|A Chain A, Structure Of Escherichia Coli Glutathione Synthetase At Ph
7.5
pdb|2GLT|A Chain A, Structure Of Escherichia Coli Glutathione Synthetase At Ph
6.0
Length = 316
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 15/69 (21%)
Query: 228 GGSIYR---GNILKIPNI-----TKTDRGTYYCVAQN---GVGRGMKRNIAVEVEFAPVI 276
G SI+R G+ PN+ T T+ GT YC+AQN + G KR + V+ E P
Sbjct: 167 GASIFRVKEGD----PNLGVIAETLTEHGTRYCMAQNYLPAIKDGDKRVLVVDGEPVPYC 222
Query: 277 TINRPRQGQ 285
P+ G+
Sbjct: 223 LARIPQGGE 231
>pdb|2QHR|H Chain H, Crystal Structure Of The 13f6-1-2 Fab Fragment Bound To
Its Ebola Virus Glycoprotein Peptide Epitope
Length = 222
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 34/144 (23%), Positives = 61/144 (42%), Gaps = 20/144 (13%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K++E + IS G + RF ++ D +T L + ++ D
Sbjct: 32 YDMSWVRQTPEKRLEWVAYISRGGGYTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDT 91
Query: 157 GIYKCEVIISLNNKVSAEVELIVRRPPI-ISDNSTRSVIV---------SEGQTVYLYCY 206
+Y C I + ++ + + +S T + V + G +V L C
Sbjct: 92 AMYYCSRHIYYGSSHYYAMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCL 151
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 152 VKGYFPEPVTLTW---NSGSLSSG 172
>pdb|4FAB|H Chain H, Three-Dimensional Structure Of A Fluorescein-Fab Complex
Crystallized In 2-Methyl-2,4-Pentanediol
Length = 216
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 30/113 (26%), Positives = 46/113 (40%), Gaps = 30/113 (26%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKC--------------EVIISLNNKVSAEVEL 177
RF ++ D S+ L + ++ D GIY C V +S + V
Sbjct: 69 RFTISRDDSKSSVYLQMNNLRVEDMGIYYCTGSYYGMDYWGQGTSVTVSSAKTTAPSVYP 128
Query: 178 IVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ P+ D + G +V L C G FP P T++W NS +LS+G
Sbjct: 129 LA---PVCGDTT--------GSSVTLGCLVKGYFPEPVTLTW---NSGSLSSG 167
>pdb|1EJO|H Chain H, Fab Fragment Of Neutralising Monoclonal Antibody 4c4
Complexed With G-H Loop From Fmdv
Length = 220
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 36/143 (25%), Positives = 60/143 (41%), Gaps = 21/143 (14%)
Query: 102 YPVIWMKMDTAKKMEPLPISMSGSLIIH-----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K++E + SG + RF ++ D ST L + ++ D
Sbjct: 32 YTMSWVRQTPEKRLEWVATISSGGAYTYYPDSVKGRFTISDDNAESTLYLQMSSLRSEDT 91
Query: 157 GIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYCYA 207
+Y C V + ++ V R +S T + V + G +V L C
Sbjct: 92 AMYYC-VRRAFDSDV-GFASWGHRTLVTVSAAKTTAPSVYPLAPVCGGTTGSSVTLGCLV 149
Query: 208 NG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 150 KGYFPEPVTLTW---NSGSLSSG 169
>pdb|1K6Q|H Chain H, Crystal Structure Of Antibody Fab Fragment D3
Length = 216
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 35/140 (25%), Positives = 57/140 (40%), Gaps = 16/140 (11%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K + +E + I I+D +FQ +T D ++T L + + D
Sbjct: 31 DYYMHWVKQRPEQGLELIGWIDPENGNTIYDPKFQDKASITADTSSNTAYLQLSSLTSED 90
Query: 156 AGIYKCEVIIS-----LNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG- 209
+Y C + + V PP + + S + V L C G
Sbjct: 91 TAVYYCARDTAAYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVKGY 149
Query: 210 FPAP-TISWRRDNSAALSTG 228
FP P T++W NS +LS+G
Sbjct: 150 FPEPVTVTW---NSGSLSSG 166
>pdb|2R0W|H Chain H, Pfa2 Fab Complexed With Abeta1-8
Length = 223
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 30/77 (38%), Gaps = 10/77 (12%)
Query: 236 ILKIPNITKTDRGTYYCV--AQNGV--------GRGMKRNIAVEVEFAPVITINRPRQGQ 285
LKI ++ D TYYCV A N V G+G ++ AP + P G
Sbjct: 81 FLKITSVDTADTATYYCVRRAHNVVLGDWFAYWGQGTLVTVSAAKTTAPSVYPLAPVCGD 140
Query: 286 ALQYDAILECHVEAYPP 302
L C V+ Y P
Sbjct: 141 TTGSSVTLGCLVKGYFP 157
>pdb|3PDO|B Chain B, Crystal Structure Of Hla-Dr1 With Clip102-120
pdb|3PGC|B Chain B, Crystal Structure Of Hla-Dr1 With Clip106-120, Flipped
Peptide Orientation
pdb|3PGC|E Chain E, Crystal Structure Of Hla-Dr1 With Clip106-120, Flipped
Peptide Orientation
pdb|3PGD|B Chain B, Crystal Structure Of Hla-Dr1 With Clip106-120, Canonical
Peptide Orientation
pdb|3PGD|E Chain E, Crystal Structure Of Hla-Dr1 With Clip106-120, Canonical
Peptide Orientation
pdb|4AEN|B Chain B, Hla-Dr1 With Covalently Linked Clip106-120 In Reversed
Orientation
Length = 199
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 251 YCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAI--VWI 308
YC GVG + V+ P +T+ P + Q LQ+ +L C V + P +I W
Sbjct: 79 YCRHNYGVGE----SFTVQRRVEPKVTVY-PSKTQPLQHHNLLVCSVSGFYPGSIEVRWF 133
Query: 309 KDG 311
++G
Sbjct: 134 RNG 136
>pdb|3N85|H Chain H, Crystallographic Trimer Of Her2 Extracellular Regions In
Complex With Tryptophan-Rich Antibody Fragment
Length = 224
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 44/108 (40%), Gaps = 19/108 (17%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTR 191
RF ++ D +T L + ++ D +Y C S + L+ +S ST+
Sbjct: 67 RFTISADTSKNTAYLQMNSLRAEDTAVYYCARWWSSAMDYWGQGTLVT-----VSSASTK 121
Query: 192 SVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
V + G T L C FP P T+SW NS AL++G
Sbjct: 122 GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 166
>pdb|8FAB|B Chain B, Crystal Structure Of The Fab Fragment From The Human
Myeloma Immunoglobulin Igg Hil At 1.8 Angstroms
Resolution
pdb|8FAB|D Chain D, Crystal Structure Of The Fab Fragment From The Human
Myeloma Immunoglobulin Igg Hil At 1.8 Angstroms
Resolution
Length = 224
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 34/148 (22%), Positives = 62/148 (41%), Gaps = 28/148 (18%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHD----SRFQLTTDPETSTYILSIKEIQETD 155
+Y + W++ K +E + I +GS + RF ++ D T + + ++ D
Sbjct: 31 NYGMHWVRQAPGKGLEWVAVIWYNGSRTYYGDSVKGRFTISRDNSKRTLYMQMNSLRTED 90
Query: 156 AGIYKC----EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVY 202
+Y C +++ + + + L+ +S ST+ V + G T
Sbjct: 91 TAVYYCARDPDILTAFSFDYWGQGVLVT-----VSSASTKGPSVFPLAPSSKSTSGGTAA 145
Query: 203 LYCYANG-FPAP-TISWRRDNSAALSTG 228
L C FP P T+SW NS AL++G
Sbjct: 146 LGCLVKDYFPEPVTVSW---NSGALTSG 170
>pdb|2W60|A Chain A, Anti Citrullinated Collagen Type 2 Antibody Acc4
Length = 218
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 39/165 (23%), Positives = 62/165 (37%), Gaps = 19/165 (11%)
Query: 79 SQEQIKDIAQTADLKC--SVQYADDYPVIWMKMDTAKKMEPLPI--SMSGSLIIHD---S 131
S ++K +T + C S DY + W+K K ++ + + +G D
Sbjct: 7 SGPELKKPGETVKISCKASGYTFTDYSIHWVKQAPGKGLKWMGWINTETGEPTYTDDFKG 66
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIIS------LNNKVSAEVELIVRRPPII 185
RF + + ST L I ++ D Y C + V PP +
Sbjct: 67 RFAFSLESSASTAFLQINNLKNEDTATYFCARATTATELAYWGQGTLVTVSAAKTTPPSV 126
Query: 186 SDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ S + V L C G FP P T++W NS +LS+G
Sbjct: 127 YPLAPGSAAQTNSM-VTLGCLVKGYFPEPVTVTW---NSGSLSSG 167
>pdb|1AQD|B Chain B, Hla-Dr1 (Dra, Drb1 0101) Human Class Ii Histocompatibility
Protein (Extracellular Domain) Complexed With Endogenous
Peptide
pdb|1AQD|E Chain E, Hla-Dr1 (Dra, Drb1 0101) Human Class Ii Histocompatibility
Protein (Extracellular Domain) Complexed With Endogenous
Peptide
pdb|1AQD|H Chain H, Hla-Dr1 (Dra, Drb1 0101) Human Class Ii Histocompatibility
Protein (Extracellular Domain) Complexed With Endogenous
Peptide
pdb|1AQD|K Chain K, Hla-Dr1 (Dra, Drb1 0101) Human Class Ii Histocompatibility
Protein (Extracellular Domain) Complexed With Endogenous
Peptide
Length = 198
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 251 YCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAI--VWI 308
YC GVG + V+ P +T+ P + Q LQ+ +L C V + P +I W
Sbjct: 78 YCRHNYGVGE----SFTVQRRVEPKVTVY-PSKTQPLQHHNLLVCSVSGFYPGSIEVRWF 132
Query: 309 KDG 311
++G
Sbjct: 133 RNG 135
>pdb|3MLR|H Chain H, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With A Ny5 V3 Peptide
pdb|3MLS|H Chain H, Crystal Structure Of Anti-Hiv-1 V3 Mab 2557 Fab In Complex
With A Hiv- 1 Gp120 V3 Mimotope
pdb|3MLS|I Chain I, Crystal Structure Of Anti-Hiv-1 V3 Mab 2557 Fab In Complex
With A Hiv- 1 Gp120 V3 Mimotope
pdb|3MLS|J Chain J, Crystal Structure Of Anti-Hiv-1 V3 Mab 2557 Fab In Complex
With A Hiv- 1 Gp120 V3 Mimotope
pdb|3MLS|K Chain K, Crystal Structure Of Anti-Hiv-1 V3 Mab 2557 Fab In Complex
With A Hiv- 1 Gp120 V3 Mimotope
pdb|3MLT|H Chain H, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With A Ug1033 V3 Peptide
pdb|3MLT|B Chain B, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With A Ug1033 V3 Peptide
pdb|3MLT|E Chain E, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With A Ug1033 V3 Peptide
pdb|3MLT|I Chain I, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With A Ug1033 V3 Peptide
pdb|3MLU|H Chain H, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With A Zam18 V3 Peptide
pdb|3MLV|H Chain H, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With An Nof V3 Peptide
pdb|3MLV|N Chain N, Crystal Structure Of Anti-Hiv-1 V3 Fab 2557 In Complex
With An Nof V3 Peptide
Length = 226
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 39/171 (22%), Positives = 67/171 (39%), Gaps = 25/171 (14%)
Query: 79 SQEQIKDIAQTADLKC---SVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIH-----D 130
S ++K Q+ + C + D + + W++ K +E + I H +
Sbjct: 7 SGGEVKQPGQSLKISCKSSGYNFLDSW-IGWVRQIPGKGLEWIGIIYPDDSDAHYSPSFE 65
Query: 131 SRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPII--SDN 188
+ ++ D ST L +Q +D G Y C + S+ + + +I S
Sbjct: 66 GQVTMSVDKSISTAYLQWTTLQASDTGKYFCTRLYLFEGAQSSNAFDLWGQGTMILVSSG 125
Query: 189 STRSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+T+ V + G T L C FP P T+SW NS AL++G
Sbjct: 126 TTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 173
>pdb|4FA8|A Chain A, Multi-Pronged Modulation Of Cytokine Signaling
pdb|4FA8|B Chain B, Multi-Pronged Modulation Of Cytokine Signaling
pdb|4FA8|D Chain D, Multi-Pronged Modulation Of Cytokine Signaling
Length = 203
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 142 STYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTV 201
+T+ L + + G Y C + + +V+ + L V +P +S +S RS + +
Sbjct: 67 NTFFLVVTAANISHDGNYLCRMKLG-ETEVTKQEHLSVVKPLTLSVHSERSQF-PDFSVL 124
Query: 202 YLYCYANGFPAPTISW 217
+ C N FP P + W
Sbjct: 125 TVTCTVNAFPHPHVQW 140
>pdb|3S35|H Chain H, Structural Basis For The Function Of Two Anti-Vegf
Receptor Antibodies
Length = 217
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 35/140 (25%), Positives = 60/140 (42%), Gaps = 16/140 (11%)
Query: 101 DYPVIWMKMDTAKKMEPLPISMSGSLII-HDSRFQ----LTTDPETSTYILSIKEIQETD 155
+Y + W+K + + +E + S II ++ +F+ LT D +ST + + + D
Sbjct: 31 EYIIHWVKQRSGQGLEWIGWLYPESNIIKYNEKFKDKATLTADKSSSTVYMELSRLTSED 90
Query: 156 AGIYKCEVIISLN-----NKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG- 209
+ +Y C N + V PP + + S + V L C G
Sbjct: 91 SAVYFCTRHDGTNFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVKGY 149
Query: 210 FPAP-TISWRRDNSAALSTG 228
FP P T++W NS +LS+G
Sbjct: 150 FPEPVTVTW---NSGSLSSG 166
>pdb|3L6F|B Chain B, Structure Of Mhc Class Ii Molecule Hla-Dr1 Complexed With
Phosphopeptide Mart-1
pdb|3S4S|B Chain B, Crystal Structure Of Cd4 Mutant Bound To Hla-Dr1
pdb|3S4S|E Chain E, Crystal Structure Of Cd4 Mutant Bound To Hla-Dr1
pdb|3S5L|B Chain B, Crystal Structure Of Cd4 Mutant Bound To Hla-Dr1
pdb|3S5L|E Chain E, Crystal Structure Of Cd4 Mutant Bound To Hla-Dr1
Length = 193
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 251 YCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAI--VWI 308
YC GVG + V+ P +T+ P + Q LQ+ +L C V + P +I W
Sbjct: 79 YCRHNYGVGE----SFTVQRRVEPKVTVY-PSKTQPLQHHNLLVCSVSGFYPGSIEVRWF 133
Query: 309 KDG 311
++G
Sbjct: 134 RNG 136
>pdb|4FQX|B Chain B, Crystal Structure Of Hla-Dm Bound To Hla-Dr1
pdb|4GBX|B Chain B, Crystal Structure Of An Immune Complex At Ph 6.5
Length = 208
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 251 YCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAI--VWI 308
YC GVG + V+ P +T+ P + Q LQ+ +L C V + P +I W
Sbjct: 84 YCRHNYGVGE----SFTVQRRVEPKVTVY-PSKTQPLQHHNLLVCSVSGFYPGSIEVRWF 138
Query: 309 KDG 311
++G
Sbjct: 139 RNG 141
>pdb|1TZI|B Chain B, Crystal Structure Of The Fab Yads2 Complexed With H-Vegf
Length = 222
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 36/145 (24%), Positives = 61/145 (42%), Gaps = 23/145 (15%)
Query: 101 DYPVIWMKMDTAKKMEPLP--ISMSGSLIIHDS---RFQLTTDPETSTYILSIKEIQETD 155
DY + W++ K +E + +G+ DS RF ++ D +T L + ++ D
Sbjct: 31 DYDIHWVRQAPGKGLEWVADIAPYAGATAYADSVKGRFTISADTSKNTAYLQMNSLRAED 90
Query: 156 AGIYKCEVIISLNNKVSAEVELIVRRPPI-ISDNSTRSVIV---------SEGQTVYLYC 205
+Y C + A ++ + + +S ST+ V + G T L C
Sbjct: 91 TAVYYCS---RSSYAYYAAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGC 147
Query: 206 YANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 148 LVKDYFPEPVTVSW---NSGALTSG 169
>pdb|1SEB|B Chain B, Complex Of The Human Mhc Class Ii Glycoprotein Hla-Dr1 And
The Bacterial Superantigen Seb
pdb|1SEB|F Chain F, Complex Of The Human Mhc Class Ii Glycoprotein Hla-Dr1 And
The Bacterial Superantigen Seb
pdb|1FYT|B Chain B, Crystal Structure Of A Complex Of A Human AlphaBETA-T Cell
Receptor, Influenza Ha Antigen Peptide, And Mhc Class Ii
Molecule, Hla-Dr1
Length = 192
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 251 YCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAI--VWI 308
YC GVG + V+ P +T+ P + Q LQ+ +L C V + P +I W
Sbjct: 78 YCRHNYGVGE----SFTVQRRVEPKVTVY-PSKTQPLQHHNLLVCSVSGFYPGSIEVRWF 132
Query: 309 KDG 311
++G
Sbjct: 133 RNG 135
>pdb|3HC3|H Chain H, Bha10 Igg1 Fab Double Mutant Variant - Antibody Directed
At Human Ltbr
Length = 217
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 37/163 (22%), Positives = 63/163 (38%), Gaps = 17/163 (10%)
Query: 79 SQEQIKDIAQTADLKC--SVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIH-----DS 131
S ++K ++ + C S Y + W++ + +E + G++
Sbjct: 7 SGAEVKKPGESVKVSCKASGYTFTTYYLHWVRQAPGQGLEWMGWIYPGNVHAQYNEKFKG 66
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKC----EVIISLNNKVSAEVELIVRRPPIISD 187
R +T D TST + + ++ D +Y C E + V + P +
Sbjct: 67 RVTITADKSTSTAYMELSSLRSEDTAVYYCARSWEGFPYWGQGTTVTVSSASTKGPSVFP 126
Query: 188 NSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ S S G T L C FP P T+SW NS AL++G
Sbjct: 127 LAPSSKSTS-GGTAALGCLVKDYFPEPVTVSW---NSGALTSG 165
>pdb|2ZUQ|C Chain C, Crystal Structure Of Dsbb-Fab Complex
pdb|2ZUQ|F Chain F, Crystal Structure Of Dsbb-Fab Complex
pdb|2LTQ|C Chain C, High Resolution Structure Of Dsbb C41s By Joint
Calculation With Solid-state Nmr And X-ray Data
pdb|2LTQ|F Chain F, High Resolution Structure Of Dsbb C41s By Joint
Calculation With Solid-state Nmr And X-ray Data
Length = 221
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 36/151 (23%), Positives = 60/151 (39%), Gaps = 38/151 (25%)
Query: 102 YPVIWMKMDTAKKMEPLPI--SMSGSLIIHDS---RFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K++E + S GS D+ RF ++ D +T L + ++ D
Sbjct: 32 YDMSWVRQTPEKRLEWVAYISSGGGSTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDT 91
Query: 157 GIYKC-----------------EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQ 199
+Y C V +S + V + P+ D + G
Sbjct: 92 AMYYCARPDYRSYAMDYWGQGTSVTVSSAKTTAPSVYPLA---PVCGDTT--------GS 140
Query: 200 TVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+V L C G FP P T++W NS +LS+G
Sbjct: 141 SVTLGCLVKGYFPEPVTLTW---NSGSLSSG 168
>pdb|3BZ4|B Chain B, Crystal Structure Of Fab F22-4 In Complex With A Shigella
Flexneri 2a O-Ag Decasaccharide
pdb|3BZ4|D Chain D, Crystal Structure Of Fab F22-4 In Complex With A Shigella
Flexneri 2a O-Ag Decasaccharide
pdb|3BZ4|F Chain F, Crystal Structure Of Fab F22-4 In Complex With A Shigella
Flexneri 2a O-Ag Decasaccharide
pdb|3BZ4|H Chain H, Crystal Structure Of Fab F22-4 In Complex With A Shigella
Flexneri 2a O-Ag Decasaccharide
pdb|3C5S|B Chain B, Crystal Structure Of Monoclonal Fab F22-4 Specific For
Shigella Flexneri 2a O-Ag
pdb|3C5S|D Chain D, Crystal Structure Of Monoclonal Fab F22-4 Specific For
Shigella Flexneri 2a O-Ag
pdb|3C6S|B Chain B, Crystal Structure Of Fab F22-4 In Complex With A Shigella
Flexneri 2a O-Ag Pentadecasaccharide
pdb|3C6S|D Chain D, Crystal Structure Of Fab F22-4 In Complex With A Shigella
Flexneri 2a O-Ag Pentadecasaccharide
pdb|3C6S|F Chain F, Crystal Structure Of Fab F22-4 In Complex With A Shigella
Flexneri 2a O-Ag Pentadecasaccharide
pdb|3C6S|H Chain H, Crystal Structure Of Fab F22-4 In Complex With A Shigella
Flexneri 2a O-Ag Pentadecasaccharide
pdb|3GGW|B Chain B, Crystal Structure Of Fab F22-4 In Complex With A
Carbohydrate-Mimetic Peptide
pdb|3GGW|D Chain D, Crystal Structure Of Fab F22-4 In Complex With A
Carbohydrate-Mimetic Peptide
Length = 217
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 43/100 (43%), Gaps = 7/100 (7%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIIS-LNNKVSAEVELIVRRPPIISDNST 190
+F ++ D S L + ++ D GIY C + + S V PP + +
Sbjct: 69 KFTISRDDSKSRLYLQMNNLRTEDTGIYYCFLPMDYWGQGTSVTVSSAKTTPPSVYPLAP 128
Query: 191 RSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
S + V L C G FP P T++W NS +LS+G
Sbjct: 129 GSAAQTNSM-VTLGCLVKGYFPEPVTVTW---NSGSLSSG 164
>pdb|3EOT|H Chain H, Crystal Structure Of Lac031, An Engineered Anti-Vla1 Fab
Length = 226
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 36/140 (25%), Positives = 57/140 (40%), Gaps = 17/140 (12%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIHDS---RFQLTTDPETSTYILSIKEIQETDAG 157
Y + W++ K +E + IS G DS RF ++ D +T L + ++ D
Sbjct: 32 YTMSWVRQAPGKGLEWVATISGGGHTYYLDSVKGRFTISRDNSKNTLYLQMNSLRAEDTA 91
Query: 158 IYKCEVIISLNN--KVSAEVELIV-----RRPPIISDNSTRSVIVSEGQTVYLYCYANG- 209
+Y C V + L+ PP + + S + V L C G
Sbjct: 92 VYYCTRGFGDGGYFDVWGQGTLVTVSSAKTTPPSVYPLAPGSAAQTN-SMVTLGCLVKGY 150
Query: 210 FPAP-TISWRRDNSAALSTG 228
FP P T++W NS +LS+G
Sbjct: 151 FPEPVTVTW---NSGSLSSG 167
>pdb|2JJV|A Chain A, Structure Of Human Signal Regulatory Protein (sirp)
Beta(2)
pdb|2JJV|B Chain B, Structure Of Human Signal Regulatory Protein (sirp)
Beta(2)
Length = 127
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 34/82 (41%), Gaps = 19/82 (23%)
Query: 191 RSVIVSEGQTVYLYCYANGF-PAPTISWRRDNSAA--------------LSTGGSIYRGN 235
+S+ V+ G++ L+C P I W R ++T + + N
Sbjct: 11 KSISVAAGESATLHCTVTSLIPVGPIQWFRGAGPGRELIYNQKEGHFPRVTTVSDLTKRN 70
Query: 236 IL----KIPNITKTDRGTYYCV 253
+ +I NIT D GTYYCV
Sbjct: 71 NMDFSIRISNITPADAGTYYCV 92
>pdb|2O5X|L Chain L, Crystal Structure Of 1e9 Leuh47trpARGH100TRP, AN
ENGINEERED DIELS- Alderase Fab With Nm Steroid-Binding
Affinity
pdb|2O5Y|L Chain L, Crystal Structure Of The 1e9 Leuh47trpARGH100TRP FAB
PROGESTERONE Complex
pdb|2O5Z|L Chain L, Crystal Structure Of The 1e9 Leuh47trpARGH100TRP FAB
5-Beta- Androstane-3,17-Dione Complex
Length = 219
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 49/207 (23%), Positives = 77/207 (37%), Gaps = 29/207 (14%)
Query: 176 ELIVRRPPI-----------ISDNSTRSVIVSEGQTVYLYCYANG------FPAPTISWR 218
EL++ + P+ IS S++S++ S G T YL+ Y F +S R
Sbjct: 1 ELVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNT-YLHWYLQKPGQSPKFLIYKVSNR 59
Query: 219 RDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAP 274
+G ILKI + D G Y+C G G K I V AP
Sbjct: 60 FSGVPDRFSGSGSGTDFILKISRVEAEDLGVYFCFQSTHFFPTFGGGTKLEIKRTVA-AP 118
Query: 275 VITINRPRQGQALQYDAILECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFS 332
+ I P Q A + C + + P + W D N SV+ + D
Sbjct: 119 SVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTY 178
Query: 333 DTSLRVITIERRQFGQ---YACKAANK 356
S +T+ + + + YAC+ ++
Sbjct: 179 SLS-STLTLSKADYEKHKVYACEVTHQ 204
>pdb|2CH8|A Chain A, Structure Of The Epstein-barr Virus Oncogene Barf1
pdb|2CH8|B Chain B, Structure Of The Epstein-barr Virus Oncogene Barf1
pdb|2CH8|C Chain C, Structure Of The Epstein-barr Virus Oncogene Barf1
pdb|2CH8|D Chain D, Structure Of The Epstein-barr Virus Oncogene Barf1
Length = 201
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 142 STYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTV 201
+T+ L + + G Y C + + +V+ + L V +P +S +S RS + +
Sbjct: 65 NTFFLVVTAANISHDGNYLCRMKLG-ETEVTKQEHLSVVKPLTLSVHSERSQF-PDFSVL 122
Query: 202 YLYCYANGFPAPTISW 217
+ C N FP P + W
Sbjct: 123 TVTCTVNAFPHPHVQW 138
>pdb|1DLH|B Chain B, Crystal Structure Of The Human Class Ii Mhc Protein
Hla-dr1 Complexed With An Influenza Virus Peptide
pdb|1DLH|E Chain E, Crystal Structure Of The Human Class Ii Mhc Protein
Hla-dr1 Complexed With An Influenza Virus Peptide
pdb|1KG0|B Chain B, Structure Of The Epstein-Barr Virus Gp42 Protein Bound To
The Mhc Class Ii Receptor Hla-Dr1
Length = 188
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 251 YCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAI--VWI 308
YC GVG + V+ P +T+ P + Q LQ+ +L C V + P +I W
Sbjct: 76 YCRHNYGVGE----SFTVQRRVEPKVTVY-PSKTQPLQHHNLLVCSVSGFYPGSIEVRWF 130
Query: 309 KDG 311
++G
Sbjct: 131 RNG 133
>pdb|1NL0|H Chain H, Crystal Structure Of Human Factor Ix Gla Domain In Complex
Of An Inhibitory Antibody, 10c12
pdb|3D69|H Chain H, Crystal Structure Of The Fab Fragment Of An Anti-Factor Ix
Antibody 10c12
pdb|3D69|B Chain B, Crystal Structure Of The Fab Fragment Of An Anti-Factor Ix
Antibody 10c12
Length = 224
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 38/145 (26%), Positives = 61/145 (42%), Gaps = 25/145 (17%)
Query: 102 YPVIWMKMDTAKKMEPLPI-SMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K +E + I S GS + RF ++ D +T L + ++ D
Sbjct: 32 YAMHWVRQAPGKGLEWVAIISYDGSKKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDT 91
Query: 157 GIYKCEVIISLNNKVSAEVELIVRRPPI--ISDNSTRSVIV---------SEGQTVYLYC 205
+Y C + + +A V R + +S ST+ V + G T L C
Sbjct: 92 AVYYC----ARASIAAARVLDYWGRGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGC 147
Query: 206 YANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 148 LVKDYFPEPVTVSW---NSGALTSG 169
>pdb|2B2X|H Chain H, Vla1 Rdeltah I-Domain Complexed With A Quadruple Mutant Of
The Aqc2 Fab
pdb|2B2X|I Chain I, Vla1 Rdeltah I-Domain Complexed With A Quadruple Mutant Of
The Aqc2 Fab
Length = 226
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 36/140 (25%), Positives = 57/140 (40%), Gaps = 17/140 (12%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIHDS---RFQLTTDPETSTYILSIKEIQETDAG 157
Y + W++ K +E + IS G DS RF ++ D +T L + ++ D
Sbjct: 32 YTMSWVRQAPGKGLEWVAVISGGGHTYYLDSVEGRFTISRDNSKNTLYLQMNSLRAEDTA 91
Query: 158 IYKCEVIISLNN--KVSAEVELIV-----RRPPIISDNSTRSVIVSEGQTVYLYCYANG- 209
+Y C V + L+ PP + + S + V L C G
Sbjct: 92 VYYCTRGFGDGGYFDVWGQGTLVTVSSAKTTPPSVYPLAPGSAAQTN-SMVTLGCLVKGY 150
Query: 210 FPAP-TISWRRDNSAALSTG 228
FP P T++W NS +LS+G
Sbjct: 151 FPEPVTVTW---NSGSLSSG 167
>pdb|3SKJ|L Chain L, Structural And Functional Characterization Of An Agonistic
Anti-Human Epha2 Monoclonal Antibody
pdb|3SKJ|M Chain M, Structural And Functional Characterization Of An Agonistic
Anti-Human Epha2 Monoclonal Antibody
Length = 214
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 30/128 (23%), Positives = 49/128 (38%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVE---FAPVITINRPRQGQALQYDAIL 293
L I + D TYYC N R + VE++ AP + I P Q A +
Sbjct: 73 LTISGLQPDDFATYYCQQYNSYSRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASV 132
Query: 294 ECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ--- 348
C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 133 VCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHKV 191
Query: 349 YACKAANK 356
YAC+ ++
Sbjct: 192 YACEVTHQ 199
>pdb|3IF1|B Chain B, Crystal Structure Of 237mab In Complex With A Galnac
pdb|3IF1|D Chain D, Crystal Structure Of 237mab In Complex With A Galnac
Length = 217
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 28/111 (25%), Positives = 44/111 (39%), Gaps = 24/111 (21%)
Query: 131 SRFQLTTDPETSTYILSIKEIQETDAGIYKC-----------EVIISLNNKVSAEVELIV 179
RF +T D S L + ++ D GIY C + + + + +
Sbjct: 68 GRFTITRDDSKSRMSLQMNSLRAEDTGIYYCSGGKVRNAYWGQGTTVTVSSKTTKAPSVY 127
Query: 180 RRPPIISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
P+ D + G +V L C G FP P T++W NS +LS+G
Sbjct: 128 PLAPVCGDTT--------GSSVTLGCLVKGYFPEPVTLTW---NSGSLSSG 167
>pdb|3IET|B Chain B, Crystal Structure Of 237mab With Antigen
pdb|3IET|D Chain D, Crystal Structure Of 237mab With Antigen
Length = 218
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 28/111 (25%), Positives = 43/111 (38%), Gaps = 24/111 (21%)
Query: 131 SRFQLTTDPETSTYILSIKEIQETDAGIYKC-----------EVIISLNNKVSAEVELIV 179
RF +T D S L + ++ D GIY C + + + +
Sbjct: 68 GRFTITRDDSKSRMSLQMNSLRAEDTGIYYCSGGKVRNAYWGQGTTVTVSSKTTTAPSVY 127
Query: 180 RRPPIISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
P+ D + G +V L C G FP P T++W NS +LS+G
Sbjct: 128 PLAPVCGDTT--------GSSVTLGCLVKGYFPEPVTLTW---NSGSLSSG 167
>pdb|3UEZ|A Chain A, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|3UEZ|B Chain B, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|3UEZ|C Chain C, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|3UEZ|D Chain D, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|A Chain A, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|B Chain B, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|C Chain C, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|D Chain D, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|E Chain E, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|F Chain F, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|M Chain M, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|N Chain N, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|O Chain O, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|P Chain P, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|Q Chain Q, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADF|R Chain R, Crystal Structure Of The Human Colony-Stimulating Factor 1
(Hcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADQ|A Chain A, Crystal Structure Of The Mouse Colony-Stimulating Factor 1
(Mcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADQ|B Chain B, Crystal Structure Of The Mouse Colony-Stimulating Factor 1
(Mcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADQ|C Chain C, Crystal Structure Of The Mouse Colony-Stimulating Factor 1
(Mcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
pdb|4ADQ|D Chain D, Crystal Structure Of The Mouse Colony-Stimulating Factor 1
(Mcsf-1) Cytokine In Complex With The Viral Receptor
Barf1
Length = 208
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 142 STYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTV 201
+T+ L + + G Y C + + +V+ + L V +P +S +S RS + +
Sbjct: 65 NTFFLVVTAANISHDGNYLCRMKLG-ETEVTKQEHLSVVKPLTLSVHSERSQF-PDFSVL 122
Query: 202 YLYCYANGFPAPTISW 217
+ C N FP P + W
Sbjct: 123 TVTCTVNAFPHPHVQW 138
>pdb|3NZH|H Chain H, Crystal Structure Of Anti-Emmprin Antibody 5f6 Fab
Length = 226
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 30/101 (29%), Positives = 43/101 (42%), Gaps = 8/101 (7%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIIS--LNNKVSAEVELIVRRPPIISDNS 189
RF ++ D S+ L + ++ D GIY C S + V + P + +
Sbjct: 70 RFTISRDDSKSSVYLQMNNLRAEDTGIYYCTPDGSDYWGQGTTLTVSSASTKGPSVFPLA 129
Query: 190 TRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
S S G T L C FP P T+SW NS AL++G
Sbjct: 130 PSSKSTS-GGTAALGCLVKDYFPEPVTVSW---NSGALTSG 166
>pdb|1HXY|B Chain B, Crystal Structure Of Staphylococcal Enterotoxin H In
Complex With Human Mhc Class Ii
pdb|1KLG|B Chain B, Crystal Structure Of Hla-Dr1TPI(23-37, Thr28-->ile Mutant)
Complexed With Staphylococcal Enterotoxin C3 Variant 3b2
(Sec3-3b2)
pdb|1KLU|B Chain B, Crystal Structure Of Hla-Dr1TPI(23-37) Complexed With
Staphylococcal Enterotoxin C3 Variant 3b2 (Sec3-3b2)
pdb|1LO5|B Chain B, Crystal Structure Of The D227a Variant Of Staphylococcal
Enterotoxin A In Complex With Human Mhc Class Ii
pdb|1JWM|B Chain B, Crystal Structure Of The Complex Of The Mhc Class Ii
Molecule Hla-Dr1(Ha Peptide 306-318) With The
Superantigen Sec3
pdb|1JWS|B Chain B, Crystal Structure Of The Complex Of The Mhc Class Ii
Molecule Hla-Dr1 (Ha Peptide 306-318) With The
Superantigen Sec3 Variant 3b1
pdb|1JWU|B Chain B, Crystal Structure Of The Complex Of The Mhc Class Ii
Molecule Hla-Dr1 (Ha Peptide 306-318) With The
Superantigen Sec3 Variant 3b2
pdb|1PYW|B Chain B, Human Class Ii Mhc Protein Hla-Dr1 Bound To A Designed
Peptide Related To Influenza Virus Hemagglutinin,
Fvkqna(Maa)al, In Complex With Staphylococcal
Enterotoxin C3 Variant 3b2 (Sec3-3b2)
pdb|1R5I|B Chain B, Crystal Structure Of The Mam-Mhc Complex
pdb|1R5I|F Chain F, Crystal Structure Of The Mam-Mhc Complex
pdb|1SJE|B Chain B, Hla-Dr1 Complexed With A 16 Residue Hiv Capsid Peptide
Bound In A Hairpin Conformation
pdb|1SJH|B Chain B, Hla-Dr1 Complexed With A 13 Residue Hiv Capsid Peptide
pdb|1T5W|B Chain B, Hla-Dr1 In Complex With A Synthetic Peptide
(Aaysdqatplllspr)
pdb|1T5W|E Chain E, Hla-Dr1 In Complex With A Synthetic Peptide
(Aaysdqatplllspr)
pdb|1T5X|B Chain B, Hla-Dr1 In Complex With A Synthetic Peptide
(Aaysdqatplllspr) And The Superantigen Sec3-3b2
pdb|2G9H|B Chain B, Crystal Structure Of Staphylococcal Enterotoxin I (Sei) In
Complex With A Human Mhc Class Ii Molecule
pdb|2OJE|B Chain B, Mycoplasma Arthritidis-Derived Mitogen Complexed With
Class Ii Mhc Molecule Hla-Dr1HA COMPLEX IN THE PRESENCE
OF EDTA
pdb|2OJE|F Chain F, Mycoplasma Arthritidis-Derived Mitogen Complexed With
Class Ii Mhc Molecule Hla-Dr1HA COMPLEX IN THE PRESENCE
OF EDTA
pdb|2IAM|B Chain B, Structural Basis For Recognition Of Mutant Self By A
Tumor- Specific, Mhc Class Ii-Restricted Tcr
pdb|2IAN|B Chain B, Structural Basis For Recognition Of Mutant Self By A
Tumor- Specific, Mhc Class Ii-Restricted Tcr
pdb|2IAN|G Chain G, Structural Basis For Recognition Of Mutant Self By A
Tumor- Specific, Mhc Class Ii-Restricted Tcr
pdb|2IAN|L Chain L, Structural Basis For Recognition Of Mutant Self By A
Tumor- Specific, Mhc Class Ii-Restricted Tcr
pdb|2IAN|Q Chain Q, Structural Basis For Recognition Of Mutant Self By A
Tumor- Specific, Mhc Class Ii-Restricted Tcr
pdb|2ICW|B Chain B, Crystal Structure Of A Complete Ternary Complex Between
Tcr, Superantigen, And Peptide-Mhc Class Ii Molecule
pdb|2ICW|E Chain E, Crystal Structure Of A Complete Ternary Complex Between
Tcr, Superantigen, And Peptide-Mhc Class Ii Molecule
pdb|2IPK|B Chain B, Crystal Structure Of The Mhc Class Ii Molecule Hla-Dr1 In
Complex With The Fluorogenic Peptide, Acpkxvkqntlklat
(X3-
[5-(Dimethylamino)-1,3-Dioxo-1,
3-Dihydro-2h-Isoindol-2-Yl]- L-Alanine) And The
Superantigen, Sec3 Variant 3b2
pdb|2XN9|E Chain E, Crystal Structure Of The Ternary Complex Between Human T
Cell Receptor, Staphylococcal Enterotoxin H And Human
Major Histocompatibility Complex Class Ii
pdb|3QXA|B Chain B, Hla-Dr1 Bound With Clip Peptide
pdb|3QXA|E Chain E, Hla-Dr1 Bound With Clip Peptide
pdb|3QXD|B Chain B, F54c Hla-Dr1 Bound With Clip Peptide
pdb|3QXD|E Chain E, F54c Hla-Dr1 Bound With Clip Peptide
pdb|4E41|B Chain B, Structural Basis For The Recognition Of Mutant Self By A
Tumor- Specific, Mhc Class Ii-Restricted T Cell Receptor
G4
pdb|4E41|G Chain G, Structural Basis For The Recognition Of Mutant Self By A
Tumor- Specific, Mhc Class Ii-Restricted T Cell Receptor
G4
Length = 190
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 251 YCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAI--VWI 308
YC GVG + V+ P +T+ P + Q LQ+ +L C V + P +I W
Sbjct: 78 YCRHNYGVGE----SFTVQRRVEPKVTVY-PSKTQPLQHHNLLVCSVSGFYPGSIEVRWF 132
Query: 309 KDG 311
++G
Sbjct: 133 RNG 135
>pdb|3MBE|C Chain C, Tcr 21.30 In Complex With Mhc Class Ii I-Ag7hel(11-27)
pdb|3MBE|G Chain G, Tcr 21.30 In Complex With Mhc Class Ii I-Ag7hel(11-27)
Length = 229
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 9/66 (13%)
Query: 198 GQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQNG 257
G+ + L+ A G ++N ST S R + L I + D GTY+C A++G
Sbjct: 41 GRLITLFYLAQG--------TKENGRLKSTFNSKERYSTLHIKDAQLEDSGTYFCAAEDG 92
Query: 258 VGRGMK 263
G G K
Sbjct: 93 -GSGNK 97
>pdb|1I7Z|B Chain B, Antibody Gnc92h2 Bound To Ligand
pdb|1I7Z|D Chain D, Antibody Gnc92h2 Bound To Ligand
Length = 220
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 41/168 (24%), Positives = 65/168 (38%), Gaps = 26/168 (15%)
Query: 79 SQEQIKDIAQTADLKCSVQ-YA-DDYPVIWMKMDTAKKMEPLPI--SMSGSLIIHD---S 131
S ++K +T + C Y+ +Y + W+K K ++ + + +G D
Sbjct: 7 SGPELKKPGETVKISCKTSGYSFTNYGMNWVKQAPGKGLKWMGWINTYTGEPTYADDFRG 66
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTR 191
RF + ST L I ++ D Y CE S + + +S ST+
Sbjct: 67 RFAFSLATSASTAYLQIINLKNEDTATYFCETYDSPLGDYWGQGTTVT-----VSSASTK 121
Query: 192 SVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
V + G T L C FP P T+SW NS AL++G
Sbjct: 122 GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 166
>pdb|3TO4|C Chain C, Structure Of Mouse
Valpha14vbeta2-Mousecd1d-Alpha-Galactosylceramide
Length = 212
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 27/72 (37%)
Query: 92 LKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYILSIKEI 151
L+C+ D + W K DT K + L + + + R+ T D + L I
Sbjct: 20 LQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGRYSATLDKDAKHSTLHITAT 79
Query: 152 QETDAGIYKCEV 163
D Y C V
Sbjct: 80 LLDDTATYICVV 91
>pdb|1J1P|L Chain L, Crystal Structure Of Hyhel-10 Fv Mutant Ls91a Complexed
With Hen Egg White Lysozyme
Length = 107
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 323 SHFATSDEFSDTSLRVITIERRQFGQYACKAANKY 357
S F+ S +D +L + ++E FG Y C+ AN +
Sbjct: 60 SRFSGSGSGTDFTLSINSVETEDFGMYFCQQANSW 94
>pdb|1A0Q|H Chain H, 29g11 Complexed With Phenyl [1-(1-N-Succinylamino)pentyl]
Phosphonate
Length = 217
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 34/142 (23%), Positives = 60/142 (42%), Gaps = 18/142 (12%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
D+ + W+K + +E + IS I ++ +F+ LT D +ST + + + D
Sbjct: 31 DHVIHWVKQKPEQGLEWIGYISPGNGDIKYNEKFKGKATLTADKSSSTAYMQLNSLTSED 90
Query: 156 AGIYKCEV-------IISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYAN 208
+ +Y C+ + + V PP + + S + V L C
Sbjct: 91 SAVYLCKRGYYGRSNVDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVK 149
Query: 209 G-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 150 GYFPEPVTVTW---NSGSLSSG 168
>pdb|4AT6|A Chain A, Fab Fragment Of Antiporphyrin Antibody 14h7
pdb|4AT6|C Chain C, Fab Fragment Of Antiporphyrin Antibody 14h7
pdb|4AT6|E Chain E, Fab Fragment Of Antiporphyrin Antibody 14h7
pdb|4AT6|G Chain G, Fab Fragment Of Antiporphyrin Antibody 14h7
pdb|4AT6|H Chain H, Fab Fragment Of Antiporphyrin Antibody 14h7
pdb|4AT6|J Chain J, Fab Fragment Of Antiporphyrin Antibody 14h7
pdb|4AT6|M Chain M, Fab Fragment Of Antiporphyrin Antibody 14h7
pdb|4AT6|O Chain O, Fab Fragment Of Antiporphyrin Antibody 14h7
Length = 217
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 32/141 (22%), Positives = 58/141 (41%), Gaps = 16/141 (11%)
Query: 100 DDYPVIWMKMDTAKKMEPLPISMSGSL-IIHDSRFQ----LTTDPETSTYILSIKEIQET 154
Y + W+K + +E + + G+ ++ +F+ LT D +ST + + +
Sbjct: 30 SSYNIHWVKQTPGQGLEWIGVIYPGNGDTSYNQKFRDKATLTADKSSSTAYMQLSSLTSE 89
Query: 155 DAGIYKCE-----VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG 209
D+ +Y C ++ V PP + + S + V L C G
Sbjct: 90 DSAVYHCARGGSGLLAYWGQGTLVTVSSAKTTPPSVYPLAPGSAAQTN-SMVTLGCLVKG 148
Query: 210 -FPAP-TISWRRDNSAALSTG 228
FP P T++W NS +LS+G
Sbjct: 149 YFPEPVTVTW---NSGSLSSG 166
>pdb|1MJ8|H Chain H, High Resolution Crystal Structure Of The Fab Fragment Of
The Esterolytic Antibody Ms6-126
Length = 230
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 36/147 (24%), Positives = 58/147 (39%), Gaps = 38/147 (25%)
Query: 106 WMKMDTAKKMEPLPISMSGSLII-HDSRFQ----LTTDPETSTYILSIKEIQETDAGIYK 160
W+K + +E + GS ++ RF+ LT D +ST + + + D+ +Y
Sbjct: 36 WVKQRPGQGLEWIGNIYPGSGYTNYNERFKSKATLTVDTSSSTAYMQLSSLTSDDSAVYY 95
Query: 161 CE-----------------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYL 203
C V +S + V + P+ D S G +V L
Sbjct: 96 CARKHYFYDGVVYWGQGTLVTVSAAKTTAPSVYPLA---PVCGDTS--------GSSVTL 144
Query: 204 YCYANG-FPAP-TISWRRDNSAALSTG 228
C G FP P T++W NS +LS+G
Sbjct: 145 GCLVKGYFPEPVTLTW---NSGSLSSG 168
>pdb|2IQ9|H Chain H, Pfa2 Fab Fragment, Triclinic Apo Form
pdb|2IQA|H Chain H, Pfa2 Fab Fragment, Monoclinic Apo Form
pdb|2IQA|B Chain B, Pfa2 Fab Fragment, Monoclinic Apo Form
Length = 223
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 30/77 (38%), Gaps = 10/77 (12%)
Query: 236 ILKIPNITKTDRGTYYCV--AQNGV--------GRGMKRNIAVEVEFAPVITINRPRQGQ 285
LKI ++ D TYYCV A N V G+G ++ AP + P G
Sbjct: 81 FLKITSVDTADTATYYCVRRAHNVVLGDWFAYWGQGTLVTVSAAKTTAPSVYPLAPVCGG 140
Query: 286 ALQYDAILECHVEAYPP 302
L C V+ Y P
Sbjct: 141 TTGSSVTLGCLVKGYFP 157
>pdb|2H9G|B Chain B, Crystal Structure Of Phage Derived Fab Bdf1 With Human
Death Receptor 5 (dr5)
pdb|2H9G|H Chain H, Crystal Structure Of Phage Derived Fab Bdf1 With Human
Death Receptor 5 (dr5)
Length = 228
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 34/142 (23%), Positives = 58/142 (40%), Gaps = 27/142 (19%)
Query: 106 WMKMDTAKKMEPLPI--SMSGSLIIHDS---RFQLTTDPETSTYILSIKEIQETDAGIYK 160
W++ K +E + + G+ DS RF ++ D +T L + ++ D +Y
Sbjct: 36 WVRQAPGKGLEWVAVIYPHDGNTAYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYY 95
Query: 161 CE---VIISLNNKVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVYLYCYAN 208
C ++ + + L+ +S ST+ V + G T L C
Sbjct: 96 CARRLALVRMWMDYWGQGTLVT-----VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVK 150
Query: 209 G-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 151 DYFPEPVTVSW---NSGALTSG 169
>pdb|1G6V|K Chain K, Complex Of The Camelid Heavy-Chain Antibody Fragment Cab-
Ca05 With Bovine Carbonic Anhydrase
Length = 126
Score = 30.0 bits (66), Expect = 2.1, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 102 YPVIWMKMDTAKKMEPLPISMSGSLIIHDS---RFQLTTDPETSTYILSIKEIQETDAGI 158
Y + W + K+ E + + GS DS RF ++ D +T L + ++ D I
Sbjct: 32 YCMGWFRQAPGKEREGVATILGGSTYYGDSVKGRFTISQDNAKNTVYLQMNSLKPEDTAI 91
Query: 159 YKC 161
Y C
Sbjct: 92 YYC 94
>pdb|4I9W|E Chain E, Human Two Pore Domain K+ Channel Traak (k2p4.1) - Fab
Complex Structure
pdb|4I9W|G Chain G, Human Two Pore Domain K+ Channel Traak (k2p4.1) - Fab
Complex Structure
Length = 217
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 35/138 (25%), Positives = 58/138 (42%), Gaps = 15/138 (10%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETDA 156
Y + W+K K +E + I+ + ++ +F+ LT D +ST + + + D+
Sbjct: 32 YIMNWVKQRHGKNLEWIGLINPNTGYTTYNQKFKGKATLTVDKSSSTAYMELLSLTSEDS 91
Query: 157 GIYKCE----VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FP 211
IY C V + V PP + + S + V L C G FP
Sbjct: 92 AIYYCTRGNYVFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVKGYFP 150
Query: 212 AP-TISWRRDNSAALSTG 228
P T++W NS +LS+G
Sbjct: 151 EPVTVTW---NSGSLSSG 165
>pdb|1A0Q|L Chain L, 29g11 Complexed With Phenyl [1-(1-N-Succinylamino)pentyl]
Phosphonate
Length = 212
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 33/127 (25%), Positives = 51/127 (40%), Gaps = 8/127 (6%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV---GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAIL 293
I N+ D TYYC+ + G G K I + AP ++I P Q A +
Sbjct: 73 FSISNLEPEDIATYYCLQYYNLRTFGGGTKLEIK-RADAAPTVSIFPPSSEQLTSGGASV 131
Query: 294 ECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI-ERRQFGQY 349
C + + I W DG + N S + + D +S +S +T E + Y
Sbjct: 132 VCFLNNFYSKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSY 191
Query: 350 ACKAANK 356
C+A +K
Sbjct: 192 TCEATHK 198
>pdb|3U1S|L Chain L, Crystal Structure Of Human Fab Pgt145, A Broadly Reactive
And Potent Hiv-1 Neutralizing Antibody
Length = 239
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 34/131 (25%), Positives = 53/131 (40%), Gaps = 15/131 (11%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV------GRGMKRNIAVEVEFAPVITINRPRQGQALQYD 290
LKI + D GTYYC+ G+ G+G K I V AP + I P Q
Sbjct: 98 LKISRVESDDVGTYYCM--QGLHSPWTFGQGTKVEIKRTVA-APSVFIFPPSDEQLKSGT 154
Query: 291 AILECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ 348
A + C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 155 ASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEK 213
Query: 349 ---YACKAANK 356
YAC+ ++
Sbjct: 214 HKVYACEVTHQ 224
>pdb|3G5V|B Chain B, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
Length = 213
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 4/88 (4%)
Query: 236 ILKIPNITKTDRGTYYCV-AQNGV---GRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
L++ ++T D TYYCV A G G+G ++ P + P G
Sbjct: 80 FLQLNSVTIEDTATYYCVTAGRGFPYWGQGTLVTVSAAKTTPPSVYPLAPGCGDTTGSSV 139
Query: 292 ILECHVEAYPPPAIVWIKDGVQIMNNQH 319
L C V+ Y P ++ + + ++ H
Sbjct: 140 TLGCLVKGYFPESVTVTANSGSLSSSVH 167
>pdb|3HC0|H Chain H, Bha10 Igg1 Wild-Type Fab - Antibody Directed At Human Ltbr
pdb|3HC0|A Chain A, Bha10 Igg1 Wild-Type Fab - Antibody Directed At Human Ltbr
Length = 217
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 29/103 (28%), Positives = 42/103 (40%), Gaps = 10/103 (9%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKC----EVIISLNNKVSAEVELIVRRPPIISD 187
R +T D TST + + ++ D +Y C E + V + P +
Sbjct: 67 RVTITADKSTSTAYMELSSLRSEDTAVYYCARSWEGFPYWGQGTTVTVSSASTKGPSVFP 126
Query: 188 NSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ S S G T L C FP P T+SW NS AL++G
Sbjct: 127 LAPSSKSTS-GGTAALGCLVKDYFPEPVTVSW---NSGALTSG 165
>pdb|2SEB|B Chain B, X-Ray Crystal Structure Of Hla-Dr4 Complexed With A
Peptide From Human Collagen Ii
pdb|1D5X|B Chain B, X-ray Crystal Structure Of Hla-dr4 Complexed With
Dipeptide Mimetic And Seb
pdb|1D5Z|B Chain B, X-Ray Crystal Structure Of Hla-Dr4 Complexed With
Peptidomimetic And Seb
pdb|1D6E|B Chain B, Crystal Structure Of Hla-Dr4 Complex With Peptidomimetic
And Seb
Length = 192
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 251 YCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAI--VWI 308
YC GVG + V+ P +T+ P + Q LQ+ +L C V + P +I W
Sbjct: 78 YCRHNYGVGE----SFTVQRRVYPEVTVY-PAKTQPLQHHNLLVCSVNGFYPGSIEVRWF 132
Query: 309 KDG 311
++G
Sbjct: 133 RNG 135
>pdb|3HE6|C Chain C, Crystal Structure Of Mouse Cd1d-Alpha-Galactosylceramide
With Mouse Valpha14-Vbeta8.2 Nkt Tcr
pdb|3HE7|C Chain C, Crystal Structure Of Mouse Cd1d-Alpha-Galactosylceramide
With Mouse Valpha14-Vbeta7 Nkt Tcr
pdb|3ARB|C Chain C, Ternary Crystal Structure Of The Nkt
Tcr-Cd1d-Alpha-Galactosylceramide Analogue-Och
pdb|3ARD|C Chain C, Ternary Crystal Structure Of The Mouse Nkt
Tcr-Cd1d-3'deoxy-Alpha- Galactosylceramide
pdb|3ARE|C Chain C, Ternary Crystal Structure Of The Mouse Nkt
Tcr-Cd1d-4'deoxy-Alpha- Galactosylceramide
pdb|3ARF|C Chain C, Ternary Crystal Structure Of The Mouse Nkt Tcr-Cd1d-C20:2
pdb|3ARG|C Chain C, Ternary Crystal Structure Of The Mouse Nkt Tcr-Cd1d-Alpha-
Glucosylceramide(C20:2)
pdb|3SCM|C Chain C, Crystal Structure Of Autoreactive-Valpha14-Vbeta6 Nkt Tcr
In Complex With Cd1d-Isoglobotrihexosylceramide
pdb|3SDA|C Chain C, Crystal Structure Of Autoreactive-Valpha14-Vbeta6 Nkt Tcr
In Complex With Cd1d-Beta-Galactosylceramide
pdb|3SDC|C Chain C, Crystal Structure Of Autoreactive-Valpha14-Vbeta6 Nkt Tcr
In Complex With Cd1d-Globotrihexosylceramide
pdb|3SDD|C Chain C, Crystal Structure Of Autoreactive-Valpha14-Vbeta6 Nkt Tcr
In Complex With Cd1d-Beta-Lactosylceramide
pdb|3TN0|C Chain C, Structure Of Mouse Va14vb8.2nkt Tcr-Mouse
Cd1d-A-C-Galactosylceramide Complex
pdb|3QI9|C Chain C, Crystal Structure Of Mouse Cd1d-Alpha-Phosphotidylinositol
With Mouse Valpha14-Vbeta6 2a3-D Nkt Tcr
Length = 207
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 27/72 (37%)
Query: 92 LKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYILSIKEI 151
L+C+ D + W K DT K + L + + + R+ T D + L I
Sbjct: 20 LQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGRYSATLDKDAKHSTLHITAT 79
Query: 152 QETDAGIYKCEV 163
D Y C V
Sbjct: 80 LLDDTATYICVV 91
>pdb|3UTZ|B Chain B, Endogenous-Like Inhibitory Antibodies Targeting Activated
Metalloproteinase Motifs Show Therapeutic Potential
pdb|3UTZ|C Chain C, Endogenous-Like Inhibitory Antibodies Targeting Activated
Metalloproteinase Motifs Show Therapeutic Potential
pdb|3UTZ|F Chain F, Endogenous-Like Inhibitory Antibodies Targeting Activated
Metalloproteinase Motifs Show Therapeutic Potential
Length = 225
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 35/141 (24%), Positives = 56/141 (39%), Gaps = 18/141 (12%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K++E + IS GS + RF ++ D +T L + ++ D
Sbjct: 32 YDMSWIRQTPEKRLEWVATISSGGSYTYYPDSVKGRFTISKDNARNTLYLQMSSLRSGDT 91
Query: 157 GIYKCE-------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG 209
+Y C + V + P + + S S G T L C
Sbjct: 92 ALYYCTRFRYDGWYFDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTS-GGTAALGCLVKD 150
Query: 210 -FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 151 YFPEPVTVSW---NSGALTSG 168
>pdb|4GOS|A Chain A, Crystal Structure Of Human B7-H4 Igv-Like Domain
Length = 125
Score = 30.0 bits (66), Expect = 2.3, Method: Composition-based stats.
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 146 LSIKEIQETDAGIYKCEVIIS 166
L +K +Q TDAG YKC +I S
Sbjct: 86 LRLKNVQLTDAGTYKCYIITS 106
>pdb|1D5M|B Chain B, X-Ray Crystal Structure Of Hla-Dr4 Complexed With Peptide
And Seb
pdb|1J8H|B Chain B, Crystal Structure Of A Complex Of A Human AlphaBETA-T Cell
Receptor, Influenza Ha Antigen Peptide, And Mhc Class Ii
Molecule, Hla-Dr4
Length = 192
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 251 YCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAI--VWI 308
YC GVG + V+ P +T+ P + Q LQ+ +L C V + P +I W
Sbjct: 78 YCRHNYGVGE----SFTVQRRVYPEVTVY-PAKTQPLQHHNLLVCSVNGFYPGSIEVRWF 132
Query: 309 KDG 311
++G
Sbjct: 133 RNG 135
>pdb|3BP5|B Chain B, Crystal Structure Of The Mouse Pd-1 And Pd-L2 Complex
pdb|3BP6|B Chain B, Crystal Structure Of The Mouse Pd-1 Mutant And Pd-L2
Complex
Length = 202
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 40/100 (40%), Gaps = 21/100 (21%)
Query: 145 ILSIKEIQETDAGIYKCEVIIS-------LNNKVSAEVELIVRRPPIISDNSTRSVIVSE 197
+ I +Q D+G Y+C VI L KV A I TR + V
Sbjct: 68 LFHIPSVQVRDSGQYRCLVICGAAWDYKYLTVKVKASYMRI----------DTRILEVPG 117
Query: 198 GQTVYLYCYANGFPAPTISWRR----DNSAALSTGGSIYR 233
V L C A G+P +SW+ N++ + T +Y+
Sbjct: 118 TGEVQLTCQARGYPLAEVSWQNVSVPANTSHIRTPEGLYQ 157
>pdb|2D9C|A Chain A, Solution Structure Of The First Ig-Like Domain Of Signal-
Regulatory Protein Beta-1 (Sirp-Beta-1)
Length = 136
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 33/82 (40%), Gaps = 19/82 (23%)
Query: 191 RSVIVSEGQTVYLYCYANGF-PAPTISWRRDNSAA--------------LSTGGSIYRGN 235
+SV V+ G++ L C P I W R A ++T + + N
Sbjct: 16 KSVSVAAGESATLRCAMTSLIPVGPIMWFRGAGAGRELIYNQKEGHFPRVTTVSELTKRN 75
Query: 236 IL----KIPNITKTDRGTYYCV 253
L I NIT D GTYYCV
Sbjct: 76 NLDFSISISNITPADAGTYYCV 97
>pdb|2NTF|H Chain H, Crystal Structure Of A Quorum-Quenching Antibody In
Complex With An N- Acyl-L-Homoserine Lactone Analog
pdb|2NTF|B Chain B, Crystal Structure Of A Quorum-Quenching Antibody In
Complex With An N- Acyl-L-Homoserine Lactone Analog
pdb|2OP4|H Chain H, Crystal Structure Of Quorum-Quenching Antibody 1g9
Length = 222
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 37/144 (25%), Positives = 59/144 (40%), Gaps = 21/144 (14%)
Query: 102 YPVIWMKMDTAKKMEPLPISMSGS-LIIHDSRFQ----LTTDPETSTYILSIKEIQETDA 156
Y + W+K + +E + GS +D +F+ LT D +ST + + + D+
Sbjct: 32 YWIHWVKQRPGQGLEWIGTIYPGSDNTYYDEKFKNKATLTVDTSSSTAFMQLSSLTSEDS 91
Query: 157 GIYKC-EVIISLNN---------KVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCY 206
+Y C + NN V PP + + S S+ V L C
Sbjct: 92 AVYFCTRGSLYYNNYGWFGYWGQGTLVTVSAAKTTPPSVYPLAPGSNAASQSM-VTLGCL 150
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 151 VKGYFPEPVTVTW---NSGSLSSG 171
>pdb|2DDQ|H Chain H, Crystal Structure Of The Fab Fragment Of A R310 Antibody
Complexed With (R)-Hne-Histidine Adduct
Length = 213
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 28/110 (25%), Positives = 46/110 (41%), Gaps = 27/110 (24%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCE-----------VIISLNNKVSAEVELIVR 180
+ LT+D +ST + + + D+ +Y C V +S + V +
Sbjct: 67 KATLTSDKSSSTAYMELSSLTSEDSAVYYCAPYGGYWGQGTTVTVSSAKTTAPSVYPLA- 125
Query: 181 RPPIISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
P+ D + G +V L C G FP P T++W NS +LS+G
Sbjct: 126 --PVCGDTT--------GSSVTLGCLVKGYFPEPVTLTW---NSGSLSSG 162
>pdb|3SN6|N Chain N, Crystal Structure Of The Beta2 Adrenergic Receptor-Gs
Protein Complex
Length = 138
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 5/66 (7%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETD 155
+Y + W++ K +E + IS SG+ I + RF ++ D +T L + ++ D
Sbjct: 31 NYKMNWVRQAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPED 90
Query: 156 AGIYKC 161
+Y C
Sbjct: 91 TAVYYC 96
>pdb|3IYW|H Chain H, West Nile Virus In Complex With Fab Fragments Of Mab
Cr4354 (Fitted Coordinates Of Envelope Proteins And Fab
Fragments Of One Icosahedral Asu)
pdb|3IYW|K Chain K, West Nile Virus In Complex With Fab Fragments Of Mab
Cr4354 (Fitted Coordinates Of Envelope Proteins And Fab
Fragments Of One Icosahedral Asu)
pdb|3N9G|H Chain H, Crystal Structure Of The Fab Fragment Of The Human
Neutralizing Anti- West Nile Virus Mab Cr4354
Length = 230
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 37/149 (24%), Positives = 60/149 (40%), Gaps = 30/149 (20%)
Query: 102 YPVIWMKMDTAKKMEPLPI-SMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETDA 156
Y + W++ + +E + I + SG + + Q +T D TST + + ++ D
Sbjct: 32 YYMHWVRQAPGQGLEWMGIINPSGGSTTYAQKLQGRVTMTRDTSTSTVYMELSSLRSEDT 91
Query: 157 GIYKCEVIISLNN------KVSAEVELIVRRPPIISDNSTRSVIV---------SEGQTV 201
+Y C N K + L+ +S ST+ V + G T
Sbjct: 92 AVYYCARDWGSNYVWGSYPKYWGQGTLVT-----VSSASTKGPSVFPLAPSSKSTSGGTA 146
Query: 202 YLYCYANG-FPAP-TISWRRDNSAALSTG 228
L C FP P T+SW NS AL++G
Sbjct: 147 ALGCLVKDYFPEPVTVSW---NSGALTSG 172
>pdb|3RNQ|B Chain B, Crystal Structure Of The Complex Between The Extracellular
Domains Of Mouse Pd-1 Mutant And Pd-L2
Length = 201
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 40/100 (40%), Gaps = 21/100 (21%)
Query: 145 ILSIKEIQETDAGIYKCEVIIS-------LNNKVSAEVELIVRRPPIISDNSTRSVIVSE 197
+ I +Q D+G Y+C VI L KV A I TR + V
Sbjct: 67 LFHIPSVQVRDSGQYRCLVICGAAWDYKYLTVKVKASYMRI----------DTRILEVPG 116
Query: 198 GQTVYLYCYANGFPAPTISWRR----DNSAALSTGGSIYR 233
V L C A G+P +SW+ N++ + T +Y+
Sbjct: 117 TGEVQLTCQARGYPLAEVSWQNVSVPANTSHIRTPEGLYQ 156
>pdb|1FBI|H Chain H, Crystal Structure Of A Cross-Reaction Complex Between Fab
F9.13.7 And Guinea-Fowl Lysozyme
pdb|1FBI|Q Chain Q, Crystal Structure Of A Cross-Reaction Complex Between Fab
F9.13.7 And Guinea-Fowl Lysozyme
Length = 221
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 36/145 (24%), Positives = 59/145 (40%), Gaps = 21/145 (14%)
Query: 101 DYPVIWMKMDTAKKMEPL-PISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
Y + W+K + +E + I S S ++ +F+ LT D +ST + + + D
Sbjct: 31 SYWMHWVKQGPGQGLEWIGEIDPSDSYPNYNEKFKGKATLTVDKSSSTAYMQLSSLTSED 90
Query: 156 AGIYKCE----------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYC 205
+ +Y C V+ S V PP + + S + V L C
Sbjct: 91 SAVYYCASLYYYGTSYGVLDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTN-SMVTLGC 149
Query: 206 YANG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 150 LVKGYFPEPVTVTW---NSGSLSSG 171
>pdb|2NYY|D Chain D, Crystal Structure Of Botulinum Neurotoxin Type A Complexed
With Monoclonal Antibody Cr1
Length = 223
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 37/141 (26%), Positives = 57/141 (40%), Gaps = 18/141 (12%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETD 155
DY + W++ K +E + IS GS + + RF + D +T L + ++ D
Sbjct: 32 DY-MYWVRQAPGKGLEWVATISDGGSYTYYSDSVEGRFTTSRDNSKNTLYLQMNSLRAED 90
Query: 156 AGIYKC------EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG 209
IY C + + V + P + + S S G T L C
Sbjct: 91 TAIYYCSRYRYDDAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTS-GGTAALGCLVKD 149
Query: 210 -FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 150 YFPEPVTVSW---NSGALTSG 167
>pdb|3O6K|H Chain H, Crystal Structure Of Anti-Tat Hiv Fab'11h6h1
pdb|3O6L|H Chain H, Anti-Tat Hiv 11h6h1 Fab' Complexed With A 15-Mer Tat
Peptide
pdb|3O6M|H Chain H, Anti-Tat Hiv 11h6h1 Fab' Complexed With A 9-Mer Tat
Peptide
Length = 219
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 35/139 (25%), Positives = 55/139 (39%), Gaps = 16/139 (11%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y + W K++E + IS GS + RF ++ D +T L + ++ D
Sbjct: 32 YDMSWFCQTPEKRLEWVASISSGGSYTYYPDSVKGRFTISRDNARNTLYLQMNSLRSEDT 91
Query: 157 GIYKCE-----VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-F 210
+Y C + S V PP + + S + V L C G F
Sbjct: 92 ALYYCARDYDYGVDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTN-SMVTLGCLVKGYF 150
Query: 211 PAP-TISWRRDNSAALSTG 228
P P T++W NS +LS+G
Sbjct: 151 PEPVTVTW---NSGSLSSG 166
>pdb|1F11|B Chain B, F124 Fab Fragment From A Monoclonal Anti-Pres2 Antibody
pdb|1F11|D Chain D, F124 Fab Fragment From A Monoclonal Anti-Pres2 Antibody
Length = 221
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 34/142 (23%), Positives = 57/142 (40%), Gaps = 18/142 (12%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K K +E + I+ + ++ +F+ LT D +ST + + + D
Sbjct: 31 DYYMKWVKQSHGKSLEWIGDINPNNGGTGYNQKFKGKATLTVDKSSSTAYMQLNSLTSED 90
Query: 156 AGIYKCE-------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYAN 208
+ +Y C V PP + + S + V L C
Sbjct: 91 SAVYYCANDYGSTYGFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTN-SMVTLGCLVK 149
Query: 209 G-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 150 GYFPEPVTVTW---NSGSLSSG 168
>pdb|3O6F|B Chain B, Crystal Structure Of A Human Autoimmune Tcr Ms2-3c8 Bound
To Mhc Class Ii Self-Ligand MbpHLA-Dr4
pdb|3O6F|F Chain F, Crystal Structure Of A Human Autoimmune Tcr Ms2-3c8 Bound
To Mhc Class Ii Self-Ligand MbpHLA-Dr4
pdb|3T0E|B Chain B, Crystal Structure Of A Complete Ternary Complex Of T Cell
Receptor, Peptide-Mhc And Cd4
Length = 221
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 251 YCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECHVEAYPPPAI--VWI 308
YC GVG + V+ P +T+ P + Q LQ+ +L C V + P +I W
Sbjct: 107 YCRHNYGVGE----SFTVQRRVYPEVTVY-PAKTQPLQHHNLLVCSVNGFYPGSIEVRWF 161
Query: 309 KDG 311
++G
Sbjct: 162 RNG 164
>pdb|3D85|A Chain A, Crystal Structure Of Il-23 In Complex With Neutralizing
Fab
Length = 214
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 49/202 (24%), Positives = 75/202 (37%), Gaps = 33/202 (16%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNS----------AALSTGGSIYR 233
I+ S ++ V+ G V L C A+ + + W R S A+ S G R
Sbjct: 2 IVMTQSPATLSVTPGDRVSLSCRASQSISDYLHWYRQKSHESPRLLIKYASQSISGIPSR 61
Query: 234 GN--------ILKIPNITKTDRGTYYCVAQNG------VGRGMKRNIAVEVEFAPVITIN 279
+ L I ++ D G YYC QNG G G K I V AP + I
Sbjct: 62 FSGSGSGSDFTLSINSVEPEDVGVYYC--QNGHSFPFTFGSGTKLEIKRTVA-APSVFIF 118
Query: 280 RPRQGQALQYDAILECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLR 337
P Q A + C + + P + W D N SV+ + D S
Sbjct: 119 PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-S 177
Query: 338 VITIERRQFGQ---YACKAANK 356
+T+ + + + YAC+ ++
Sbjct: 178 TLTLSKADYEKHKVYACEVTHQ 199
>pdb|3O2V|L Chain L, Crystal Structure Of 1e9 Phel89serLEUH47TRPMETH100BPHE, AN
Engineered Diels-Alderase Fab With Modified Specificity
And Catalytic Activity
pdb|3O2W|L Chain L, Crystal Structure Of The 1e9 Phel89serLEUH47TRPMETH100BPHE
FAB IN Complex With A 39a11 Transition State Analog
Length = 219
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 49/207 (23%), Positives = 77/207 (37%), Gaps = 29/207 (14%)
Query: 176 ELIVRRPPI-----------ISDNSTRSVIVSEGQTVYLYCYANG------FPAPTISWR 218
EL++ + P+ IS S++S++ S G T YL+ Y F +S R
Sbjct: 1 ELVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNT-YLHWYLQKPGQSPKFLIYKVSNR 59
Query: 219 RDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAP 274
+G ILKI + D G Y+C G G K I V AP
Sbjct: 60 FSGVPDRFSGSGSGTDFILKISRVEAEDLGVYFCSQSTHFFPTFGGGTKLEIKRTVA-AP 118
Query: 275 VITINRPRQGQALQYDAILECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFS 332
+ I P Q A + C + + P + W D N SV+ + D
Sbjct: 119 SVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTY 178
Query: 333 DTSLRVITIERRQFGQ---YACKAANK 356
S +T+ + + + YAC+ ++
Sbjct: 179 SLS-STLTLSKADYEKHKVYACEVTHQ 204
>pdb|2PCP|B Chain B, Antibody Fab Complexed With Phencyclidine
pdb|2PCP|D Chain D, Antibody Fab Complexed With Phencyclidine
Length = 215
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 56/140 (40%), Gaps = 16/140 (11%)
Query: 101 DYPVIWMKMDTAKKMEPLPI---SMSGSLIIHD--SRFQLTTDPETSTYILSIKEIQETD 155
DY + W K K +E + + G+ H + LT D +ST + ++ + D
Sbjct: 31 DYYIHWNKQSHGKSLEWIGYIYPNNGGNGYNHKFKGKATLTVDKSSSTAYMDVRTLTSED 90
Query: 156 AGIYKC-----EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG- 209
+ +Y C + + V PP + + S + V L C G
Sbjct: 91 SAVYYCGRSTWDDFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTN-SMVTLGCLVKGY 149
Query: 210 FPAP-TISWRRDNSAALSTG 228
FP P T++W NS +LS+G
Sbjct: 150 FPEPVTLTW---NSGSLSSG 166
>pdb|1DBA|H Chain H, Three-Dimensional Structure Of An Anti-Steroid Fab' And
Progesterone-Fab' Complex
pdb|1DBB|H Chain H, Three-Dimensional Structure Of An Anti-Steroid Fab' And
Progesterone-Fab' Complex
pdb|1DBJ|H Chain H, Molecular Basis Of Cross-Reactivity And The Limits Of
Antibody-Antigen Complementarity
pdb|1DBK|H Chain H, Molecular Basis Of Cross-Reactivity And The Limits Of
Antibody-Antigen Complementarity
pdb|1DBM|H Chain H, Molecular Basis Of Cross-Reactivity And The Limits Of
Antibody-Antigen Complementarity
pdb|2DBL|H Chain H, Molecular Basis Of Cross-Reactivity And The Limits Of
Antibody-Antigen Complementarity
Length = 219
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 41/166 (24%), Positives = 65/166 (39%), Gaps = 20/166 (12%)
Query: 79 SQEQIKDIAQTADLKCSVQ-YA-DDYPVIWMKMDTAKKMEPLP---ISMSGSLIIHD--S 131
S ++K +T + C YA +Y V W+K K+++ + I + D
Sbjct: 7 SGPELKKPGETVKISCKASGYAFTNYGVNWVKEAPGKELKWMGWINIYTGEPTYVDDFKG 66
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLN-------NKVSAEVELIVRRPPI 184
RF + + ST L I ++ D Y C +N + V PP
Sbjct: 67 RFAFSLETSASTAYLEINNLKNEDTATYFCTRGDYVNWYFDVWGAGTTVTVSSAKTTPPS 126
Query: 185 ISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ + S + V L C G FP P T++W NS +LS+G
Sbjct: 127 VYPLAPGSAAQTNSM-VTLGCLVKGYFPEPVTVTW---NSGSLSSG 168
>pdb|3O8X|C Chain C, Recognition Of Glycolipid Antigen By Inkt Cell Tcr
pdb|3O9W|C Chain C, Recognition Of A Glycolipid Antigen By The Inkt Cell Tcr
pdb|3QUX|C Chain C, Structure Of The Mouse Cd1d-Alpha-C-Galcer-Inkt Tcr
Complex
pdb|3QUY|C Chain C, Structure Of The Mouse Cd1d-Bnnh-Gsl-1'-Inkt Tcr Complex
pdb|3QUZ|C Chain C, Structure Of The Mouse Cd1d-Nu-Alpha-Galcer-Inkt Tcr
Complex
pdb|3RZC|C Chain C, Structure Of The Self-Antigen Igb3 Bound To Mouse Cd1d And
In Complex With The Inkt Tcr
pdb|3TA3|C Chain C, Structure Of The Mouse Cd1d-Glc-Dag-S2-Inkt Tcr Complex
pdb|3TVM|C Chain C, Structure Of The Mouse Cd1d-Smc124-Inkt Tcr Complex
pdb|3TVM|G Chain G, Structure Of The Mouse Cd1d-Smc124-Inkt Tcr Complex
pdb|3RTQ|C Chain C, Structure Of The Mouse Cd1d-Hs44-Inkt Tcr Complex
Length = 209
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 27/72 (37%)
Query: 92 LKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYILSIKEI 151
L+C+ D + W K DT K + L + + + R+ T D + L I
Sbjct: 22 LQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGRYSATLDKDAKHSTLHITAT 81
Query: 152 QETDAGIYKCEV 163
D Y C V
Sbjct: 82 LLDDTATYICVV 93
>pdb|2LE9|A Chain A, Ragec2-S100a13 Tetrameric Complex
pdb|2LE9|D Chain D, Ragec2-S100a13 Tetrameric Complex
Length = 93
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 27/60 (45%), Gaps = 5/60 (8%)
Query: 195 VSEGQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVA 254
V+ G TV L C P+P I W +D +L +P I D+GTY CVA
Sbjct: 15 VAPGGTVTLTCEVPAQPSPQIHWMKDGVPLPLPPSP-----VLILPEIGPQDQGTYSCVA 69
Score = 29.3 bits (64), Expect = 4.0, Method: Composition-based stats.
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 293 LECHVEAYPPPAIVWIKDGV 312
L C V A P P I W+KDGV
Sbjct: 23 LTCEVPAQPSPQIHWMKDGV 42
>pdb|1AD0|B Chain B, Fab Fragment Of Engineered Human Monoclonal Antibody A5b7
pdb|1AD0|D Chain D, Fab Fragment Of Engineered Human Monoclonal Antibody A5b7
Length = 220
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 56/144 (38%), Gaps = 20/144 (13%)
Query: 101 DYPVIWMKMDTAKKMEPLPI---SMSGSLIIHDS----RFQLTTDPETSTYILSIKEIQE 153
DY + W++ K +E L +G + + RF ++ D ST L + +Q
Sbjct: 31 DYYMNWVRQAPGKGLEWLGFIGNKANGYTTEYSASVKGRFTISRDKSKSTLYLQMNTLQA 90
Query: 154 TDAGIYKCEVIISL-------NNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCY 206
D+ IY C L V + P + + S SE T L C
Sbjct: 91 EDSAIYYCTRDRGLRFYFDYWGQGTLVTVSSASTKGPSVFPLAPCSRSTSE-STAALGCL 149
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 150 VKDYFPEPVTVSW---NSGALTSG 170
>pdb|2EH8|L Chain L, Crystal Structure Of The Complex Of Humanized Kr127 Fab
And Pres1 Peptide Epitope
Length = 218
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 30/128 (23%), Positives = 49/128 (38%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVE---FAPVITINRPRQGQALQYDAIL 293
LKI + D G YYCV + VE++ AP + I P Q A +
Sbjct: 78 LKISRVEAEDVGVYYCVQGTHFPQTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASV 137
Query: 294 ECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ--- 348
C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 138 VCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHKV 196
Query: 349 YACKAANK 356
YAC+ ++
Sbjct: 197 YACEVTHQ 204
>pdb|3LD8|B Chain B, Structure Of Jmjd6 And Fab Fragments
pdb|3LDB|B Chain B, Structure Of Jmjd6 Complexd With Alpha-Ketoglutarate And
Fab Fragment
Length = 220
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 36/84 (42%), Gaps = 6/84 (7%)
Query: 144 YILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRP---PIISDNSTRSVIVSEGQT 200
Y L+I +Q D G Y C+ IS A +L ++R P +S S + G
Sbjct: 77 YTLTITSVQAEDMGQYFCQQGISNPYTFGAGTKLEIKRADAKPTVSIFPPSSEQLGTGSA 136
Query: 201 VYLYCYANGFPAPTIS--WRRDNS 222
L C+ N F I+ W+ D S
Sbjct: 137 T-LVCFVNNFYPKDINVKWKVDGS 159
>pdb|3QEH|B Chain B, Crystal Structure Of Human N12-I15, An Adcc And
Non-Neutralizing Anti- Hiv-1 Env Antibody
pdb|3QEH|D Chain D, Crystal Structure Of Human N12-I15, An Adcc And
Non-Neutralizing Anti- Hiv-1 Env Antibody
pdb|3QEH|F Chain F, Crystal Structure Of Human N12-I15, An Adcc And
Non-Neutralizing Anti- Hiv-1 Env Antibody
pdb|3QEH|H Chain H, Crystal Structure Of Human N12-I15, An Adcc And
Non-Neutralizing Anti- Hiv-1 Env Antibody
Length = 218
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 32/128 (25%), Positives = 50/128 (39%), Gaps = 10/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQN---GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAIL 293
LKI + D G YYC+ G+G K I V AP + I P Q A +
Sbjct: 78 LKISRVEAEDVGVYYCMQAKESPTFGQGTKVEIKRTVA-APSVFIFPPSDEQLKSGTASV 136
Query: 294 ECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ--- 348
C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 137 VCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHKV 195
Query: 349 YACKAANK 356
YAC+ ++
Sbjct: 196 YACEVTHQ 203
>pdb|1HXM|B Chain B, Crystal Structure Of A Human Vgamma9VDELTA2 T CELL
RECEPTOR
pdb|1HXM|D Chain D, Crystal Structure Of A Human Vgamma9VDELTA2 T CELL
RECEPTOR
pdb|1HXM|F Chain F, Crystal Structure Of A Human Vgamma9VDELTA2 T CELL
RECEPTOR
pdb|1HXM|H Chain H, Crystal Structure Of A Human Vgamma9VDELTA2 T CELL
RECEPTOR
Length = 242
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 46/95 (48%), Gaps = 10/95 (10%)
Query: 77 YISQEQI---KDIAQTADLKCSVQ--YADDYPVIWMKMDTAKKMEPL-PISMSGSLI--- 127
++ Q QI K +++TA L+C V V W + + ++ L IS G++
Sbjct: 3 HLEQPQISSTKTLSKTARLECVVSGITISATSVYWYRERPGEVIQFLVSISYDGTVRKES 62
Query: 128 -IHDSRFQLTTDPETSTYILSIKEIQETDAGIYKC 161
I +F++ PETST L+I +++ D Y C
Sbjct: 63 GIPSGKFEVDRIPETSTSTLTIHNVEKQDIATYYC 97
>pdb|1KCS|H Chain H, Crystal Structure Of Antibody Pc282 In Complex With Ps1
Peptide
pdb|1KCV|H Chain H, Crystal Structure Of Antibody Pc282
Length = 217
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 34/83 (40%), Gaps = 7/83 (8%)
Query: 236 ILKIPNITKTDRGTYYCVAQNGVG---RGMKRNIAVEVE--FAPVITINRPRQGQALQYD 290
L++ ++T D TYYC A+ G G G N+ V AP + P A
Sbjct: 80 FLQLNSVTTDDTATYYC-ARGGTGFPYWGTGTNVTVSAASTTAPSVFPLVPGSATAAASA 138
Query: 291 AILECHVEAY-PPPAIVWIKDGV 312
L C V+ Y P P V +G
Sbjct: 139 VTLGCLVKGYFPEPVTVAWNEGA 161
>pdb|3IY1|B Chain B, Variable Domains Of The Wam Of Fab B Fitted Into The
Cryoem Reconstruction Of The Virus-Fab B Complex
Length = 109
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 5/66 (7%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
+Y + W+K T + +E + IS ++ +F+ LT D +ST + + + D
Sbjct: 25 NYYISWIKQTTGQGLEYVGYISTGSGGTNYNEKFKGKATLTVDKSSSTTFMQLSSLTPDD 84
Query: 156 AGIYKC 161
+ +Y C
Sbjct: 85 SAVYYC 90
>pdb|1KAC|B Chain B, Knob Domain From Adenovirus Serotype 12 In Complex With
Domain 1 Of Its Cellular Receptor Car
pdb|1P69|B Chain B, Structural Basis For Variation In Adenovirus Affinity For
The Cellular Receptor Car (P417s Mutant)
pdb|1P6A|B Chain B, Structural Basis For Variation In Asdenovirus Affinity For
The Cellular Receptor Car (S489y Mutant)
Length = 124
Score = 29.6 bits (65), Expect = 3.1, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 324 HFATSD-EFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
HF ++D + D S+ V ++ G Y CK G A K+I L
Sbjct: 72 HFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHL 115
>pdb|2EH7|L Chain L, Crystal Structure Of Humanized Kr127 Fab
Length = 219
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 30/128 (23%), Positives = 49/128 (38%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVE---FAPVITINRPRQGQALQYDAIL 293
LKI + D G YYCV + VE++ AP + I P Q A +
Sbjct: 78 LKISRVEAEDVGVYYCVQGTHFPQTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASV 137
Query: 294 ECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ--- 348
C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 138 VCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHKV 196
Query: 349 YACKAANK 356
YAC+ ++
Sbjct: 197 YACEVTHQ 204
>pdb|3JWD|H Chain H, Structure Of Hiv-1 Gp120 With Gp41-Interactive Region:
Layered Architecture And Basis Of Conformational
Mobility
pdb|3JWD|P Chain P, Structure Of Hiv-1 Gp120 With Gp41-Interactive Region:
Layered Architecture And Basis Of Conformational
Mobility
pdb|3JWO|H Chain H, Structure Of Hiv-1 Gp120 With Gp41-Interactive Region:
Layered Architecture And Basis Of Conformational
Mobility
Length = 220
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 42/170 (24%), Positives = 69/170 (40%), Gaps = 28/170 (16%)
Query: 79 SQEQIKDIAQTADLKC--SVQYADDYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ- 134
S ++K T + C S D+ + W++ K +E + I + ++ +F+
Sbjct: 7 SGAEVKKPGATVKISCKASGYTFSDFYMYWVRQAPGKGLEWMGLIDPEDADTMYAEKFRG 66
Query: 135 ---LTTDPETSTYILSIKEIQETDAGIYKCEV-IISLNN-KVSAEVELIVRRPPIISDNS 189
+T D T T L + ++ D +Y C LN V + L+ +S S
Sbjct: 67 RVTITADTSTDTGYLELSSLRSEDTAVYYCAADPWELNAFNVWGQGTLVS-----VSSAS 121
Query: 190 TRSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
T+ V + G T L C FP P T+SW NS AL++G
Sbjct: 122 TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 168
>pdb|1SBS|H Chain H, Crystal Structure Of An Anti-Hcg Fab
Length = 222
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 43/108 (39%), Gaps = 15/108 (13%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCE---------VIISLNNKVSAEVELIVRRP 182
RF ++ D S+ L + ++ D GIY C + S V P
Sbjct: 69 RFTISRDDSKSSVYLQMNNLRAEDTGIYYCTRGAYYRYDYAMDYWGQGTSVTVSSAKTTP 128
Query: 183 PIISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
P + + S + V L C G FP P T++W NS +LS+G
Sbjct: 129 PSVYPLAPGSAAQTN-SMVTLGCLVKGYFPEPVTVTW---NSGSLSSG 172
>pdb|3QPQ|L Chain L, Crystal Structure Of Anti-Tlr3 Antibody C1068 Fab
pdb|3QPQ|E Chain E, Crystal Structure Of Anti-Tlr3 Antibody C1068 Fab
pdb|3QPQ|C Chain C, Crystal Structure Of Anti-Tlr3 Antibody C1068 Fab
pdb|3QPQ|I Chain I, Crystal Structure Of Anti-Tlr3 Antibody C1068 Fab
pdb|3ULU|E Chain E, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form1)
pdb|3ULV|E Chain E, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form2)
Length = 215
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 44/192 (22%), Positives = 74/192 (38%), Gaps = 28/192 (14%)
Query: 192 SVIVSEGQTVYLYCYANGFPAPTISWRRD-----------NSAALSTG-GSIYRGN---- 235
S+ S G+TV + C A+G ++W + N+ L+ G S + G+
Sbjct: 10 SLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYNAKTLADGVPSRFSGSESGT 69
Query: 236 --ILKIPNITKTDRGTYYC----VAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQY 289
LKI ++ D G+YYC G G K + AP + I P Q
Sbjct: 70 QYSLKINSLQPEDFGSYYCQHFWSTPFTFGSGTKLELKRGTVAAPSVFIFPPSDEQLKSG 129
Query: 290 DAILECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFG 347
A + C + + P + W D N SV+ + D S +T+ + +
Sbjct: 130 TASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYE 188
Query: 348 Q---YACKAANK 356
+ YAC+ ++
Sbjct: 189 KHKVYACEVTHQ 200
>pdb|1RIH|L Chain L, Crystal Structure Of Fab 14f7, A Unique Anti-Tumor
Antibody Specific For N-Glycolyl Gm3
Length = 214
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 21/35 (60%)
Query: 323 SHFATSDEFSDTSLRVITIERRQFGQYACKAANKY 357
S F+ S +D +L + ++E FG Y C+ +N++
Sbjct: 60 SRFSGSGSGTDFTLSISSVETEDFGMYFCQQSNRW 94
>pdb|1RZ7|H Chain H, Crystal Structure Of Human Anti-Hiv-1 Gp120-Reactive
Antibody 48d
pdb|4DVR|H Chain H, Crystal Structure Of Yu2 Gp120 Core In Complex With Fab
48d And Nbd- 557
Length = 219
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 42/170 (24%), Positives = 69/170 (40%), Gaps = 28/170 (16%)
Query: 79 SQEQIKDIAQTADLKC--SVQYADDYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ- 134
S ++K T + C S D+ + W++ K +E + I + ++ +F+
Sbjct: 7 SGAEVKKPGATVKISCKASGYTFSDFYMYWVRQAPGKGLEWMGLIDPEDADTMYAEKFRG 66
Query: 135 ---LTTDPETSTYILSIKEIQETDAGIYKCEV-IISLNN-KVSAEVELIVRRPPIISDNS 189
+T D T T L + ++ D +Y C LN V + L+ +S S
Sbjct: 67 RVTITADTSTDTGYLELSSLRSEDTAVYYCAADPWELNAFNVWGQGTLVS-----VSSAS 121
Query: 190 TRSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
T+ V + G T L C FP P T+SW NS AL++G
Sbjct: 122 TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 168
>pdb|1JEW|R Chain R, Cryo-Em Structure Of Coxsackievirus B3(M Strain) With Its
Cellular Receptor, Coxsackievirus And Adenovirus
Receptor (Car)
Length = 120
Score = 29.3 bits (64), Expect = 3.4, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 324 HFATSD-EFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
HF ++D + D S+ V ++ G Y CK G A K+I L
Sbjct: 72 HFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHL 115
>pdb|1OPG|L Chain L, Opg2 Fab Fragment
pdb|1BM3|L Chain L, Immunoglobulin Opg2 Fab-Peptide Complex
Length = 214
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 323 SHFATSDEFSDTSLRVITIERRQFGQYACKAANKY-----GSAQKEIELFD 368
S F+ S +D +L + ++E FG Y C+ +N + G ++ EI+ D
Sbjct: 60 SRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPLTFGGGSKLEIKRAD 110
>pdb|2QQN|H Chain H, Neuropilin-1 B1 Domain In Complex With A Vegf-Blocking Fab
Length = 230
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 62/144 (43%), Gaps = 20/144 (13%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K +E + IS +G + RF ++ D +T L + ++ D
Sbjct: 32 YAMSWVRQAPGKGLEWVSQISPAGGYTNYADSVKGRFTISADTSKNTAYLQMNSLRAEDT 91
Query: 157 GIYKCEVIISLNNKVSAEVELIVRRPPI-ISDNSTRSVIV---------SEGQTVYLYCY 206
+Y C ++S +++ + + +S ST+ V + G T L C
Sbjct: 92 AVYYCARGELPYYRMSKVMDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCL 151
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 152 VKDYFPEPVTVSW---NSGALTSG 172
>pdb|4FNL|L Chain L, Crystal Structure Of Broadly Neutralizing Antibody C05
pdb|4FNL|M Chain M, Crystal Structure Of Broadly Neutralizing Antibody C05
pdb|4FP8|L Chain L, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin, Ha1 Subunit
pdb|4FP8|M Chain M, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin, Ha1 Subunit
pdb|4FP8|N Chain N, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin, Ha1 Subunit
pdb|4FP8|O Chain O, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin, Ha1 Subunit
pdb|4FQR|BB Chain b, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|DD Chain d, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|FF Chain f, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|HH Chain h, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|JJ Chain j, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|LL Chain l, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|NN Chain n, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|PP Chain p, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|RR Chain r, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|TT Chain t, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|VV Chain v, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
pdb|4FQR|XX Chain x, Crystal Structure Of Broadly Neutralizing Antibody C05
Bound To H3 Influenza Hemagglutinin
Length = 214
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 35/139 (25%), Positives = 55/139 (39%), Gaps = 11/139 (7%)
Query: 227 TGGSIYRGNILKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPR 282
+GG L I ++ D GTYYC +G+ G G K I V AP + I P
Sbjct: 63 SGGGSGTDFTLIISSLQPEDVGTYYCQQYDGLPFTFGGGTKVVIKRTVA-APSVFIFPPS 121
Query: 283 QGQALQYDAILECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVIT 340
Q A + C + + P + W D N SV+ + D S +T
Sbjct: 122 DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLT 180
Query: 341 IERRQFGQ---YACKAANK 356
+ + + + YAC+ ++
Sbjct: 181 LSKADYEKHKVYACEVTHQ 199
>pdb|4D9Q|D Chain D, Inhibiting Alternative Pathway Complement Activation By
Targeting The Exosite On Factor D
pdb|4D9Q|L Chain L, Inhibiting Alternative Pathway Complement Activation By
Targeting The Exosite On Factor D
Length = 213
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 31/129 (24%), Positives = 52/129 (40%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I ++ D TYYC+ + + G+G K I V AP + I P Q A
Sbjct: 73 LTISSLQPEDVATYYCLQSDSLPYTFGQGTKVEIKRTVA-APSVFIFPPSDEQLKSGTAS 131
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 132 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 190
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 191 VYACEVTHQ 199
>pdb|4HC1|H Chain H, Crystal Structure Of A Loop Deleted Mutant Of Human
Madcam-1 D1d2 Complexed With Fab 10g3
pdb|4HC1|M Chain M, Crystal Structure Of A Loop Deleted Mutant Of Human
Madcam-1 D1d2 Complexed With Fab 10g3
Length = 220
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 20/90 (22%), Positives = 33/90 (36%), Gaps = 6/90 (6%)
Query: 236 ILKIPNITKTDRGTYYCVAQNGV------GRGMKRNIAVEVEFAPVITINRPRQGQALQY 289
LK+ ++T D TYYC + G+G ++ AP + P G
Sbjct: 80 FLKLSSVTTEDTATYYCARASDSDGFAYWGQGTLVTVSAAKTTAPSVYPLAPVCGGTTGS 139
Query: 290 DAILECHVEAYPPPAIVWIKDGVQIMNNQH 319
L C V+ Y P + + + + H
Sbjct: 140 SVTLGCLVKGYFPEPVTLTWNSGSLSSGVH 169
>pdb|2R0L|H Chain H, Short Form Hgfa With Inhibitory Fab75
Length = 220
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 28/109 (25%), Positives = 44/109 (40%), Gaps = 19/109 (17%)
Query: 131 SRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNST 190
RF ++ D +T L + ++ D +Y C + + L+ +S ST
Sbjct: 66 GRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFWWRSFDYWGQGTLVT-----VSSAST 120
Query: 191 RSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ V + G T L C FP P T+SW NS AL++G
Sbjct: 121 KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 166
>pdb|1QNZ|H Chain H, Nmr Structure Of The 0.5b Anti-Hiv Antibody Complex With
The Gp120 V3 Peptide
Length = 119
Score = 29.3 bits (64), Expect = 3.7, Method: Composition-based stats.
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 11/70 (15%)
Query: 102 YPVIWMKMDTAKKMEPL----PISMSGSLIIHDSRF----QLTTDPETSTYILSIKEIQE 153
YP+ WMK + K +E + P S + ++ +F +LT + +ST L +
Sbjct: 32 YPIEWMKQNHGKSLEWIGNFHPYSDDTN---YNEKFKGKAKLTVEKSSSTVYLEFSRLTS 88
Query: 154 TDAGIYKCEV 163
D+ +Y C +
Sbjct: 89 DDSAVYYCAI 98
>pdb|1XQ4|A Chain A, Crystal Structure Of The Putative Apaa Protein From
Bordetella Pertussis, Northeast Structural Genomics
Target Ber40
pdb|1XQ4|B Chain B, Crystal Structure Of The Putative Apaa Protein From
Bordetella Pertussis, Northeast Structural Genomics
Target Ber40
pdb|1XQ4|C Chain C, Crystal Structure Of The Putative Apaa Protein From
Bordetella Pertussis, Northeast Structural Genomics
Target Ber40
pdb|1XQ4|D Chain D, Crystal Structure Of The Putative Apaa Protein From
Bordetella Pertussis, Northeast Structural Genomics
Target Ber40
Length = 139
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 239 IPNITKTDRGTYYCVAQNGV 258
+P T RGTY+CV +NG+
Sbjct: 94 LPTPIGTXRGTYHCVGENGI 113
>pdb|3PNW|B Chain B, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
pdb|3PNW|E Chain E, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
pdb|3PNW|H Chain H, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
pdb|3PNW|K Chain K, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
pdb|3PNW|N Chain N, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
pdb|3PNW|Q Chain Q, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
pdb|3PNW|T Chain T, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
pdb|3PNW|W Chain W, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
Length = 246
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 39/148 (26%), Positives = 60/148 (40%), Gaps = 33/148 (22%)
Query: 106 WMKMDTAKKMEPLP-ISMS-GSLIIHDS---RFQLTTDPETSTYILSIKEIQETDAGIYK 160
W++ K +E + IS S GS DS RF ++ D +T L + ++ D +Y
Sbjct: 39 WVRQAPGKGLEWVASISSSYGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYY 98
Query: 161 CEVIISLNNK---------VSAEVELIVRRPPIISDNSTRSVIV---------SEGQTVY 202
C + + K + L+ +S ST+ V + G T
Sbjct: 99 CARTVRGSKKPYFSGWAMDYWGQGTLVT-----VSSASTKGPSVFPLAPSSKSTSGGTAA 153
Query: 203 LYCYANG-FPAP-TISWRRDNSAALSTG 228
L C FP P T+SW NS AL++G
Sbjct: 154 LGCLVKDYFPEPVTVSW---NSGALTSG 178
>pdb|3LMJ|H Chain H, Structure Of Human Anti Hiv 21c Fab
pdb|3LQA|H Chain H, Crystal Structure Of Clade C Gp120 In Complex With Scd4
And
Length = 231
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 49/120 (40%), Gaps = 21/120 (17%)
Query: 127 IIHDSRFQ----LTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRP 182
II+ +FQ +T D T+T + + ++ D +Y C + N + L
Sbjct: 58 IIYAQKFQGRVSMTEDTSTNTAYMELSSLRSEDTAVYYCATGGNYYNLWTGYYPLAYWGQ 117
Query: 183 P---IISDNSTRSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+S ST+ V + G T L C FP P T+SW NS AL++G
Sbjct: 118 GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 174
>pdb|4DTG|L Chain L, Hemostatic Effect Of A Monoclonal Antibody Mab 2021
Blocking The Interaction Between Fxa And Tfpi In A
Rabbit Hemophilia Model
Length = 219
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 29/128 (22%), Positives = 49/128 (38%), Gaps = 9/128 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVE---FAPVITINRPRQGQALQYDAIL 293
LKI + D G YYC+ + VE++ AP + I P Q A +
Sbjct: 78 LKISRVEAEDVGVYYCLQATHFPQTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASV 137
Query: 294 ECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ--- 348
C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 138 VCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHKV 196
Query: 349 YACKAANK 356
YAC+ ++
Sbjct: 197 YACEVTHQ 204
>pdb|3RPI|L Chain L, Crystal Structure Of Fab From 3bnc60, Highly Potent
Anti-Hiv Antibody
pdb|3RPI|B Chain B, Crystal Structure Of Fab From 3bnc60, Highly Potent
Anti-Hiv Antibody
Length = 206
Score = 29.3 bits (64), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 44/186 (23%), Positives = 69/186 (37%), Gaps = 37/186 (19%)
Query: 198 GQTVYLYCYANGFPAPTISW---RRDNSAAL--STGGSIYRG-------------NILKI 239
G TV + C ANG+ ++W RR + L G + RG L I
Sbjct: 16 GDTVTITCQANGY----LNWYQQRRGKAPKLLIYDGSKLERGVPARFSGRRWGQEYNLTI 71
Query: 240 PNITKTDRGTYYCVAQN----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILEC 295
N+ D TY+C G +KR +A AP + I P Q A + C
Sbjct: 72 NNLQPEDVATYFCQVYEFIVPGTRLDLKRTVA-----APSVFIFPPSDEQLKSGTASVVC 126
Query: 296 HVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ---YA 350
+ + P + W D N SV+ + D S +T+ + + + YA
Sbjct: 127 LLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHKVYA 185
Query: 351 CKAANK 356
C+ ++
Sbjct: 186 CEVTHQ 191
>pdb|4D9R|L Chain L, Inhibiting Alternative Pathway Complement Activation By
Targeting The Exosite On Factor D
pdb|4D9R|D Chain D, Inhibiting Alternative Pathway Complement Activation By
Targeting The Exosite On Factor D
Length = 214
Score = 29.3 bits (64), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 31/129 (24%), Positives = 52/129 (40%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I ++ D TYYC+ + + G+G K I V AP + I P Q A
Sbjct: 73 LTISSLQPEDVATYYCLQSDSLPYTFGQGTKVEIKRTVA-APSVFIFPPSDEQLKSGTAS 131
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 132 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 190
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 191 VYACEVTHQ 199
>pdb|1HCF|X Chain X, Crystal Structure Of Trkb-D5 Bound To Neurotrophin-45
pdb|1HCF|Y Chain Y, Crystal Structure Of Trkb-D5 Bound To Neurotrophin-45
Length = 101
Score = 29.3 bits (64), Expect = 3.9, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 4/70 (5%)
Query: 297 VEAYPPPAIVWIKDGVQIMNNQHYSVS--HFATSDEFSDTSLRVITIERRQFGQYACKAA 354
V+ P PA+ W +G I+N Y + H E+ L++ G Y A
Sbjct: 25 VKGNPKPALQWFYNGA-ILNESKYICTKIHVTNHTEYHGC-LQLDNPTHMNNGDYTLIAK 82
Query: 355 NKYGSAQKEI 364
N+YG +K+I
Sbjct: 83 NEYGKDEKQI 92
>pdb|3R1G|H Chain H, Structure Basis Of Allosteric Inhibition Of Bace1 By An
Exosite- Binding Antibody
Length = 222
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 36/142 (25%), Positives = 55/142 (38%), Gaps = 18/142 (12%)
Query: 101 DYPVIWMKMDTAKKMEPLPI--SMSGSLIIHDS---RFQLTTDPETSTYILSIKEIQETD 155
Y + W++ K +E + GS DS RF ++ D +T L + ++ D
Sbjct: 31 GYGIHWVRQAPGKGLEWVGWISPAGGSTDYADSVKGRFTISADTSKNTAYLQMNSLRAED 90
Query: 156 AGIYKCE-------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYAN 208
+Y C V+ V + P + + S S G T L C
Sbjct: 91 TAVYYCARGPFSPWVMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTS-GGTAALGCLVK 149
Query: 209 G-FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 150 DYFPEPVTVSW---NSGALTSG 168
>pdb|2JIX|A Chain A, Crystal Structure Of Abt-007 Fab Fragment With The Soluble
Domain Of Epo Receptor
pdb|2JIX|G Chain G, Crystal Structure Of Abt-007 Fab Fragment With The Soluble
Domain Of Epo Receptor
pdb|2JIX|L Chain L, Crystal Structure Of Abt-007 Fab Fragment With The Soluble
Domain Of Epo Receptor
Length = 214
Score = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 51/129 (39%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQN----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I ++ D TYYC+ N G+G K I V AP + I P Q A
Sbjct: 73 LTISSLQPEDFATYYCLQHNTYPPTFGQGTKVEIKRTVA-APSVFIFPPSDEQLKSGTAS 131
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 132 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 190
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 191 VYACEVTHQ 199
>pdb|2CMR|H Chain H, Crystal Structure Of The Hiv-1 Neutralizing Antibody D5
Fab Bound To The Gp41 Inner-Core Mimetic 5-Helix
Length = 217
Score = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 39/161 (24%), Positives = 65/161 (40%), Gaps = 30/161 (18%)
Query: 90 ADLKCSVQYADD----YPVIWMKMDTAKKMEPL----PISMSGSLI-IHDSRFQLTTDPE 140
A +K S + + D Y + W++ + +E + PI + + R +T +
Sbjct: 16 ASVKVSCKASGDTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANYAQAFQGRVTITANES 75
Query: 141 TSTYILSIKEIQETDAGIYKC--EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV--- 195
TST + + ++ D IY C + L + L+ +S ST+ V
Sbjct: 76 TSTAYMELSSLRSEDTAIYYCARDNPTLLGSDYWGAGTLVT-----VSSASTKGPSVFPL 130
Query: 196 ------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ G T L C FP P T+SW NS AL++G
Sbjct: 131 APCSRSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 168
>pdb|3HFM|L Chain L, Structure Of An Antibody-Antigen Complex. Crystal
Structure Of The HyHEL-10 Fab-Lysozyme Complex
Length = 214
Score = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 323 SHFATSDEFSDTSLRVITIERRQFGQYACKAANKY-----GSAQKEIELFD 368
S F+ S +D +L + ++E FG Y C+ +N + G + EI+ D
Sbjct: 60 SRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPYTFGGGTKLEIKRAD 110
>pdb|3LEX|H Chain H, 2f5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal
Antibody 11f10 In Complex With Hiv-1 Gp41
pdb|3LEX|A Chain A, 2f5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal
Antibody 11f10 In Complex With Hiv-1 Gp41
Length = 221
Score = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/88 (21%), Positives = 34/88 (38%), Gaps = 4/88 (4%)
Query: 236 ILKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
L++ ++T D TY+C N + G+G ++ AP + P G
Sbjct: 80 FLQLHSVTPEDTATYFCAYGNYLPAYWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSV 139
Query: 292 ILECHVEAYPPPAIVWIKDGVQIMNNQH 319
L C V+ Y P + + + + H
Sbjct: 140 TLGCLVKGYFPEPVTLTWNSGSLSSGVH 167
>pdb|3D9A|L Chain L, High Resolution Crystal Structure Structure Of Hyhel10 Fab
Complexed To Hen Egg Lysozyme
Length = 213
Score = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 323 SHFATSDEFSDTSLRVITIERRQFGQYACKAANKY-----GSAQKEIELFD 368
S F+ S +D +L + ++E FG Y C+ +N + G + EI+ D
Sbjct: 60 SRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPYTFGGGTKLEIKRAD 110
>pdb|3BFO|A Chain A, Crystal Structure Of Ig-Like C2-Type 2 Domain Of The Human
Mucosa-Associated Lymphoid Tissue Lymphoma Translocation
Protein 1
pdb|3BFO|B Chain B, Crystal Structure Of Ig-Like C2-Type 2 Domain Of The Human
Mucosa-Associated Lymphoid Tissue Lymphoma Translocation
Protein 1
pdb|3BFO|C Chain C, Crystal Structure Of Ig-Like C2-Type 2 Domain Of The Human
Mucosa-Associated Lymphoid Tissue Lymphoma Translocation
Protein 1
pdb|3BFO|D Chain D, Crystal Structure Of Ig-Like C2-Type 2 Domain Of The Human
Mucosa-Associated Lymphoid Tissue Lymphoma Translocation
Protein 1
Length = 91
Score = 29.3 bits (64), Expect = 4.1, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 5/59 (8%)
Query: 198 GQTVYLYCYANGFPAPTISWRRDNSAALSTGGSIYRGNILKIPNITKTDRGTYYCVAQN 256
G T+ L C A G P P W ++ +Y +P + +GTY+C N
Sbjct: 18 GSTLVLQCVAVGSPIPHYQWFKNELPLTHETKKLY-----MVPYVDLEHQGTYWCHVYN 71
>pdb|2PYE|D Chain D, Crystal Structures Of High Affinity Human T-Cell Receptors
Bound To Pmhc Revealnative Diagonal Binding Geometry Tcr
Clone C5c1 Complexed With Mhc
Length = 195
Score = 29.3 bits (64), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 27/72 (37%)
Query: 92 LKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYILSIKEI 151
L CS + Y + W + D K + L + S R + D + + L I
Sbjct: 22 LNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGSSTLYIAAS 81
Query: 152 QETDAGIYKCEV 163
Q D+ Y C V
Sbjct: 82 QPGDSATYLCAV 93
>pdb|1UYW|H Chain H, Crystal Structure Of The Antiflavivirus Fab4g2
pdb|1UYW|M Chain M, Crystal Structure Of The Antiflavivirus Fab4g2
Length = 218
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 29/113 (25%), Positives = 46/113 (40%), Gaps = 27/113 (23%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKV------------SAEVELIV 179
+ LT D +ST + ++ + D+ +Y C I + SA+
Sbjct: 66 KATLTVDKSSSTAYMDLRSLSSEDSAVYFCARIYHYDGYFDVWGAGTAVTVSSAKTTAPS 125
Query: 180 RRP--PIISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
P P+ D + G +V L C G FP P T++W NS +LS+G
Sbjct: 126 VYPLAPVCGDTT--------GSSVTLGCLVKGYFPEPVTLTW---NSGSLSSG 167
>pdb|1IQW|H Chain H, Crystal Structure Of The Fab Fragment Of The Mouse Anti-
Human Fas Antibody Hfe7a
Length = 230
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 37/142 (26%), Positives = 61/142 (42%), Gaps = 18/142 (12%)
Query: 102 YPVIWMKMDTAKKMEPL-PISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETDA 156
Y + W+K + +E + I S S ++ +F+ LT D +ST + + + D+
Sbjct: 32 YWMQWVKQRPGQGLEWIGEIDPSDSYTNYNQKFKGKATLTVDTSSSTAYMQLSSLTSEDS 91
Query: 157 GIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVIV-----SEGQT---VYLYCYAN 208
+Y C +N +V + S +T + S QT V L C
Sbjct: 92 AVYYCARNRDYSNNWYFDVWGTGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVK 151
Query: 209 G-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 152 GYFPEPVTVTW---NSGSLSSG 170
>pdb|2ZNW|A Chain A, Crystal Structure Of Scfv10 In Complex With Hen Egg
Lysozyme
pdb|2ZNW|B Chain B, Crystal Structure Of Scfv10 In Complex With Hen Egg
Lysozyme
Length = 242
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 323 SHFATSDEFSDTSLRVITIERRQFGQYACKAANKY 357
S F+ S +D +L + ++E FG Y C+ +N +
Sbjct: 60 SRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSW 94
>pdb|2PYF|A Chain A, Crystal Structures Of High Affinity Human T-Cell Receptors
Bound To Pmhc Revealnative Diagonal Binding Geometry
Unbound Tcr Clone 5-1
Length = 205
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 27/72 (37%)
Query: 92 LKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYILSIKEI 151
L CS + Y + W + D K + L + S R + D + + L I
Sbjct: 21 LNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGSSTLYIAAS 80
Query: 152 QETDAGIYKCEV 163
Q D+ Y C V
Sbjct: 81 QPGDSATYLCAV 92
>pdb|4HPY|H Chain H, Crystal Structure Of Rv144-elicited Antibody Ch59 In
Complex With V2 Peptide
Length = 225
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 38/150 (25%), Positives = 62/150 (41%), Gaps = 31/150 (20%)
Query: 100 DDYPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQET 154
DD + W++ K +E + IS + ++I + RF ++ D ++ L + ++
Sbjct: 30 DDGAMHWVRQAPGKGLEWVSGISWNSNIIAYADSVKGRFTISRDNAKNSLYLEMNSLRVE 89
Query: 155 DAGIYKCEVIISLNNKVSAEVELIVRRPP-----IISDNSTRSVIV---------SEGQT 200
D +Y C K S EL + +S ST+ V + G T
Sbjct: 90 DTALYYCA-------KDSPRGELPLNYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGT 142
Query: 201 VYLYCYANG-FPAP-TISWRRDNSAALSTG 228
L C FP P T+SW NS AL++G
Sbjct: 143 AALGCLVKDYFPEPVTVSW---NSGALTSG 169
>pdb|2JB5|H Chain H, Fab Fragment In Complex With Small Molecule Hapten,
Crystal Form-1
pdb|2JB6|B Chain B, Fab Fragment In Complex With Small Molecule Hapten,
Crystal Form-2
pdb|2JB6|H Chain H, Fab Fragment In Complex With Small Molecule Hapten,
Crystal Form-2
Length = 244
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 36/171 (21%), Positives = 63/171 (36%), Gaps = 29/171 (16%)
Query: 79 SQEQIKDIAQTADLKCSVQYA--DDYPVIWMKMDTAKKMEPLP-----ISMSGSLIIHDS 131
S ++K + + C +Y + W++ + +E + +
Sbjct: 7 SGAEVKKPGSSVKVSCKASGGTFSNYAINWVRQAPGQGLEWMGNIEPYFGTANYAQKFQG 66
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVS---AEVELIVRRPPIISDN 188
R +T D TST + + ++ D +Y C +S + L+ +S
Sbjct: 67 RVTITADESTSTAYMELSSLRSEDTAVYYCARYFMSYKHLSDYWGQGTLVT-----VSSA 121
Query: 189 STRSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
ST+ V + G T L C FP P T+SW NS AL++G
Sbjct: 122 STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 169
>pdb|1DQJ|A Chain A, Crystal Structure Of The Anti-Lysozyme Antibody Hyhel-63
Complexed With Hen Egg White Lysozyme
pdb|1DQM|L Chain L, Crystal Structure Of Anti-Lysozyme Antibody
pdb|1DQQ|A Chain A, Crystal Structure Of Anti-Lysozyme Antibody Hyhel-63
pdb|1DQQ|C Chain C, Crystal Structure Of Anti-Lysozyme Antibody Hyhel-63
pdb|1NBY|A Chain A, Crystal Structure Of Hyhel-63 Complexed With Hel Mutant
K96a
pdb|1NBZ|A Chain A, Crystal Structure Of Hyhel-63 Complexed With Hel Mutant
K97a
pdb|1NDG|A Chain A, Crystal Structure Of Fab Fragment Of Antibody Hyhel-8
Complexed With Its Antigen Lysozyme
pdb|1NDM|A Chain A, Crystal Structure Of Fab Fragment Of Antibody Hyhel-26
Complexed With Lysozyme
pdb|1XGU|A Chain A, Structure For Antibody Hyhel-63 Y33f Mutant Complexed With
Hen Egg Lysozyme
Length = 214
Score = 28.9 bits (63), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 323 SHFATSDEFSDTSLRVITIERRQFGQYACKAANKY-----GSAQKEIELFD 368
S F+ S +D +L + ++E FG Y C+ +N + G + EI+ D
Sbjct: 60 SRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPYTFGGGTKLEIKRAD 110
>pdb|1XGP|A Chain A, Structure For Antibody Hyhel-63 Y33a Mutant Complexed With
Hen Egg Lysozyme
pdb|1XGQ|A Chain A, Structure For Antibody Hyhel-63 Y33v Mutant Complexed With
Hen Egg Lysozyme
pdb|1XGR|A Chain A, Structure For Antibody Hyhel-63 Y33i Mutant Complexed With
Hen Egg Lysozyme
pdb|1XGT|A Chain A, Structure For Antibody Hyhel-63 Y33l Mutant Complexed With
Hen Egg Lysozyme
Length = 215
Score = 28.9 bits (63), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 323 SHFATSDEFSDTSLRVITIERRQFGQYACKAANKY-----GSAQKEIELFD 368
S F+ S +D +L + ++E FG Y C+ +N + G + EI+ D
Sbjct: 61 SRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPYTFGGGTKLEIKRAD 111
>pdb|3NPS|B Chain B, Crystal Structure Of Membrane-Type Serine Protease 1
(Mt-Sp1) In Complex With The Fab Inhibitor S4
Length = 226
Score = 28.9 bits (63), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 29/112 (25%), Positives = 44/112 (39%), Gaps = 18/112 (16%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPP----IISD 187
R +T D TST + + ++ D +Y C + S + + +S
Sbjct: 66 RVTITADESTSTAYMELSSLRSEDTAVYYCARTFHIRRYRSGYYDKMDHWGQGTLVTVSS 125
Query: 188 NSTRSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
ST+ V + G T L C FP P T+SW NS AL++G
Sbjct: 126 ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 174
>pdb|2DQI|L Chain L, Crystal Structure Of Hyhel-10 Fv Mutant (Ly50a) Complexed
With Hen Egg Lysozyme
Length = 107
Score = 28.9 bits (63), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 323 SHFATSDEFSDTSLRVITIERRQFGQYACKAANKY 357
S F+ S +D +L + ++E FG Y C+ +N +
Sbjct: 60 SRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSW 94
>pdb|3A6B|L Chain L, Crystal Structure Of Hyhel-10 Fv Mutant Ln32d Complexed
With White Lysozyme
Length = 107
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 323 SHFATSDEFSDTSLRVITIERRQFGQYACKAANKY 357
S F+ S +D +L + ++E FG Y C+ +N +
Sbjct: 60 SRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSW 94
>pdb|3A67|L Chain L, Crystal Structure Of Hyhel-10 Fv Mutant Ln31d Complexed
With White Lysozyme
Length = 107
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 323 SHFATSDEFSDTSLRVITIERRQFGQYACKAANKY 357
S F+ S +D +L + ++E FG Y C+ +N +
Sbjct: 60 SRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSW 94
>pdb|1J1O|L Chain L, Crystal Structure Of Hyhel-10 Fv Mutant Ly50f Complexed
With Hen Egg White Lysozyme
Length = 107
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 323 SHFATSDEFSDTSLRVITIERRQFGQYACKAANKY 357
S F+ S +D +L + ++E FG Y C+ +N +
Sbjct: 60 SRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSW 94
>pdb|1C08|A Chain A, Crystal Structure Of Hyhel-10 Fv-Hen Lysozyme Complex
pdb|1IC4|L Chain L, Crystal Structure Of Hyhel-10 Fv Mutant(Hd32a)-Hen
Lysozyme Complex
pdb|1IC5|L Chain L, Crystal Structure Of Hyhel-10 Fv Mutant(Hd99a)-Hen
Lysozyme Complex
pdb|1IC7|L Chain L, Crystal Structure Of Hyhel-10 Fv Mutant(Hd32a99a)-Hen
Lysozyme Complex
pdb|1UA6|L Chain L, Crystal Structure Of Hyhel-10 Fv Mutant Sfsf Complexed
With Hen Egg White Lysozyme Complex
pdb|1UAC|L Chain L, Crystal Structure Of Hyhel-10 Fv Mutant Sfsf Complexed
With Turkey White Lysozyme
pdb|2DQC|L Chain L, Crystal Structure Of Hyhel-10 Fv Mutant(Hy33f) Complexed
With Hen Egg Lysozyme
pdb|2DQD|L Chain L, Crystal Structure Of Hyhel-10 Fv Mutant (Hy50f) Complexed
With Hen Egg Lysozyme
pdb|2DQE|L Chain L, Crystal Structure Of Hyhel-10 Fv Mutant (Hy53a) Complexed
With Hen Egg Lysozyme
pdb|2DQF|A Chain A, Crystal Structure Of Hyhel-10 Fv Mutant (Y33ay53a)
Complexed With Hen Egg Lysozyme
pdb|2DQF|D Chain D, Crystal Structure Of Hyhel-10 Fv Mutant (Y33ay53a)
Complexed With Hen Egg Lysozyme
pdb|2DQG|L Chain L, Crystal Structure Of Hyhel-10 Fv Mutant (Hy53f) Complexed
With Hen Egg Lysozyme
pdb|2DQH|L Chain L, Crystal Structure Of Hyhel-10 Fv Mutant (Hy58a) Complexed
With Hen Egg Lysozyme
pdb|2DQJ|L Chain L, Crystal Structure Of Hyhel-10 Fv (Wild-Type) Complexed
With Hen Egg Lysozyme At 1.8a Resolution
Length = 107
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 323 SHFATSDEFSDTSLRVITIERRQFGQYACKAANKY 357
S F+ S +D +L + ++E FG Y C+ +N +
Sbjct: 60 SRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSW 94
>pdb|1CLZ|H Chain H, Igg Fab (Igg3, Kappa) Fragment (Mbr96) Complexed With
Lewis Y Nonoate Methyl Ester
Length = 218
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 35/145 (24%), Positives = 58/145 (40%), Gaps = 25/145 (17%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETD 155
DY + W++ K++E + IS G + + RF ++ D ++ L + ++ D
Sbjct: 31 DYYMYWVRQTPEKRLEWVAYISQGGDITDYPDTVKGRFTISRDNAKNSLYLQMSRLKSED 90
Query: 156 AGIYKCEVIIS-------LNNKVSAEVELIVRRP---PIISDNSTRSVIVSEGQTVYLYC 205
+Y C + V + P P++ S S G +V L C
Sbjct: 91 TAMYYCARGLDDGAWFAYWGQGTLVTVSVTTTAPSVYPLVPGCSDTS-----GSSVTLGC 145
Query: 206 YANG-FPAP-TISWRRDNSAALSTG 228
G FP P T+ W N ALS+G
Sbjct: 146 LVKGYFPEPVTVKW---NYGALSSG 167
>pdb|3UMT|A Chain A, Scfv12, Anti-Bcla Antibody Single Chain Variable Fragment
Length = 256
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
+Y + W+K K +E + I+ + ++ +F+ LT D +ST L ++ + D
Sbjct: 33 EYTMHWVKQSHGKSLEWIGGINPNNGGTSYNQKFKGKAILTVDKSSSTAYLELRSLTSED 92
Query: 156 AGIYKC 161
+ +Y C
Sbjct: 93 SAVYYC 98
>pdb|1IND|H Chain H, How The Anti-(Metal Chelate) Antibody Cha255 Is Specific
For The Metal Ion Of Its Antigen: X-Ray Structures For
Two Fab'(Slash)hapten Complexes With Different Metals In
The Chelate
pdb|1INE|H Chain H, How The Anti-(Metal Chelate) Antibody Cha255 Is Specific
For The Metal Ion Of Its Antigen: X-Ray Structures For
Two Fab'(Slash)hapten Complexes With Different Metals In
The Chelate
Length = 226
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 31/131 (23%), Positives = 56/131 (42%), Gaps = 12/131 (9%)
Query: 106 WMKMDTAKKMEPLPISMSGSLIIHDS-----RFQLTTDPETSTYILSIKEIQETDAGIYK 160
W++ K++E + ++SG S RF ++ D + L + ++ D +Y
Sbjct: 36 WVRQTPEKRLEWVATTLSGGGFTFYSASVKGRFTISRDNAQNNLYLQLNSLRSEDTALYF 95
Query: 161 CEVIISLNNKVSAEVELIVR-RPPIISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISW 217
C ++ V + + PP + + S + V L C G FP P T++W
Sbjct: 96 CASHRFVHWGHGTLVTVSAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVKGYFPEPVTVTW 154
Query: 218 RRDNSAALSTG 228
NS +LS+G
Sbjct: 155 ---NSGSLSSG 162
>pdb|1MLB|A Chain A, Monoclonal Antibody Fab D44.1 Raised Against Chicken Egg-
White Lysozyme
pdb|1MLC|A Chain A, Monoclonal Antibody Fab D44.1 Raised Against Chicken Egg-
White Lysozyme Complexed With Lysozyme
pdb|1MLC|C Chain C, Monoclonal Antibody Fab D44.1 Raised Against Chicken Egg-
White Lysozyme Complexed With Lysozyme
Length = 214
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 323 SHFATSDEFSDTSLRVITIERRQFGQYACKAANKY-----GSAQKEIELFD 368
S F+ S +D +L + ++E FG Y C+ +N + G + EI+ D
Sbjct: 60 SRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPRTFGGGTKLEIKRAD 110
>pdb|1Z3G|H Chain H, Crystal Structure Of Complex Between Pvs25 And Fab
Fragment Of Malaria Transmission Blocking Antibody 2a8
pdb|1Z3G|I Chain I, Crystal Structure Of Complex Between Pvs25 And Fab
Fragment Of Malaria Transmission Blocking Antibody 2a8
Length = 216
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 34/138 (24%), Positives = 57/138 (41%), Gaps = 14/138 (10%)
Query: 101 DYPVIWMKMDTAKKMEPLPI--SMSGSLIIHD---SRFQLTTDPETSTYILSIKEIQETD 155
Y + W+K + +E + + SGS ++ S+ LT D +ST + + + D
Sbjct: 31 SYWMHWVKQRPGQGLEWIGMIHPHSGSTNYNEKFKSKATLTVDKSSSTAYMQLSSLTSED 90
Query: 156 AGIYKCEV---IISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FP 211
+ +Y C + V PP + + S + V L C G FP
Sbjct: 91 SAVYYCARGWDVAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVKGYFP 149
Query: 212 AP-TISWRRDNSAALSTG 228
P T++W NS +LS+G
Sbjct: 150 EPVTVTW---NSGSLSSG 164
>pdb|3S62|H Chain H, Structure Of Fab Fragment Of Malaria Transmission Blocking
Antibody 2a8 Against P. Vivax P25 Protein
Length = 216
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 34/138 (24%), Positives = 57/138 (41%), Gaps = 14/138 (10%)
Query: 101 DYPVIWMKMDTAKKMEPLPI--SMSGSLIIHD---SRFQLTTDPETSTYILSIKEIQETD 155
Y + W+K + +E + + SGS ++ S+ LT D +ST + + + D
Sbjct: 31 SYWMHWVKQRPGQGLEWIGMIHPHSGSTNYNEKFKSKATLTVDKSSSTAYMQLSSLTSED 90
Query: 156 AGIYKCEV---IISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FP 211
+ +Y C + V PP + + S + V L C G FP
Sbjct: 91 SAVYYCARGADVAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVKGYFP 149
Query: 212 AP-TISWRRDNSAALSTG 228
P T++W NS +LS+G
Sbjct: 150 EPVTVTW---NSGSLSSG 164
>pdb|1KCU|L Chain L, Crystal Structure Of Antibody Pc287
pdb|1KC5|L Chain L, Crystal Structure Of Antibody Pc287 In Complex With Ps1
Peptide
Length = 214
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 49/216 (22%), Positives = 81/216 (37%), Gaps = 36/216 (16%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISW---RRDNSAALS-------------- 226
I+ S +S+ +S G+ V L C A+ +SW R + AL
Sbjct: 2 IVLTQSPKSMSMSVGEKVTLSCKASENVDTYVSWYQQRPEQPPALLIYGASNRYTGVPDR 61
Query: 227 -TGGSIYRGNILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRP 281
TG L I ++ D Y+C G G K + + AP ++I P
Sbjct: 62 FTGSGSATDFTLTISSVQAEDLADYHCGQSYSYPLTFGGGTKLELK-RADAAPTVSIFPP 120
Query: 282 RQGQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDEFSD------ 333
Q A + C + + P I W DG + N V++ T+ + D
Sbjct: 121 SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNG----VANSWTAQDSKDSTYSMS 176
Query: 334 TSLRVITIERRQFGQYACKAANKYGSAQKEIELFDR 369
++L + E + Y C+A +K S ++ F+R
Sbjct: 177 STLTLTKDEYERHNSYTCEATHK-TSTSPVVKSFNR 211
>pdb|3SQO|H Chain H, Pcsk9 J16 Fab Complex
Length = 219
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 30/106 (28%), Positives = 43/106 (40%), Gaps = 12/106 (11%)
Query: 131 SRFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISL------NNKVSAEVELIVRRPPI 184
SR +T D TST + + ++ D +Y C L + V + P
Sbjct: 66 SRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARERPLYASDLWGQGTTVTVSSASTKGPS 125
Query: 185 ISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ + S SE T L C FP P T+SW NS AL++G
Sbjct: 126 VFPLAPSSRSTSE-STAALGCLVKDYFPEPVTVSW---NSGALTSG 167
>pdb|1YUH|H Chain H, Fab Fragment
pdb|1YUH|B Chain B, Fab Fragment
Length = 218
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 28/106 (26%), Positives = 43/106 (40%), Gaps = 12/106 (11%)
Query: 131 SRFQLTTDPETSTYILSIKEIQETDAGIY------KCEVIISLNNKVSAEVELIVRRPPI 184
S+ LT D +ST + + + D+ +Y C + + V PP
Sbjct: 66 SKATLTVDKPSSTAYMELSSLTSEDSAVYYCARYAYCRPMDYWGQGTTVTVSSAATTPPS 125
Query: 185 ISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ + S + V L C G FP P T++W NS ALS+G
Sbjct: 126 VYPLAPGSAAQTNSM-VTLGCLVKGYFPEPVTVTW---NSGALSSG 167
>pdb|2F54|D Chain D, Directed Evolution Of Human T Cell Receptor Cdr2 Residues
By Phage Display Dramatically Enhances Affinity For
Cognate Peptide-Mhc Without Increasing Apparent
Cross-Reactivity
pdb|2F54|K Chain K, Directed Evolution Of Human T Cell Receptor Cdr2 Residues
By Phage Display Dramatically Enhances Affinity For
Cognate Peptide-Mhc Without Increasing Apparent
Cross-Reactivity
Length = 206
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 26/72 (36%)
Query: 92 LKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYILSIKEI 151
L CS + Y + W + D K+ L + S R + D + L I
Sbjct: 21 LNCSFTDSAIYNLQWFRQDPGGKLTSLLLIQSSQREQTSGRLNASLDKSAGSSTLYIAAS 80
Query: 152 QETDAGIYKCEV 163
Q D+ Y C V
Sbjct: 81 QPGDSATYLCAV 92
>pdb|3FO0|L Chain L, Crystal Structure Of Hapten Complex Of Catalytic
Elimination Antibody 13g5 (Wild-Type)
Length = 219
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 50/129 (38%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + + G G K I V AP + I P Q A
Sbjct: 78 LKINRVEAEDLGVYYCFQGSHLPPTFGGGTKLEIKRTVA-APSVFIFPPSDEQLKSGTAS 136
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 137 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 195
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 196 VYACEVTHQ 204
>pdb|1A4J|L Chain L, Diels Alder Catalytic Antibody Germline Precursor
pdb|1A4J|A Chain A, Diels Alder Catalytic Antibody Germline Precursor
Length = 217
Score = 28.9 bits (63), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 49/129 (37%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G Y+C V G G K I V AP + I P Q A
Sbjct: 78 LKISRVEAEDLGVYFCSQSTHVPPTFGGGTKLEIKRTVA-APSVFIFPPSDEQLKSGTAS 136
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 137 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 195
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 196 VYACEVTHQ 204
>pdb|2UYL|B Chain B, Crystal Structure Of A Monoclonal Antibody Directed
Against An Antigenic Determinant Common To Ogawa And
Inaba Serotypes Of Vibrio Cholerae O1
pdb|2UYL|N Chain N, Crystal Structure Of A Monoclonal Antibody Directed
Against An Antigenic Determinant Common To Ogawa And
Inaba Serotypes Of Vibrio Cholerae O1
pdb|2UYL|W Chain W, Crystal Structure Of A Monoclonal Antibody Directed
Against An Antigenic Determinant Common To Ogawa And
Inaba Serotypes Of Vibrio Cholerae O1
pdb|2UYL|Y Chain Y, Crystal Structure Of A Monoclonal Antibody Directed
Against An Antigenic Determinant Common To Ogawa And
Inaba Serotypes Of Vibrio Cholerae O1
Length = 221
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 36/137 (26%), Positives = 57/137 (41%), Gaps = 18/137 (13%)
Query: 106 WMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETDAGIYK 160
W+K + +E + IS S ++ +F+ LT D +ST + + + D+ +Y
Sbjct: 36 WVKQRPGQGLEWIGHISPGSSSTNYNEKFKSKATLTVDTSSSTAYMQLSSLTSDDSAVYY 95
Query: 161 C----EVIISLNN---KVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG-FPA 212
C V S N V PP + + S + V L C G FP
Sbjct: 96 CGREETVRASFGNWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVKGYFPE 154
Query: 213 P-TISWRRDNSAALSTG 228
P T++W NS +LS+G
Sbjct: 155 PVTVTW---NSGSLSSG 168
>pdb|3PP3|H Chain H, Epitope Characterization And Crystal Structure Of Ga101
Provide Insights Into The Molecular Basis For The Type I
TYPE II Distinction Of Anti- Cd20 Antibodies
pdb|3PP3|I Chain I, Epitope Characterization And Crystal Structure Of Ga101
Provide Insights Into The Molecular Basis For The Type I
TYPE II Distinction Of Anti- Cd20 Antibodies
pdb|3PP4|H Chain H, Epitope Characterization And Crystal Structure Of Ga101
Provide Insights Into The Molecular Basis For The Type I
TYPE II Distinction Of Anti- Cd20 Antibodies
Length = 224
Score = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 38/166 (22%), Positives = 65/166 (39%), Gaps = 20/166 (12%)
Query: 79 SQEQIKDIAQTADLKCSVQ-YADDYPVI-WMKMDTAKKMEPLPISMSGSLII-HDSRFQ- 134
S ++K + + C YA Y I W++ + +E + G ++ +F+
Sbjct: 7 SGAEVKKPGSSVKVSCKASGYAFSYSWINWVRQAPGQGLEWMGRIFPGDGDTDYNGKFKG 66
Query: 135 ---LTTDPETSTYILSIKEIQETDAGIYKCE-------VIISLNNKVSAEVELIVRRPPI 184
+T D TST + + ++ D +Y C ++ V + P
Sbjct: 67 RVTITADKSTSTAYMELSSLRSEDTAVYYCARNVFDGYWLVYWGQGTLVTVSSASTKGPS 126
Query: 185 ISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ + S S G T L C FP P T+SW NS AL++G
Sbjct: 127 VFPLAPSSKSTS-GGTAALGCLVKDYFPEPVTVSW---NSGALTSG 168
>pdb|3NVQ|A Chain A, Molecular Mechanism Of Guidance Cue Recognition
pdb|3NVQ|E Chain E, Molecular Mechanism Of Guidance Cue Recognition
Length = 590
Score = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 29/68 (42%), Gaps = 2/68 (2%)
Query: 191 RSVIVSEGQTVYLYCYANGFPAPTISWR-RDNSAALSTGGSIYRGNILKIPNITKTDRGT 249
+ V ++ YL C A T SWR ++N G IL I N+T G
Sbjct: 508 QKVSLAPNSRYYLSCPMESRHA-TYSWRHKENVEQSCEPGHQSPNCILFIENLTAQQYGH 566
Query: 250 YYCVAQNG 257
Y+C AQ G
Sbjct: 567 YFCEAQEG 574
>pdb|2RCS|H Chain H, Immunoglobulin 48g7 Germline Fab-Affinity Maturation Of An
Esterolytic Antibody
pdb|1AJ7|H Chain H, Immunoglobulin 48g7 Germline Fab Antibody Complexed With
Hapten 5-(Para-Nitrophenyl Phosphonate)-Pentanoic Acid.
Affinity Maturation Of An Esterolytic Antibody
Length = 217
Score = 28.9 bits (63), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 30/108 (27%), Positives = 45/108 (41%), Gaps = 12/108 (11%)
Query: 129 HDSRFQ----LTTDPETSTYILSIKEIQETDAGIYKCEVI--ISLNNKVSAEVELIVRRP 182
+D +FQ +T D ++T L + + D +Y C I + V +
Sbjct: 60 YDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCASYYGIYWGQGTTLTVSSASTKG 119
Query: 183 PIISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
P + + S S G T L C FP P T+SW NS AL++G
Sbjct: 120 PSVFPLAPSSKSTSGG-TAALGCLVKDYFPEPVTVSW---NSGALTSG 163
>pdb|3FO1|L Chain L, Crystal Structure Of Hapten Complex Of Catalytic
Elimination Antibody 13g5 (Glu(L39)ala Mutant)
pdb|3FO1|A Chain A, Crystal Structure Of Hapten Complex Of Catalytic
Elimination Antibody 13g5 (Glu(L39)ala Mutant)
Length = 219
Score = 28.9 bits (63), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 50/129 (38%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + + G G K I V AP + I P Q A
Sbjct: 78 LKINRVEAEDLGVYYCFQGSHLPPTFGGGTKLEIKRTVA-APSVFIFPPSDEQLKSGTAS 136
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 137 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 195
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 196 VYACEVTHQ 204
>pdb|2KDG|A Chain A, Solution Structure Of The 1st Ig Domain Of Myotilin
Length = 100
Score = 28.9 bits (63), Expect = 5.6, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 9/74 (12%)
Query: 195 VSEGQTVYLYCYANGFPAPTISW-------RRDNSAALSTGGSIYRGNILKIPNITKTDR 247
+ EG+ + +G PAP +SW + D+ + I ++ + +D
Sbjct: 17 IDEGRFCRMDFKVSGLPAPDVSWYLNGRTVQSDDLHKMIVSEKGLHSLIFEV--VRASDA 74
Query: 248 GTYYCVAQNGVGRG 261
G Y CVA+N G
Sbjct: 75 GAYACVAKNRAGEA 88
>pdb|3FO2|L Chain L, Crystal Structure Of Hapten Complex Of Catalytic
Elimination Antibody 13g5 (Glu(L39)gln Mutant)
pdb|3FO2|A Chain A, Crystal Structure Of Hapten Complex Of Catalytic
Elimination Antibody 13g5 (Glu(L39)gln Mutant)
Length = 219
Score = 28.5 bits (62), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 50/129 (38%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC + + G G K I V AP + I P Q A
Sbjct: 78 LKINRVEAEDLGVYYCFQGSHLPPTFGGGTKLEIKRTVA-APSVFIFPPSDEQLKSGTAS 136
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 137 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 195
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 196 VYACEVTHQ 204
>pdb|3G5Y|B Chain B, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
Length = 216
Score = 28.5 bits (62), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 4/88 (4%)
Query: 236 ILKIPNITKTDRGTYYCV-AQNGV---GRGMKRNIAVEVEFAPVITINRPRQGQALQYDA 291
L++ ++T D TYYC A G G+G ++ AP + P G
Sbjct: 80 FLQLNSVTVEDTATYYCATAGRGFPYWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSV 139
Query: 292 ILECHVEAYPPPAIVWIKDGVQIMNNQH 319
L C V+ Y P + + + + H
Sbjct: 140 TLGCLVKGYFPEPVTLTWNSGSLSSGVH 167
>pdb|2YPV|H Chain H, Crystal Structure Of The Meningococcal Vaccine Antigen
Factor H Binding Protein In Complex With A Bactericidal
Antibody
Length = 218
Score = 28.5 bits (62), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 5/66 (7%)
Query: 101 DYPVIWMKMDTAKKMEPLPI-SMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K K +E + I I ++ +F+ LT D +ST + + + D
Sbjct: 31 DYNMSWVKQSNGKSLEWIGIIDPKYGTINYNQKFKGKATLTVDQASSTAYMQLNSLTSED 90
Query: 156 AGIYKC 161
+ +Y C
Sbjct: 91 SAVYYC 96
>pdb|3E4C|A Chain A, Procaspase-1 Zymogen Domain Crystal Strucutre
pdb|3E4C|B Chain B, Procaspase-1 Zymogen Domain Crystal Strucutre
Length = 302
Score = 28.5 bits (62), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 303 PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIER 343
P +VW KD V + N T++EF D +++ IE+
Sbjct: 188 PGVVWFKDSVGVSGNL-----SLPTTEEFEDDAIKKAHIEK 223
>pdb|3U0T|C Chain C, Fab-Antibody Complex
pdb|3U0T|A Chain A, Fab-Antibody Complex
Length = 219
Score = 28.5 bits (62), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 31/129 (24%), Positives = 50/129 (38%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI + D G YYC+ G+G + I V AP + I P Q A
Sbjct: 78 LKISRVEAEDVGVYYCLQGTHYPVLFGQGTRLEIKRTVA-APSVFIFPPSDEQLKSGTAS 136
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 137 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 195
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 196 VYACEVTHQ 204
>pdb|3VFG|L Chain L, Crystal Structure Of Monoclonal Anitbody 3f8 Fab Fragment
That Binds To Gd2 Ganglioside
Length = 211
Score = 28.5 bits (62), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 41/196 (20%), Positives = 71/196 (36%), Gaps = 24/196 (12%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALS----------------- 226
I+ + + ++VS G V + C A+ + ++W + +
Sbjct: 2 IVMTQTPKFLLVSAGDRVTITCKASQSVSNDVTWYQQKAGQSPKLLIYSASNRYSGVPDR 61
Query: 227 -TGGSIYRGNILKIPNITKTDRGTYYCVAQ-NGVGRGMKRNIAVEVEFAPVITINRPRQG 284
TG I + D Y+C + G G K I + AP ++I P
Sbjct: 62 FTGSGYGTAFTFTISTVQAEDLAVYFCQQDYSSFGGGTKLEIK-RADAAPTVSIFPPSSE 120
Query: 285 QALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRVITI 341
Q A + C + + P I W DG + N S + + D +S +S +T
Sbjct: 121 QLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTK 180
Query: 342 -ERRQFGQYACKAANK 356
E + Y C+A +K
Sbjct: 181 DEYERHNSYTCEATHK 196
>pdb|1CR9|H Chain H, Crystal Structure Of The Anti-Prion Fab 3f4
pdb|1CU4|H Chain H, Crystal Structure Of The Anti-Prion Fab 3f4 In Complex
With Its Peptide Epitope
Length = 217
Score = 28.5 bits (62), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 36/146 (24%), Positives = 57/146 (39%), Gaps = 31/146 (21%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
DY + W+K + +E + I + RFQ +T D ++T L + + D
Sbjct: 31 DYYIQWVKQRPEQGLEWIGWIDPENGNSEYAPRFQGKATMTADTLSNTAYLQLSSLTSED 90
Query: 156 AGIYKCEVIISLNNKVSAEVELIVRR-----------PPIISDNSTRSVIVSEGQTVYLY 204
+Y C L++ L V P+ D + G +V L
Sbjct: 91 TAVYYCNA--DLHDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTT--------GSSVTLG 140
Query: 205 CYANG-FPAP-TISWRRDNSAALSTG 228
C G FP P T++W NS +LS+G
Sbjct: 141 CLVKGYFPEPVTLTW---NSGSLSSG 163
>pdb|3EO0|B Chain B, Structure Of The Transforming Growth Factor-Beta
Neutralizing Antibody Gc-1008
pdb|3EO0|D Chain D, Structure Of The Transforming Growth Factor-Beta
Neutralizing Antibody Gc-1008
Length = 225
Score = 28.5 bits (62), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 29/107 (27%), Positives = 42/107 (39%), Gaps = 14/107 (13%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISL--------NNKVSAEVELIVRRPP 183
R +T D TST + + ++ D +Y C + L V + P
Sbjct: 67 RVTITADESTSTTYMELSSLRSEDTAVYYCASTLGLVLDAMDYWGQGTLVTVSSASTKGP 126
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ + S SE T L C FP P T+SW NS AL++G
Sbjct: 127 SVFPLAPCSRSTSE-STAALGCLVKDYFPEPVTVSW---NSGALTSG 169
>pdb|3EO1|B Chain B, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
pdb|3EO1|E Chain E, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
pdb|3EO1|H Chain H, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
pdb|3EO1|K Chain K, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
Length = 225
Score = 28.5 bits (62), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 29/107 (27%), Positives = 42/107 (39%), Gaps = 14/107 (13%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCEVIISL--------NNKVSAEVELIVRRPP 183
R +T D TST + + ++ D +Y C + L V + P
Sbjct: 67 RVTITADESTSTTYMELSSLRSEDTAVYYCASTLGLVLDAMDYWGQGTLVTVSSASTKGP 126
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ + S SE T L C FP P T+SW NS AL++G
Sbjct: 127 SVFPLAPCSRSTSE-STAALGCLVKDYFPEPVTVSW---NSGALTSG 169
>pdb|3HAE|H Chain H, Rational Development Of High-Affinity T-Cell Receptor-Like
Antibodies
pdb|3HAE|I Chain I, Rational Development Of High-Affinity T-Cell Receptor-Like
Antibodies
pdb|3HAE|O Chain O, Rational Development Of High-Affinity T-Cell Receptor-Like
Antibodies
pdb|3HAE|T Chain T, Rational Development Of High-Affinity T-Cell Receptor-Like
Antibodies
Length = 220
Score = 28.5 bits (62), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 46/111 (41%), Gaps = 21/111 (18%)
Query: 131 SRFQLTTDPETSTYILSIKEIQETDAGIYKC--EVIISLNNKVSAEVELIVRRPPIISDN 188
RF ++ D +T L + ++ D +Y C E++ V + + +S
Sbjct: 66 GRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAGELLPYYGMDVWGQGTTVT-----VSSA 120
Query: 189 STRSVIV---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
ST+ V + G T L C FP P T+SW NS AL++G
Sbjct: 121 STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW---NSGALTSG 168
>pdb|1GAF|H Chain H, 48g7 Hybridoma Line Fab Complexed With Hapten 5-(Para-
Nitrophenyl Phosphonate)-Pentanoic Acid
pdb|1HKL|H Chain H, Free And Liganded Form Of An Esterolytic Catalytic
Antibody
Length = 217
Score = 28.5 bits (62), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 30/108 (27%), Positives = 44/108 (40%), Gaps = 12/108 (11%)
Query: 129 HDSRFQ----LTTDPETSTYILSIKEIQETDAGIYKCEVI--ISLNNKVSAEVELIVRRP 182
+D +FQ +T D + T L + + D +Y C I + V +
Sbjct: 60 YDPKFQDKATITADTSSKTTYLQLSSLTSEDTAVYYCASYYGIYWGQGTTLTVSSASTKG 119
Query: 183 PIISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
P + + S S G T L C FP P T+SW NS AL++G
Sbjct: 120 PSVFPLAPSSKSTSGG-TAALGCLVKDYFPEPVTVSW---NSGALTSG 163
>pdb|2VC2|H Chain H, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist L-739758
pdb|2VDK|H Chain H, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece
pdb|2VDL|H Chain H, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece
pdb|2VDM|H Chain H, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist Tirofiban
pdb|2VDN|H Chain H, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist Eptifibatide
pdb|2VDO|H Chain H, Integrin Alphaiibbeta3 Headpiece Bound To Fibrinogen Gamma
Chain Peptide, Hhlggakqagdv
pdb|2VDP|H Chain H, Integrin Alphaiibbeta3 Headpiece Bound To Fibrinogen Gamma
Chain Peptide,Lggakqagdv
pdb|2VDQ|H Chain H, Integrin Alphaiibbeta3 Headpiece Bound To A Chimeric
Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv
pdb|2VDR|H Chain H, Integrin Alphaiibbeta3 Headpiece Bound To A Chimeric
Fibrinogen Gamma Chain Peptide, Lggakqrgdv
pdb|3NID|E Chain E, The Closed Headpiece Of Integrin Alphaiib Beta3 And Its
Complex With An Alpahiib Beta3 -Specific Antagonist That
Does Not Induce Opening
pdb|3NID|H Chain H, The Closed Headpiece Of Integrin Alphaiib Beta3 And Its
Complex With An Alpahiib Beta3 -Specific Antagonist That
Does Not Induce Opening
pdb|3NIF|E Chain E, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIF|H Chain H, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIG|E Chain E, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIG|H Chain H, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3T3M|E Chain E, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3M|H Chain H, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3P|E Chain E, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3P|H Chain H, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
Length = 221
Score = 28.5 bits (62), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 20/90 (22%), Positives = 34/90 (37%), Gaps = 7/90 (7%)
Query: 237 LKIPNITKTDRGTYYCV-------AQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQY 289
L++ ++T D YYCV A + G+G ++ AP + P G
Sbjct: 81 LQLSSLTSEDTAVYYCVRPLYDYYAMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGS 140
Query: 290 DAILECHVEAYPPPAIVWIKDGVQIMNNQH 319
L C V+ Y P + + + + H
Sbjct: 141 SVTLGCLVKGYFPEPVTLTWNSGSLSSGVH 170
>pdb|3UJT|H Chain H, Structure Of The Fab Fragment Of Ab-52, An Antibody That
Binds The O- Antigen Of Francisella Tularensis
pdb|3UJT|I Chain I, Structure Of The Fab Fragment Of Ab-52, An Antibody That
Binds The O- Antigen Of Francisella Tularensis
Length = 213
Score = 28.5 bits (62), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 28/110 (25%), Positives = 45/110 (40%), Gaps = 27/110 (24%)
Query: 132 RFQLTTDPETSTYILSIKEIQETDAGIYKCE-----------VIISLNNKVSAEVELIVR 180
+ LT D +ST + + + D+ +Y C V +S + V +
Sbjct: 67 KATLTVDTSSSTAYVDLSSLTSEDSAVYYCVRGFAYWGQGTLVTVSAAKTTAPSVYPLA- 125
Query: 181 RPPIISDNSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
P+ D + G +V L C G FP P T++W NS +LS+G
Sbjct: 126 --PVCGDTT--------GSSVTLGCLVKGYFPEPVTLTW---NSGSLSSG 162
>pdb|2H1P|H Chain H, The Three-Dimensional Structures Of A Polysaccharide
Binding Antibody To Cryptococcus Neoformans And Its
Complex With A Peptide From A Phage Display Library:
Implications For The Identification Of Peptide Mimotopes
Length = 220
Score = 28.5 bits (62), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 35/142 (24%), Positives = 59/142 (41%), Gaps = 19/142 (13%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIH----DSRFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K++E + I+ +G H RF ++ D +T L + ++ D
Sbjct: 32 YFLSWVRQTPEKRLELVATINSNGDKTYHPDTMKGRFTISRDNAKNTLYLQMSSLKSEDT 91
Query: 157 GIYKC---EVIISL-----NNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYAN 208
+Y C + SL + V PP + + S + V L C
Sbjct: 92 ALYYCARRDSSASLYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSM-VTLGCLVK 150
Query: 209 G-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 151 GYFPEPVTVTW---NSGSLSSG 169
>pdb|3PHQ|B Chain B, Crystal Structure Of S64-4 In Complex With Kdo
Length = 222
Score = 28.5 bits (62), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 39/144 (27%), Positives = 59/144 (40%), Gaps = 19/144 (13%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHD------SRFQLTTDPETSTYILSIKEIQE 153
DY + W++ K +E L I G+ + RF ++ D S L + ++
Sbjct: 31 DYYMSWVRQPPGKALEWLGFIRNKGNGYTTEYSTSVKGRFTISRDNSQSAVYLQMNTLRA 90
Query: 154 TDAGIYKCEVIISLNNKVSA---EVELIVRRPPIISDNSTRSVI-VSEGQT---VYLYCY 206
D+ Y C I N A + L+ I+ S + S QT V L C
Sbjct: 91 EDSATYYCARDIGYGNSPFAYWGQGTLVTVSAASITPPSVYPLAPGSAAQTNSMVTLGCL 150
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 151 VKGYFPEPVTVTW---NSGSLSSG 171
>pdb|3JZ7|A Chain A, Crystal Structure Of The Extracellular Domains Of
Coxsackie & Adenovirus Receptor From Mouse (Mcar)
Length = 214
Score = 28.5 bits (62), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 305 IVWIKDGVQIMNNQHYSVS---HFATSD-EFSDTSLRVITIERRQFGQYACKAANKYGSA 360
++ + G +I +N + + HF ++D + D S+ V ++ G Y CK G A
Sbjct: 51 VIILYSGDKIYDNYYPDLKGRVHFTSNDVKSGDASINVTNLQLSDIGTYQCKVKKAPGVA 110
Query: 361 QKEIEL 366
K+ L
Sbjct: 111 NKKFLL 116
>pdb|3EO9|L Chain L, Crystal Structure The Fab Fragment Of Efalizumab
pdb|3EOA|L Chain L, Crystal Structure The Fab Fragment Of Efalizumab In
Complex With Lfa-1 I Domain, Form I
pdb|3EOA|A Chain A, Crystal Structure The Fab Fragment Of Efalizumab In
Complex With Lfa-1 I Domain, Form I
pdb|3EOB|L Chain L, Crystal Structure The Fab Fragment Of Efalizumab In
Complex With Lfa-1 I Domain, Form Ii
pdb|3EOB|A Chain A, Crystal Structure The Fab Fragment Of Efalizumab In
Complex With Lfa-1 I Domain, Form Ii
Length = 214
Score = 28.5 bits (62), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 50/129 (38%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQN----GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I ++ D TYYC N G+G K I V AP + I P Q A
Sbjct: 73 LTISSLQPEDFATYYCQQHNEYPLTFGQGTKVEIKRTVA-APSVFIFPPSDEQLKSGTAS 131
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 132 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 190
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 191 VYACEVTHQ 199
>pdb|1BBJ|L Chain L, Crystal Structure Of A Chimeric Fab' Fragment Of An
Antibody Binding Tumour Cells
pdb|1BBJ|A Chain A, Crystal Structure Of A Chimeric Fab' Fragment Of An
Antibody Binding Tumour Cells
Length = 211
Score = 28.5 bits (62), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 31/129 (24%), Positives = 51/129 (39%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
LKI ++ D G+YYC G G G + I + AP + I P Q A
Sbjct: 73 LKINSLQSEDFGSYYCQHFWGTPYTFGGGTRLEIK-RADAAPTVFIFPPSDEQLKSGTAS 131
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 132 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 190
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 191 VYACEVTHQ 199
>pdb|1FSK|B Chain B, Complex Formation Between A Fab Fragment Of A Monoclonal
Igg Antibody And The Major Allergen From Birch Pollen
Bet V 1
pdb|1FSK|E Chain E, Complex Formation Between A Fab Fragment Of A Monoclonal
Igg Antibody And The Major Allergen From Birch Pollen
Bet V 1
pdb|1FSK|H Chain H, Complex Formation Between A Fab Fragment Of A Monoclonal
Igg Antibody And The Major Allergen From Birch Pollen
Bet V 1
pdb|1FSK|K Chain K, Complex Formation Between A Fab Fragment Of A Monoclonal
Igg Antibody And The Major Allergen From Birch Pollen
Bet V 1
Length = 214
Score = 28.5 bits (62), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 48/199 (24%), Positives = 73/199 (36%), Gaps = 27/199 (13%)
Query: 184 IISDNSTRSVIVSEGQTVYLYCYANGFPAPTISW---RRDNSAALS-------------- 226
I+ S +S+ VS G+ V L C A+ + W + D S L
Sbjct: 2 IVLTQSPKSMSVSVGERVTLSCKASENVDTYVFWFQQKPDQSPKLLLYGPSNRYTGVPDR 61
Query: 227 -TGGSIYRGNILKIPNITKTDRGTYYCVAQNG----VGRGMKRNIAVEVEFAPVITINRP 281
TG L I ++ D Y+C G G K I + AP ++I P
Sbjct: 62 FTGSGSTTDFTLTISSVQAEDLADYHCGQSYSYPYTFGGGTKLEIK-RADAAPTVSIFPP 120
Query: 282 RQGQALQYDAILECHVEAYPPPAI--VWIKDGVQIMNNQHYSVSHFATSDE-FSDTSLRV 338
Q A + C + + P I W DG + N S + + D +S +S
Sbjct: 121 SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT 180
Query: 339 ITI-ERRQFGQYACKAANK 356
+T E + Y C+A +K
Sbjct: 181 LTKDEYERHNSYTCEATHK 199
>pdb|3OKK|B Chain B, Crystal Structure Of S25-39 In Complex With Kdo(2.4)kdo
pdb|3OKL|B Chain B, Crystal Structure Of S25-39 In Complex With Kdo(2.8)kdo
pdb|3OKM|B Chain B, Crystal Structure Of Unliganded S25-39
pdb|3OKN|B Chain B, Crystal Structure Of S25-39 In Complex With
Kdo(2.4)kdo(2.4)kdo
pdb|3OKO|B Chain B, Crystal Structure Of S25-39 In Complex With
Kdo(2.8)kdo(2.4)kdo
Length = 222
Score = 28.5 bits (62), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 35/145 (24%), Positives = 54/145 (37%), Gaps = 21/145 (14%)
Query: 101 DYPVIWMKMDTAKKMEPLPI---SMSGSLIIHDS----RFQLTTDPETSTYILSIKEIQE 153
DY + W++ K +E L G + + RF ++ D S+ L + ++
Sbjct: 31 DYYMSWVRQPPGKALEWLGFIRNKAKGYTTEYSASVKGRFTISRDNSQSSLYLQMNTLRA 90
Query: 154 TDAGIYKC--------EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYC 205
D+ Y C E V PP + + S + V L C
Sbjct: 91 EDSATYYCARDHDGYYERFAYWGQGTLVTVSAAATTPPSVYPLAPGSAAQTNSM-VTLGC 149
Query: 206 YANG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LSTG
Sbjct: 150 LVKGYFPEPVTVTW---NSGSLSTG 171
>pdb|3MJ7|B Chain B, Crystal Structure Of The Complex Of Jaml And Coxsackie And
Adenovirus Receptor, Car
Length = 225
Score = 28.5 bits (62), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 324 HFATSD-EFSDTSLRVITIERRQFGQYACKAANKYGSAQKEIEL 366
HF ++D + D S+ V ++ G Y CK G A K+ L
Sbjct: 75 HFTSNDVKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKFLL 118
>pdb|2A6D|H Chain H, Crystal Structure Analysis Of The Anti-Arsonate Germline
Antibody 36-65 In Complex With A Phage Display Derived
Dodecapeptide Rlliadppspre
pdb|2A6D|B Chain B, Crystal Structure Analysis Of The Anti-Arsonate Germline
Antibody 36-65 In Complex With A Phage Display Derived
Dodecapeptide Rlliadppspre
pdb|2A6I|B Chain B, Crystal Structure Analysis Of The Anti-Arsonate Germline
Antibody 36-65 In Complex With A Phage Display Derived
Dodecapeptide Klasipthtspl
pdb|2A6J|H Chain H, Crystal Structure Analysis Of The Anti-Arsonate Germline
Antibody 36- 65
pdb|2A6J|B Chain B, Crystal Structure Analysis Of The Anti-Arsonate Germline
Antibody 36- 65
pdb|2A6K|B Chain B, Crystal Structure Analysis Of The Germline Antibody 36-65
Fab In Complex With The Dodecapeptide Slgdnltnhnlr
pdb|2A6K|H Chain H, Crystal Structure Analysis Of The Germline Antibody 36-65
Fab In Complex With The Dodecapeptide Slgdnltnhnlr
Length = 222
Score = 28.5 bits (62), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 32/144 (22%), Positives = 58/144 (40%), Gaps = 20/144 (13%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
Y + W+K + +E + I+ ++ +F+ LT D +ST + ++ + D
Sbjct: 31 SYGINWVKQRPGQGLEWIGYINPGNGYTKYNEKFKGKTTLTVDKSSSTAYMQLRSLTSED 90
Query: 156 AGIYKCEVIISLNNK---------VSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCY 206
+ +Y C + + V PP + + S + V L C
Sbjct: 91 SAVYFCARSVYYGGSYYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTN-SMVTLGCL 149
Query: 207 ANG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 150 VKGYFPEPVTVTW---NSGSLSSG 170
>pdb|3NCJ|L Chain L, Crystal Structure Of Fab15 Mut8
Length = 214
Score = 28.1 bits (61), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 51/129 (39%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I ++ D TYYC N + G+G K I V AP + I P Q A
Sbjct: 73 LTISSLQPEDFATYYCQQGNTLPYTFGQGTKVEIKRTVA-APSVFIFPPSDEQLKSGTAS 131
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 132 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 190
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 191 VYACEVTHQ 199
>pdb|3OKD|B Chain B, Crystal Structure Of S25-39 In Complex With Kdo
pdb|3OKE|B Chain B, Crystal Structure Of S25-39 In Complex With Ko
Length = 222
Score = 28.1 bits (61), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 35/145 (24%), Positives = 54/145 (37%), Gaps = 21/145 (14%)
Query: 101 DYPVIWMKMDTAKKMEPLPI---SMSGSLIIHDS----RFQLTTDPETSTYILSIKEIQE 153
DY + W++ K +E L G + + RF ++ D S+ L + ++
Sbjct: 31 DYYMSWVRQPPGKALEWLGFIRNKAKGYTTEYSASVKGRFTISRDNSQSSLYLQMNTLRA 90
Query: 154 TDAGIYKC--------EVIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYC 205
D+ Y C E V PP + + S + V L C
Sbjct: 91 EDSATYYCARDHDGYYERFAYWGQGTLVTVSAAATTPPSVYPLAPGSAAQTNSM-VTLGC 149
Query: 206 YANG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LSTG
Sbjct: 150 LVKGYFPEPVTVTW---NSGSLSTG 171
>pdb|3ULU|F Chain F, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form1)
pdb|3ULV|F Chain F, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form2)
Length = 223
Score = 28.1 bits (61), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 36/141 (25%), Positives = 61/141 (43%), Gaps = 18/141 (12%)
Query: 102 YPVIWMKMDTAKKMEPL-PISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETDA 156
Y + W+K + +E + I+ + I ++ +F+ LT D +ST + + + D+
Sbjct: 32 YWIHWVKQRPGQGLEWIGEINPNNGRINYNEKFKTKATLTVDKSSSTAYMQLSSLTSEDS 91
Query: 157 GIYKCE---VIIS----LNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG 209
+Y C V+I+ V + P + + S SE T L C
Sbjct: 92 AVYYCTRVGVMITTFPYWGQGTLVTVSAASTKGPSVFPLAPCSRSTSE-STAALGCLVKD 150
Query: 210 -FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 151 YFPEPVTVSW---NSGALTSG 168
>pdb|3NA9|L Chain L, Crystal Structure Of Fab15
pdb|3NAA|L Chain L, Crystal Structure Of Fab15 Mut5
pdb|3NAB|L Chain L, Crystal Structure Of Fab15 Mut6
pdb|3NAC|L Chain L, Crystal Structure Of Fab15 Mut7
pdb|3ULU|L Chain L, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form1)
pdb|3ULV|L Chain L, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form2)
Length = 214
Score = 28.1 bits (61), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 51/129 (39%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I ++ D TYYC N + G+G K I V AP + I P Q A
Sbjct: 73 LTISSLQPEDFATYYCQQGNTLSYTFGQGTKVEIKRTVA-APSVFIFPPSDEQLKSGTAS 131
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 132 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 190
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 191 VYACEVTHQ 199
>pdb|3V4P|H Chain H, Crystal Structure Of A4b7 Headpiece Complexed With Fab
Act-1
pdb|3V4P|M Chain M, Crystal Structure Of A4b7 Headpiece Complexed With Fab
Act-1
pdb|3V4V|H Chain H, Crystal Structure Of A4b7 Headpiece Complexed With Fab
Act-1 And Ro0505376
pdb|3V4V|M Chain M, Crystal Structure Of A4b7 Headpiece Complexed With Fab
Act-1 And Ro0505376
Length = 219
Score = 28.1 bits (61), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 36/143 (25%), Positives = 58/143 (40%), Gaps = 20/143 (13%)
Query: 102 YPVIWMKMDTAKKMEPL-PISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETDA 156
Y + W+K + +E + I S S ++ +F+ LT D +ST + + + D+
Sbjct: 32 YWMHWVKQRPGQGLEWIGEIDPSESNTNYNQKFKGKATLTVDISSSTAYMQLSSLTSEDS 91
Query: 157 GIYKCE---------VIISLNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYA 207
+Y C I S V PP + + S + V L C
Sbjct: 92 AVYYCARGGYDGWDYAIDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTN-SMVTLGCLV 150
Query: 208 NG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 151 KGYFPEPVTVTW---NSGSLSSG 170
>pdb|3QYC|A Chain A, Structure Of A Dimeric Anti-Her2 Single Domain Antibody
pdb|3QYC|B Chain B, Structure Of A Dimeric Anti-Her2 Single Domain Antibody
Length = 146
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 102 YPVIWMKMDTAKKMEPLPI--SMSGSLIIHDS---RFQLTTDPETSTYILSIKEIQETDA 156
Y + W++ K +E + S GS DS RF ++ D +T L + ++ D
Sbjct: 34 YDMAWVRQAPGKGLEWVSAISSSGGSTYYADSVKGRFTISRDNSKNTVYLQMNSLRAEDT 93
Query: 157 GIYKC 161
+Y C
Sbjct: 94 AVYYC 98
>pdb|3QPQ|H Chain H, Crystal Structure Of Anti-Tlr3 Antibody C1068 Fab
pdb|3QPQ|F Chain F, Crystal Structure Of Anti-Tlr3 Antibody C1068 Fab
pdb|3QPQ|D Chain D, Crystal Structure Of Anti-Tlr3 Antibody C1068 Fab
pdb|3QPQ|J Chain J, Crystal Structure Of Anti-Tlr3 Antibody C1068 Fab
Length = 223
Score = 28.1 bits (61), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 36/141 (25%), Positives = 61/141 (43%), Gaps = 18/141 (12%)
Query: 102 YPVIWMKMDTAKKMEPL-PISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETDA 156
Y + W+K + +E + I+ + I ++ +F+ LT D +ST + + + D+
Sbjct: 32 YWIHWVKQRPGQGLEWIGEINPNNGRINYNEKFKTKATLTVDKSSSTAYMQLSSLTSEDS 91
Query: 157 GIYKCE---VIIS----LNNKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYANG 209
+Y C V+I+ V + P + + S SE T L C
Sbjct: 92 AVYYCTRVGVMITTFPYWGQGTLVTVSAASTKGPSVFPLAPCSRSTSE-STAALGCLVKD 150
Query: 210 -FPAP-TISWRRDNSAALSTG 228
FP P T+SW NS AL++G
Sbjct: 151 YFPEPVTVSW---NSGALTSG 168
>pdb|3RBG|A Chain A, Crystal Structure Analysis Of Class-I Mhc Restricted
T-Cell Associated Molecule
pdb|3RBG|B Chain B, Crystal Structure Analysis Of Class-I Mhc Restricted
T-Cell Associated Molecule
pdb|3RBG|C Chain C, Crystal Structure Analysis Of Class-I Mhc Restricted
T-Cell Associated Molecule
pdb|3RBG|D Chain D, Crystal Structure Analysis Of Class-I Mhc Restricted
T-Cell Associated Molecule
Length = 124
Score = 28.1 bits (61), Expect = 8.4, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 13/79 (16%)
Query: 188 NSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSAALSTG------GSIYR-----GNI 236
N T ++ V EGQT+ L C + ++ W + + S Y+ N
Sbjct: 6 NHTETITVEEGQTLTLKCVTSLRKNSSLQWLTPSGFTIFLNEYPVLKNSKYQLLHHSANQ 65
Query: 237 LKI--PNITKTDRGTYYCV 253
L I PN+T D G Y C+
Sbjct: 66 LSITVPNVTLQDEGVYKCL 84
>pdb|3GRW|H Chain H, Fgfr3 In Complex With A Fab
Length = 235
Score = 28.1 bits (61), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 35/146 (23%), Positives = 58/146 (39%), Gaps = 24/146 (16%)
Query: 104 VIWMKMDTAKKMEPLP--ISMSGSLIIHDS---RFQLTTDPETSTYILSIKEIQETDAGI 158
+ W++ K +E + +GS DS RF ++ D +T L + ++ D +
Sbjct: 34 ISWVRQAPGKGLEWVGRIYPTNGSTNYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAV 93
Query: 159 YKCEVIISLNNKVSAEVELIVRRPP-----IISDNSTRSVIV---------SEGQTVYLY 204
Y C + + E ++ +S ST+ V + G T L
Sbjct: 94 YYCARTYGIYDLYVDYTEYVMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALG 153
Query: 205 CYANG-FPAP-TISWRRDNSAALSTG 228
C FP P T+SW NS AL++G
Sbjct: 154 CLVKDYFPEPVTVSW---NSGALTSG 176
>pdb|3HFM|H Chain H, Structure Of An Antibody-Antigen Complex. Crystal
Structure Of The HyHEL-10 Fab-Lysozyme Complex
Length = 215
Score = 28.1 bits (61), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 7/80 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNG--VGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI-- 292
L + ++T D TYYC +G G+G ++ P + P G A Q +++
Sbjct: 80 LDLNSVTTEDTATYYCANWDGDYWGQGTLVTVSAAKTTPPSVYPLAP--GSAAQTNSMVT 137
Query: 293 LECHVEAY-PPPAIVWIKDG 311
L C V+ Y P P V G
Sbjct: 138 LGCLVKGYFPEPVTVTWNSG 157
>pdb|2R0Z|H Chain H, Pfa1 Fab Complexed With Gripi Peptide Fragment
Length = 223
Score = 28.1 bits (61), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 29/77 (37%), Gaps = 10/77 (12%)
Query: 236 ILKIPNITKTDRGTYYCV--AQNGV--------GRGMKRNIAVEVEFAPVITINRPRQGQ 285
L+I ++ D TYYCV A V G+G ++ AP + P G
Sbjct: 81 FLRITSVDTADTATYYCVRRAHTTVLGDWFAYWGQGTLVTVSAAKTTAPSVYPLAPVCGD 140
Query: 286 ALQYDAILECHVEAYPP 302
L C V+ Y P
Sbjct: 141 TTGSSVTLGCLVKGYFP 157
>pdb|1JN6|B Chain B, Crystal Structure Of Fab-Estradiol Complexes
pdb|1JNH|B Chain B, Crystal Structure Of Fab-Estradiol Complexes
pdb|1JNH|D Chain D, Crystal Structure Of Fab-Estradiol Complexes
pdb|1JNH|F Chain F, Crystal Structure Of Fab-Estradiol Complexes
pdb|1JNH|H Chain H, Crystal Structure Of Fab-Estradiol Complexes
Length = 218
Score = 28.1 bits (61), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 29/103 (28%), Positives = 41/103 (39%), Gaps = 13/103 (12%)
Query: 135 LTTDPETSTYILSIKEIQETDAGIYKCEVIISL-------NNKVSAEVELIVRRPPIISD 187
LT D +S L + + D+ +Y C SL S V PP +
Sbjct: 70 LTADRSSSIVYLQLNSLTSEDSAVYSCSRGRSLYYTMDYWGQGTSVTVSSAKTTPPSVYP 129
Query: 188 NSTRSVIVSEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
+ S + V L C G FP P T+SW N+ +LS+G
Sbjct: 130 LAPGSAAQTNSM-VTLGCLVKGYFPEPVTVSW---NTGSLSSG 168
>pdb|1DFB|L Chain L, Structure Of A Human Monoclonal Antibody Fab Fragment
Against Gp41 Of Human Immunodeficiency Virus Type I
Length = 212
Score = 28.1 bits (61), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 32/127 (25%), Positives = 50/127 (39%), Gaps = 9/127 (7%)
Query: 237 LKIPNITKTDRGTYYCVAQN--GVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILE 294
L I ++ D TYYC N G G K +I V AP + I P Q A +
Sbjct: 73 LTISSLQPDDFATYYCQQYNSYSFGPGTKVDIKRTVA-APSVFIFPPSDEQLKSGTASVV 131
Query: 295 CHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ---Y 349
C + + P + W D N SV+ + D S +T+ + + + Y
Sbjct: 132 CLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHKVY 190
Query: 350 ACKAANK 356
AC+ ++
Sbjct: 191 ACEVTHQ 197
>pdb|2Q86|A Chain A, Structure Of The Mouse Invariant Nkt Cell Receptor
Valpha14
pdb|2Q86|C Chain C, Structure Of The Mouse Invariant Nkt Cell Receptor
Valpha14
Length = 229
Score = 28.1 bits (61), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 27/72 (37%)
Query: 92 LKCSVQYADDYPVIWMKMDTAKKMEPLPISMSGSLIIHDSRFQLTTDPETSTYILSIKEI 151
L+C+ D + W K DT K + L + + + R+ T D + L I
Sbjct: 21 LQCNYSVTPDNHLRWYKQDTGKGLVLLTVLVDQKDKTSNGRYSATLDKDAKHSTLHITAT 80
Query: 152 QETDAGIYKCEV 163
D Y C V
Sbjct: 81 LLDDTATYFCVV 92
>pdb|2FGW|L Chain L, X-Ray Structures Of Fragments From Binding And Nonbinding
Versions Of A Humanized Anti-Cd18 Antibody: Structural
Indications Of The Key Role Of Vh Residues 59 To 65
Length = 214
Score = 28.1 bits (61), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 51/129 (39%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I ++ D TYYC N + G+G K I V AP + I P Q A
Sbjct: 73 LTISSLQPEDFATYYCQQGNTLPPTFGQGTKVEIKRTVA-APSVFIFPPSDEQLKSGTAS 131
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 132 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 190
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 191 VYACEVTHQ 199
>pdb|1MIE|H Chain H, Crystal Structure Of The Fab Fragment Of Esterolytic
Antibody Ms5-393
pdb|1MJ7|H Chain H, Crystal Structure Of The Complex Of The Fab Fragment Of
Esterolytic Antibody Ms5-393 And A Transition-State
Analog
Length = 228
Score = 28.1 bits (61), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 31/141 (21%), Positives = 53/141 (37%), Gaps = 32/141 (22%)
Query: 194 IVSEGQTVYLYCYANG--FPAPTISW-RRDNSAALSTGGSIYRGN--------------- 235
+V G +V L C A+G F + I+W ++ L G++Y G+
Sbjct: 11 LVKPGASVKLSCKASGYTFTSSWINWVKQRPGQGLEWIGNVYPGSSSTNYNEKFKNKATL 70
Query: 236 ---------ILKIPNITKTDRGTYYCVAQNGV-----GRGMKRNIAVEVEFAPVITINRP 281
+++ ++T D YYCV ++ G+G ++ AP + P
Sbjct: 71 TVDTSSSTAYMQLSSLTSDDSAFYYCVRKDYSWFPYWGQGTLVTVSAAKTTAPSVYPLAP 130
Query: 282 RQGQALQYDAILECHVEAYPP 302
G L C V+ Y P
Sbjct: 131 VCGDTSGSSVTLGCLVKGYFP 151
>pdb|1D5I|L Chain L, Unliganded Germline Precursor Of An Oxy-Cope Catalytic
Antibody
pdb|1D6V|L Chain L, Conformation Effects In Biological Catalysis Introduced By
Oxy-Cope Antibody Maturation
Length = 211
Score = 28.1 bits (61), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 39/97 (40%), Gaps = 18/97 (18%)
Query: 144 YILSIKEIQETDAGIYKC----EVIISLNNKVSAEVELIVRRPPII----SDNSTRSVIV 195
Y L+I ++ D GIY C E + + E++ V P + SD +S
Sbjct: 71 YSLTISSLEYEDMGIYYCLQYDEFPYTFGSGTKLEIKRTVAAPSVFIFPPSDEQLKSGTA 130
Query: 196 SEGQTVYLYCYANGF--PAPTISWRRDNSAALSTGGS 230
S + C N F + W+ DN AL +G S
Sbjct: 131 S------VVCLLNNFYPREAKVQWKVDN--ALQSGNS 159
>pdb|3H3B|C Chain C, Crystal Structure Of The Single-Chain Fv (Scfv) Fragment
Of An Anti- Erbb2 Antibody Cha21 In Complex With
Residues 1-192 Of Erbb2 Extracellular Domain
pdb|3H3B|D Chain D, Crystal Structure Of The Single-Chain Fv (Scfv) Fragment
Of An Anti- Erbb2 Antibody Cha21 In Complex With
Residues 1-192 Of Erbb2 Extracellular Domain
Length = 259
Score = 28.1 bits (61), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 102 YPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETDA 156
Y + W+K ++ K E + IS S + ++ +F+ T D +ST + + + D+
Sbjct: 171 YFINWVKKNSGKSPEWIGHISSSYATSTYNQKFKNKAAFTVDTSSSTAFMQLNSLTSEDS 230
Query: 157 GIYKC 161
+Y C
Sbjct: 231 AVYYC 235
>pdb|2VWE|E Chain E, Crystal Structure Of Vascular Endothelial Growth Factor-B
In Complex With A Neutralizing Antibody Fab Fragment
pdb|2VWE|L Chain L, Crystal Structure Of Vascular Endothelial Growth Factor-B
In Complex With A Neutralizing Antibody Fab Fragment
Length = 219
Score = 28.1 bits (61), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 45/105 (42%), Gaps = 16/105 (15%)
Query: 135 LTTDPETSTYILSIKEIQETDAGIYKCEVIISLNNKVSAEVELIVRRPPIISDNSTRSVI 194
LT D +ST + + + D+ +Y C S +N V A +S T +
Sbjct: 70 LTVDKSSSTAYMQLSSLTSEDSAVYYCAR--SYSNYVRAMDYWGQGTSVTVSSAKTTAPS 127
Query: 195 V---------SEGQTVYLYCYANG-FPAP-TISWRRDNSAALSTG 228
V + G +V L C G FP P T++W NS +LS+G
Sbjct: 128 VYPLVPVCGGTTGSSVTLGCLVKGYFPEPVTLTW---NSGSLSSG 169
>pdb|1D5B|A Chain A, Unliganded Mature Oxy-Cope Catalytic Antibody
pdb|1D5B|L Chain L, Unliganded Mature Oxy-Cope Catalytic Antibody
Length = 211
Score = 28.1 bits (61), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 39/97 (40%), Gaps = 18/97 (18%)
Query: 144 YILSIKEIQETDAGIYKC----EVIISLNNKVSAEVELIVRRPPII----SDNSTRSVIV 195
Y L+I ++ D GIY C E + + E++ V P + SD +S
Sbjct: 71 YSLTISSLEYEDMGIYYCLQYDEFPYTFGSGTKLEIKRTVAAPSVFIFPPSDEQLKSGTA 130
Query: 196 SEGQTVYLYCYANGF--PAPTISWRRDNSAALSTGGS 230
S + C N F + W+ DN AL +G S
Sbjct: 131 S------VVCLLNNFYPREAKVQWKVDN--ALQSGNS 159
>pdb|1E6J|H Chain H, Crystal Structure Of Hiv-1 Capsid Protein (P24) In Complex
With Fab13b5
pdb|1E6O|H Chain H, Crystal Structure Of Fab13b5 Against Hiv-1 Capsid Protein
P24
Length = 219
Score = 28.1 bits (61), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 35/143 (24%), Positives = 60/143 (41%), Gaps = 19/143 (13%)
Query: 101 DYPVIWMKMDTAKKMEPLP-ISMSGSLIIHDSRFQ----LTTDPETSTYILSIKEIQETD 155
Y + W+K + +E + I+ S ++ +F+ LT D +ST + + + D
Sbjct: 31 SYTMHWVKQRPGQGLEWIGYINPSSGYSNYNQKFKDKATLTADKSSSTAYMQLSSLTSED 90
Query: 156 AGIYKCE---VIISLN-----NKVSAEVELIVRRPPIISDNSTRSVIVSEGQTVYLYCYA 207
+ +Y C V + N + V PP + + S + V L C
Sbjct: 91 SAVYYCSRPVVRLGYNFDYWGQGSTLTVSSAKTTPPSVYPLAPGSAAQTNSM-VTLGCLV 149
Query: 208 NG-FPAP-TISWRRDNSAALSTG 228
G FP P T++W NS +LS+G
Sbjct: 150 KGYFPEPVTVTW---NSGSLSSG 169
>pdb|2WUB|L Chain L, Crystal Structure Of Hgfa In Complex With The Allosteric
Non-Inhibitory Antibody Fab40.Deltatrp
pdb|2WUB|Q Chain Q, Crystal Structure Of Hgfa In Complex With The Allosteric
Non-Inhibitory Antibody Fab40.Deltatrp
pdb|2WUC|L Chain L, Crystal Structure Of Hgfa In Complex With The Allosteric
Non- Inhibitory Antibody Fab40.Deltatrp And
Ac-Kqlr-Chloromethylketone
pdb|3K2U|L Chain L, Crystal Structure Of Hgfa In Complex With The Allosteric
Inhibitory Antibody Fab40
Length = 214
Score = 28.1 bits (61), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 50/129 (38%), Gaps = 11/129 (8%)
Query: 237 LKIPNITKTDRGTYYCVAQNGV----GRGMKRNIAVEVEFAPVITINRPRQGQALQYDAI 292
L I ++ D TYYC N G+G K I V AP + I P Q A
Sbjct: 73 LTISSLQPEDFATYYCQQSNRAPATFGQGTKVEIKRTVA-APSVFIFPPSDEQLKSGTAS 131
Query: 293 LECHVEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ-- 348
+ C + + P + W D N SV+ + D S +T+ + + +
Sbjct: 132 VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHK 190
Query: 349 -YACKAANK 356
YAC+ ++
Sbjct: 191 VYACEVTHQ 199
>pdb|4HWE|L Chain L, Crystal Structure Of Ectodomain 3 Of The Il-13 Receptor
Alpha1 In Complex With A Human Neutralizing Monoclonal
Antibody Fragment
Length = 211
Score = 28.1 bits (61), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 30/125 (24%), Positives = 47/125 (37%), Gaps = 7/125 (5%)
Query: 237 LKIPNITKTDRGTYYCVAQNGVGRGMKRNIAVEVEFAPVITINRPRQGQALQYDAILECH 296
L I + D YYC G+G K I V AP + I P Q A + C
Sbjct: 74 LTISRLEPEDFAVYYCQQYETFGQGTKVEIKRTVA-APSVFIFPPSDEQLKSGTASVVCL 132
Query: 297 VEAYPP--PAIVWIKDGVQIMNNQHYSVSHFATSDEFSDTSLRVITIERRQFGQ---YAC 351
+ + P + W D N SV+ + D S +T+ + + + YAC
Sbjct: 133 LNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS-STLTLSKADYEKHKVYAC 191
Query: 352 KAANK 356
+ ++
Sbjct: 192 EVTHQ 196
>pdb|4DKD|C Chain C, Crystal Structure Of Human Interleukin-34 Bound To Human
Csf-1r
Length = 292
Score = 27.7 bits (60), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 33/72 (45%), Gaps = 10/72 (13%)
Query: 183 PIISDNSTRSVIVSEGQTVYLYCYANGFPAPTISWRRDNSA--ALSTGGSIYRGNILKIP 240
P+I + S ++V G TV L C NG ++ W S L + GS +IL
Sbjct: 5 PVI-EPSVPELVVKPGATVTLRCVGNG----SVEWDGPPSPHWTLYSDGS---SSILSTN 56
Query: 241 NITKTDRGTYYC 252
N T + GTY C
Sbjct: 57 NATFQNTGTYRC 68
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
0.319 0.134 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,919,564
Number of Sequences: 62578
Number of extensions: 430622
Number of successful extensions: 3327
Number of sequences better than 100.0: 765
Number of HSP's better than 100.0 without gapping: 113
Number of HSP's successfully gapped in prelim test: 652
Number of HSP's that attempted gapping in prelim test: 2514
Number of HSP's gapped (non-prelim): 1209
length of query: 384
length of database: 14,973,337
effective HSP length: 101
effective length of query: 283
effective length of database: 8,652,959
effective search space: 2448787397
effective search space used: 2448787397
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)