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= psy5600
(413 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HL4|A Chain A, Crystal Structure Of A Mammalian Ctp:phosphocholine
Cytidylyltransferase With Cdp-Choline
pdb|3HL4|B Chain B, Crystal Structure Of A Mammalian Ctp:phosphocholine
Cytidylyltransferase With Cdp-Choline
Length = 236
Score = 241 bits (614), Expect = 8e-64, Method: Compositional matrix adjust.
Identities = 120/212 (56%), Positives = 136/212 (64%), Gaps = 48/212 (22%)
Query: 45 ASRKVRVYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSDALTHRKKGRTVMNDIER 104
R VRVYADGI+D+FH GH+R LMQAKN+FPN YLIVGVCSD LTH KG TVMN+ ER
Sbjct: 73 CERPVRVYADGIFDLFHSGHARALMQAKNLFPNTYLIVGVCSDELTHNFKGFTVMNENER 132
Query: 105 YEAVRHCRYVDEVVRDAPWETDDEFLAKHKESTSSISITKPAPFSDEPEAVEERNQCNYE 164
Y+AV+HCRYVDEVVR+APW EFLA+H
Sbjct: 133 YDAVQHCRYVDEVVRNAPWTLTPEFLAEH------------------------------- 161
Query: 165 QRITYDDAKQGKGKAWERIDFIAHDDIPYMSEFGTDVYAHLKARGMFVATQRTEGVSTSD 224
RIDF+AHDDIPY S DVY H+K GMF TQRTEG+STSD
Sbjct: 162 -----------------RIDFVAHDDIPYSSAGSDDVYKHIKEAGMFAPTQRTEGISTSD 204
Query: 225 IVARIVRDYDIYVRRNLARGYTAKDLNVSFLN 256
I+ RIVRDYD+Y RRNL RGYTAK+LNVSF+N
Sbjct: 205 IITRIVRDYDVYARRNLQRGYTAKELNVSFIN 236
Score = 97.8 bits (242), Expect = 9e-21, Method: Compositional matrix adjust.
Identities = 42/59 (71%), Positives = 50/59 (84%)
Query: 260 RKVRVYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSDALTHRKKGRTVMNDEKKF 318
R VRVYADGI+D+FH GH+R LMQAKN+FPN YLIVGVCSD LTH KG TVMN+ +++
Sbjct: 75 RPVRVYADGIFDLFHSGHARALMQAKNLFPNTYLIVGVCSDELTHNFKGFTVMNENERY 133
>pdb|3ELB|A Chain A, Human Ctp: Phosphoethanolamine Cytidylyltransferase In
Complex With Cmp
Length = 341
Score = 84.0 bits (206), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 80/297 (26%), Positives = 117/297 (39%), Gaps = 90/297 (30%)
Query: 47 RKVRVYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSDALTHRKKGRTVMNDIERYE 106
R VRV+ DG YD H GHS QL QA+ YLIVGV +D + KG V ERY+
Sbjct: 6 RAVRVWCDGCYDXVHYGHSNQLRQARAX--GDYLIVGVHTDEEIAKHKGPPVFTQEERYK 63
Query: 107 AVRHCRYVDEVVRDAPWETDDEFLAKHKESTSSISITKPAPFSDEPEAVEERNQCNYEQR 166
V+ ++VDEVV AP+ T E L K+
Sbjct: 64 XVQAIKWVDEVVPAAPYVTTLETLDKYN-------------------------------- 91
Query: 167 ITYDDAKQGKGKAWERIDFIAHDDIPYMSEFGTDVYAHLKARGMFVATQRTEGVSTSDIV 226
DF H + ++ G D Y +K G + +RT+GVST+D+V
Sbjct: 92 ----------------CDFCVHGNDITLTVDGRDTYEEVKQAGRYRECKRTQGVSTTDLV 135
Query: 227 ARIV----------------RDY-DIYVR----RNLARGYTAKDLNVSFLNVTSRKVR-- 263
R + R+Y D + + RN G + FL + + ++
Sbjct: 136 GRXLLVTKAHHSSQEXSSEYREYADSFGKCPGGRNPWTGVS------QFLQTSQKIIQFA 189
Query: 264 -----------VYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSDALTHRKKGR 309
+Y G +D+FH GH L + + Y+I G+ D + KG+
Sbjct: 190 SGKEPQPGETVIYVAGAFDLFHIGHVDFLEKVHRLAERPYIIAGLHFDQEVNHYKGK 246
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 28/66 (42%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 260 RKVRVYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSDALTHRKKGRTVMNDEKKFR 319
R VRV+ DG YD H GHS QL QA+ YLIVGV +D + KG V E++++
Sbjct: 6 RAVRVWCDGCYDXVHYGHSNQLRQARAX--GDYLIVGVHTDEEIAKHKGPPVFTQEERYK 63
Query: 320 FQNKIE 325
I+
Sbjct: 64 XVQAIK 69
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 34/109 (31%), Positives = 50/109 (45%), Gaps = 2/109 (1%)
Query: 51 VYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSDALTHRKKGRT--VMNDIERYEAV 108
+Y G +D+FH GH L + + Y+I G+ D + KG+ + N ER +V
Sbjct: 201 IYVAGAFDLFHIGHVDFLEKVHRLAERPYIIAGLHFDQEVNHYKGKNYPIXNLHERTLSV 260
Query: 109 RHCRYVDEVVRDAPWETDDEFLAKHKESTSSISITKPAPFSDEPEAVEE 157
CRYV EVV AP+ E L+ K T+ P D + +E
Sbjct: 261 LACRYVSEVVIGAPYAVTAELLSHFKVDLVCHGKTEIIPDRDGSDPYQE 309
>pdb|1COZ|A Chain A, Ctp:glycerol-3-Phosphate Cytidylyltransferase From
Bacillus Subtilis
pdb|1COZ|B Chain B, Ctp:glycerol-3-Phosphate Cytidylyltransferase From
Bacillus Subtilis
pdb|1N1D|A Chain A, Glycerol-3-phosphate Cytidylyltransferase Complexed With
Cdp-glycerol
pdb|1N1D|B Chain B, Glycerol-3-phosphate Cytidylyltransferase Complexed With
Cdp-glycerol
pdb|1N1D|C Chain C, Glycerol-3-phosphate Cytidylyltransferase Complexed With
Cdp-glycerol
pdb|1N1D|D Chain D, Glycerol-3-phosphate Cytidylyltransferase Complexed With
Cdp-glycerol
Length = 129
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 26/87 (29%), Positives = 44/87 (50%), Gaps = 4/87 (4%)
Query: 47 RKVRVYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSDALTHRKKGRTVMNDIERYE 106
+KV Y G +D+ H GH + L +AK + YL+V + +D +K+ + + R
Sbjct: 2 KKVITY--GTFDLLHWGHIKLLERAKQL--GDYLVVAISTDEFNLQKQKKAYHSYEHRKL 57
Query: 107 AVRHCRYVDEVVRDAPWETDDEFLAKH 133
+ RYVDEV+ + WE + + H
Sbjct: 58 ILETIRYVDEVIPEKNWEQKKQDIIDH 84
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 37/127 (29%), Positives = 61/127 (48%), Gaps = 28/127 (22%)
Query: 260 RKVRVYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSDALTHRKKGRTVMNDEKKFR 319
+KV Y G +D+ H GH + L +AK + YL+V + +D +K+ + + E +
Sbjct: 2 KKVITY--GTFDLLHWGHIKLLERAKQL--GDYLVVAISTDEFNLQKQKKAYHSYEHR-- 55
Query: 320 FQNKIEEFKDRSKRVMENIGERRVDMI---QKWEEKSRDIIDTFLLLFGREGRLKHMWNE 376
K ++E I R VD + + WE+K +DIID + +F + W E
Sbjct: 56 ------------KLILETI--RYVDEVIPEKNWEQKKQDIIDHNIDVF----VMGDDW-E 96
Query: 377 GKGKFLQ 383
GK FL+
Sbjct: 97 GKFDFLK 103
>pdb|2B7L|A Chain A, Crystal Structure Of Ctp:glycerol-3-Phosphate
Cytidylyltransferase From Staphylococcus Aureus
pdb|2B7L|B Chain B, Crystal Structure Of Ctp:glycerol-3-Phosphate
Cytidylyltransferase From Staphylococcus Aureus
pdb|2B7L|C Chain C, Crystal Structure Of Ctp:glycerol-3-Phosphate
Cytidylyltransferase From Staphylococcus Aureus
pdb|2B7L|D Chain D, Crystal Structure Of Ctp:glycerol-3-Phosphate
Cytidylyltransferase From Staphylococcus Aureus
Length = 132
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 50 RVYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSDALTHRKKGRTVMNDIERYEAVR 109
RV G YD+ H GH L +A+ + YLIV + +D K ++ + +R +
Sbjct: 3 RVITYGTYDLLHYGHIELLRRAREM--GDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLE 60
Query: 110 HCRYVDEVVRDAPW 123
RYVD V+ + W
Sbjct: 61 SIRYVDLVIPEKGW 74
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 36/141 (25%), Positives = 61/141 (43%), Gaps = 34/141 (24%)
Query: 263 RVYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSDALTHRKKGRTVMNDEKKFRFQN 322
RV G YD+ H GH L +A+ + YLIV + +D K ++ + E++
Sbjct: 3 RVITYGTYDLLHYGHIELLRRAREM--GDYLIVALSTDEFNQIKHKKSYYDYEQR----- 55
Query: 323 KIEEFKDRSKRVMENIGERRVDMI---QKWEEKSRDI----IDTFLLLFGREGRLKHMWN 375
K ++E+I R VD++ + W +K D+ +D F+ + H W
Sbjct: 56 ---------KMMLESI--RYVDLVIPEKGWGQKEDDVEKFDVDVFV--------MGHDW- 95
Query: 376 EGKGKFLQAFSPPASPTRSRG 396
EG+ FL+ R+ G
Sbjct: 96 EGEFDFLKDKCEVIYLKRTEG 116
>pdb|1MPA|H Chain H, Bactericidal Antibody Against Neisseria Meningitidis
pdb|1MNU|H Chain H, Unliganded Bactericidal Antibody Against Neisseria
Meningitidis
pdb|2MPA|H Chain H, Bactericidal Antibody Against Neisseria Meningitidis
Length = 225
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 52 YADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSD 87
YAD I D + QG + + AK P+VY + VC D
Sbjct: 103 YADFIMDYWGQGTTVTVSSAKTTAPSVYPLAPVCGD 138
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 265 YADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSD 300
YAD I D + QG + + AK P+VY + VC D
Sbjct: 103 YADFIMDYWGQGTTVTVSSAKTTAPSVYPLAPVCGD 138
>pdb|4F2M|A Chain A, Crystal Structure Of A Tgev Coronavirus Spike Fragment In
Complex With The Tgev Neutralizing Monoclonal Antibody
1af10
pdb|4F2M|C Chain C, Crystal Structure Of A Tgev Coronavirus Spike Fragment In
Complex With The Tgev Neutralizing Monoclonal Antibody
1af10
Length = 221
Score = 33.1 bits (74), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 26 HIPSLNNGVDEALFHDNNNASRKVRVYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVC 85
H+ SL + VD A++ R YA D + QG S + AK P+VY + VC
Sbjct: 82 HLSSLTS-VDSAVYFCARGGYRYDPYYA---MDYWGQGTSVTVSSAKTTAPSVYPLAPVC 137
Query: 86 SD 87
D
Sbjct: 138 GD 139
>pdb|4DVZ|A Chain A, Crystal Structure Of The Helicobacter Pylori Caga
Oncoprotein
Length = 569
Score = 32.7 bits (73), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 31/49 (63%)
Query: 312 MNDEKKFRFQNKIEEFKDRSKRVMENIGERRVDMIQKWEEKSRDIIDTF 360
+++++K +FQN+IE+F+ SK ++ +G R+ + K + K +I F
Sbjct: 158 LSEKEKEKFQNEIEDFQKDSKAYLDALGNDRIAFVSKKDTKHSALITEF 206
>pdb|3GLV|A Chain A, Crystal Structure Of The Lipopolysaccharide Core
Biosynthesis Protein From Thermoplasma Volcanium Gss1
pdb|3GLV|B Chain B, Crystal Structure Of The Lipopolysaccharide Core
Biosynthesis Protein From Thermoplasma Volcanium Gss1
Length = 143
Score = 32.7 bits (73), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 262 VRVYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSDALTHRKKGRTVMNDE 315
+RV A G++D+ H GH L ++K + L+V V D+ T R G+ + DE
Sbjct: 3 IRVMATGVFDILHLGHIHYLKESKKLGDE--LVVVVARDS-TARNNGKIPIFDE 53
Score = 32.7 bits (73), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 49 VRVYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSDALTHRKKGRT-VMNDIERYEA 107
+RV A G++D+ H GH L ++K + L+V V D+ T R G+ + ++ R
Sbjct: 3 IRVMATGVFDILHLGHIHYLKESKKLGDE--LVVVVARDS-TARNNGKIPIFDENSRLAL 59
Query: 108 VRHCRYVDEVV 118
+ + VD +
Sbjct: 60 ISELKVVDRAI 70
>pdb|4G0H|A Chain A, Crystal Structure Of The N-Terminal Domain Of Helicobacter
Pylori Caga Protein
Length = 916
Score = 32.3 bits (72), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 31/49 (63%)
Query: 312 MNDEKKFRFQNKIEEFKDRSKRVMENIGERRVDMIQKWEEKSRDIIDTF 360
+++++K +FQN+IE+F+ SK ++ +G R+ + K + K +I F
Sbjct: 418 LSEKEKEKFQNEIEDFQKDSKAYLDALGNDRIAFVSKKDTKHSALITEF 466
>pdb|4DVY|P Chain P, Crystal Structure Of The Helicobacter Pylori Caga
Oncoprotein
Length = 876
Score = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 31/49 (63%)
Query: 312 MNDEKKFRFQNKIEEFKDRSKRVMENIGERRVDMIQKWEEKSRDIIDTF 360
+++++K +FQN+IE+F+ SK ++ +G R+ + K + K +I F
Sbjct: 418 LSEKEKEKFQNEIEDFQKDSKAYLDALGNDRIAFVSKKDTKHSALITEF 466
>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 = 32.0 bits (71), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 50 RVY-ADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSD 87
R+Y DG +D++ G + + AK P+VY + VC D
Sbjct: 97 RIYHYDGYFDVWGAGTAVTVSSAKTTAPSVYPLAPVCGD 135
Score = 32.0 bits (71), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 263 RVY-ADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSD 300
R+Y DG +D++ G + + AK P+VY + VC D
Sbjct: 97 RIYHYDGYFDVWGAGTAVTVSSAKTTAPSVYPLAPVCGD 135
>pdb|2BDN|H Chain H, Crystal Structure Of Human Mcp-1 Bound To A Blocking
Antibody, 11k2
Length = 217
Score = 31.6 bits (70), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 251 NVSFL---NVTSRKVRVY-----ADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSD 300
N ++L ++TS VY G +D + QG + + AK P+VY + VC D
Sbjct: 77 NTAYLQLSSLTSEDTAVYYCARGVFGFFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGD 134
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 55 GIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSD 87
G +D + QG + + AK P+VY + VC D
Sbjct: 102 GFFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGD 134
>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 = 31.6 bits (70), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 44/105 (41%), Gaps = 9/105 (8%)
Query: 196 EFGTDVYAHLKARGMFVATQRTEGVSTSDIVARIVRDYDIYVRRNLARGYTAKDLNVSFL 255
E G + A ++ + AT E V ++R +Y++ N R A+D + +
Sbjct: 42 EKGLEWVAEIRLKSNNYATHYAESVKGRFTISRDDSKSSVYLQMNNLR---AEDTGIYYC 98
Query: 256 NVTSRKVRVYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSD 300
R A G D + QG S + A P+VY +V CSD
Sbjct: 99 T------RGGAVGAMDYWGQGTSVTVSSATTTAPSVYPLVPGCSD 137
>pdb|1OB1|B Chain B, Crystal Structure Of A Fab Complex Whith Plasmodium
Falciparum Msp1-19
pdb|1OB1|E Chain E, Crystal Structure Of A Fab Complex Whith Plasmodium
Falciparum Msp1-19
Length = 219
Score = 31.6 bits (70), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 54 DGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSD 87
DG D + QG S + AK P+VY + VC D
Sbjct: 104 DGGMDFWGQGTSVTVSSAKTTAPSVYPLAPVCGD 137
Score = 31.6 bits (70), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 267 DGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSD 300
DG D + QG S + AK P+VY + VC D
Sbjct: 104 DGGMDFWGQGTSVTVSSAKTTAPSVYPLAPVCGD 137
>pdb|1PEI|A Chain A, Nmr Structure Of The Membrane-Binding Domain Of Ctp
Phosphocholine Cytidylyltransferase, 10 Structures
Length = 24
Score = 31.2 bits (69), Expect = 0.98, Method: Composition-based stats.
Identities = 12/22 (54%), Positives = 18/22 (81%)
Query: 338 IGERRVDMIQKWEEKSRDIIDT 359
+ E+ +D+IQKWEEKSR+ I +
Sbjct: 2 VEEKSIDLIQKWEEKSREFIGS 23
>pdb|1PZ5|B Chain B, Structural Basis Of Peptide-Carbohydrate Mimicry In An
Antibody Combining Site
Length = 220
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 44/105 (41%), Gaps = 9/105 (8%)
Query: 196 EFGTDVYAHLKARGMFVATQRTEGVSTSDIVARIVRDYDIYVRRNLARGYTAKDLNVSFL 255
E G + A ++ + AT E V ++R +Y++ N R A+D + +
Sbjct: 42 EKGLEWVAEIRLKSNNYATHYAESVKGRFTISRDDSKSSVYLQMNNLR---AEDTGIYYC 98
Query: 256 NVTSRKVRVYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSD 300
R A G D + QG S + A P+VY +V CSD
Sbjct: 99 T------RGGAVGAMDYWGQGTSVTVSSATTTAPSVYPLVPGCSD 137
>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 = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 7/56 (12%)
Query: 251 NVSFL---NVTSRKVRVY---ADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSD 300
N ++L ++TS VY AD ++D + QG + + AK P+VY + VC D
Sbjct: 77 NTAYLQLSSLTSEDTAVYYCNAD-LHDYWGQGTTLTVSSAKTTAPSVYPLAPVCGD 131
>pdb|1PMI|A Chain A, Candida Albicans Phosphomannose Isomerase
Length = 440
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 43/91 (47%), Gaps = 8/91 (8%)
Query: 302 LTHRKKGRTVMNDEKKFRFQN-KIEEFKDRSKRVMENIGERRVDMIQKWEEKSRDIIDTF 360
L + G+ + D+ + Q K+ E DR +V ++I R ++IQ+ ++ + I F
Sbjct: 200 LLQKVFGKLMNTDDDVIKQQTAKLLERTDREPQVFKDIDSRLPELIQRLNKQFPNDIGLF 259
Query: 361 --LLLFGREGRLKHMWNEGKGKFLQAFSPPA 389
LL G N+G+ FLQA P A
Sbjct: 260 CGCLLLNHVG-----LNKGEAMFLQAKDPHA 285
>pdb|3U9U|A Chain A, Crystal Structure Of Extracellular Domain Of Human
Erbb4HER4 IN Complex With The Fab Fragment Of Mab1479
pdb|3U9U|C Chain C, Crystal Structure Of Extracellular Domain Of Human
Erbb4HER4 IN Complex With The Fab Fragment Of Mab1479
Length = 224
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 50 RVYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSD 87
R+ D +D + QG + + AK P+VY + VC D
Sbjct: 99 RIPDDHYFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGD 136
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 263 RVYADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCSD 300
R+ D +D + QG + + AK P+VY + VC D
Sbjct: 99 RIPDDHYFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGD 136
>pdb|1IAI|H Chain H, Idiotype-Anti-Idiotype Fab Complex
Length = 219
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 26/68 (38%), Gaps = 9/68 (13%)
Query: 29 SLNNGVDEALFHDNNNASRKVRVYA---DGIY------DMFHQGHSRQLMQAKNVFPNVY 79
SL A NN + Y DG Y D + QG S + AK P+VY
Sbjct: 71 SLETSASTAYLQINNLKNEDTATYFCARDGYYENYYAMDYWGQGTSVTVSSAKTTAPSVY 130
Query: 80 LIVGVCSD 87
+ VC D
Sbjct: 131 PLAPVCGD 138
>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 = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 3/61 (4%)
Query: 29 SLNNGVDEALFHDNNNASRKVRVY--ADGIYDMFHQGHSRQLMQAKNVFPNVYLIVGVCS 86
SL+ A H +N + Y A G+ D + QG S + AK P+VY + C
Sbjct: 71 SLDTSASTAYLHISNLKNEDTATYFCARGL-DSWGQGTSVTVSSAKTTPPSVYPLAPGCG 129
Query: 87 D 87
D
Sbjct: 130 D 130
>pdb|1FLR|H Chain H, 4-4-20 Fab Fragment
Length = 219
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 265 YADGIY---DMFHQGHSRQLMQAKNVFPNVYLIVGVCSDA 301
Y G Y D + QG S + AK P+VY + VC D
Sbjct: 97 YCTGSYYGMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDT 136
>pdb|3ULQ|A Chain A, Crystal Structure Of The Anti-Activator Rapf Complexed
With The Response Regulator Coma Dna Binding Domain
Length = 383
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 265 YADGIYDMF--HQGHSRQLMQAKNVFPNVYLIVGVCSDALTHRKKGRTVMNDEKK 317
YA Y+++ H+ ++ +L+Q ++F +L + DA++H +K ++ EK+
Sbjct: 165 YARQAYEIYKEHEAYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQ 219
>pdb|4FAB|H Chain H, Three-Dimensional Structure Of A Fluorescein-Fab Complex
Crystallized In 2-Methyl-2,4-Pentanediol
Length = 216
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 265 YADGIY---DMFHQGHSRQLMQAKNVFPNVYLIVGVCSDA 301
Y G Y D + QG S + AK P+VY + VC D
Sbjct: 97 YCTGSYYGMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDT 136
>pdb|4F4C|A Chain A, The Crystal Structure Of The Multi-Drug Transporter
Length = 1321
Score = 28.5 bits (62), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 190 DIPYMSEFGTDVYAHLKARGMFVATQRTEGVSTSDIVARIVRDYDIYVRRNLARGYTAKD 249
D+P + V A G VA + G S I++ ++R YD+ + G +D
Sbjct: 430 DVPILRGMNLRVNA-----GQTVALVGSSGCGKSTIISLLLRYYDVLKGKITIDGVDVRD 484
Query: 250 LNVSFL 255
+N+ FL
Sbjct: 485 INLEFL 490
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
0.318 0.134 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,620,068
Number of Sequences: 62578
Number of extensions: 533309
Number of successful extensions: 1493
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1448
Number of HSP's gapped (non-prelim): 55
length of query: 413
length of database: 14,973,337
effective HSP length: 101
effective length of query: 312
effective length of database: 8,652,959
effective search space: 2699723208
effective search space used: 2699723208
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)