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= psy17790
(2564 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1LI1|A Chain A, The 1.9-A Crystal Structure Of The Noncollagenous (Nc1)
Domain Of Human Placenta Collagen Iv Shows Stabilization
Via A Novel Type Of Covalent Met-Lys Cross-Link
pdb|1LI1|B Chain B, The 1.9-A Crystal Structure Of The Noncollagenous (Nc1)
Domain Of Human Placenta Collagen Iv Shows Stabilization
Via A Novel Type Of Covalent Met-Lys Cross-Link
pdb|1LI1|D Chain D, The 1.9-A Crystal Structure Of The Noncollagenous (Nc1)
Domain Of Human Placenta Collagen Iv Shows Stabilization
Via A Novel Type Of Covalent Met-Lys Cross-Link
pdb|1LI1|E Chain E, The 1.9-A Crystal Structure Of The Noncollagenous (Nc1)
Domain Of Human Placenta Collagen Iv Shows Stabilization
Via A Novel Type Of Covalent Met-Lys Cross-Link
Length = 229
Score = 294 bits (753), Expect = 4e-79, Method: Composition-based stats.
Identities = 125/224 (55%), Positives = 171/224 (76%)
Query: 2218 GFFLTFHSQTDMEPECPRYTSKLWSGYSLLHISGDNKAHTQDLGSPGSCLPRFSTMPFLF 2277
GF +T HSQT +P+CP T L+ GYSLL++ G+ +AH QDLG+ GSCL +FSTMPFLF
Sbjct: 5 GFLVTRHSQTIDDPQCPSGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTMPFLF 64
Query: 2278 CSLTQTCDYASRGDNSYWLSSTEPMLKTMEPIPSADLKKYVSRCSVCESTTRAIAIHSQS 2337
C++ C++ASR D SYWLS+ EPM +M PI +++ ++SRC+VCE+ +A+HSQ+
Sbjct: 65 CNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGENIRPFISRCAVCEAPAMVMAVHSQT 124
Query: 2338 VTIPSCPGGWEELWVGFSFLMHTDAGSGGGGQSLISPGSCLQDFRPTPFIQCHGVGSCNY 2397
+ IP CP GW LW+G+SF+MHT AG+ G GQ+L SPGSCL++FR PFI+CHG G+CNY
Sbjct: 125 IQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECHGRGTCNY 184
Query: 2398 YSTASSFWLATLDDRDQWRKPRPQTLKANDLKTRISRCAVCLRR 2441
Y+ A SFWLAT++ + ++KP P TLKA +L+T +SRC VC+RR
Sbjct: 185 YANAYSFWLATIERSEMFKKPTPSTLKAGELRTHVSRCQVCMRR 228
Score = 79.0 bits (193), Expect = 3e-14, Method: Composition-based stats.
Identities = 45/113 (39%), Positives = 60/113 (53%), Gaps = 6/113 (5%)
Query: 2221 LTFHSQTDMEPECPRYTSKLWSGYS-LLHISGDNKAHTQDLGSPGSCLPRFSTMPFLFCS 2279
+ HSQT P CP S LW GYS ++H S + Q L SPGSCL F + PF+ C
Sbjct: 118 MAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECH 177
Query: 2280 LTQTCDYASRGDNSYWLSSTEPMLKTMEPIPS----ADLKKYVSRCSVCESTT 2328
TC+Y + S+WL++ E +P PS +L+ +VSRC VC T
Sbjct: 178 GRGTCNYYANA-YSFWLATIERSEMFKKPTPSTLKAGELRTHVSRCQVCMRRT 229
>pdb|1M3D|A Chain A, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|B Chain B, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|D Chain D, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|E Chain E, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|G Chain G, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|H Chain H, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|J Chain J, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|K Chain K, Structure Of Type Iv Collagen Nc1 Domains
pdb|1T60|A Chain A, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|B Chain B, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|D Chain D, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|E Chain E, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|G Chain G, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|H Chain H, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|J Chain J, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|K Chain K, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|M Chain M, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|N Chain N, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|P Chain P, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|Q Chain Q, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|S Chain S, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|T Chain T, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|V Chain V, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|W Chain W, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T61|A Chain A, Crystal Structure Of Collagen Iv Nc1 Domain From Placenta
Basement Membrane
pdb|1T61|B Chain B, Crystal Structure Of Collagen Iv Nc1 Domain From Placenta
Basement Membrane
pdb|1T61|D Chain D, Crystal Structure Of Collagen Iv Nc1 Domain From Placenta
Basement Membrane
pdb|1T61|E Chain E, Crystal Structure Of Collagen Iv Nc1 Domain From Placenta
Basement Membrane
Length = 229
Score = 294 bits (753), Expect = 4e-79, Method: Composition-based stats.
Identities = 125/224 (55%), Positives = 171/224 (76%)
Query: 2218 GFFLTFHSQTDMEPECPRYTSKLWSGYSLLHISGDNKAHTQDLGSPGSCLPRFSTMPFLF 2277
GF +T HSQT +P+CP T L+ GYSLL++ G+ +AH QDLG+ GSCL +FSTMPFLF
Sbjct: 5 GFLVTRHSQTTDDPQCPPGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTMPFLF 64
Query: 2278 CSLTQTCDYASRGDNSYWLSSTEPMLKTMEPIPSADLKKYVSRCSVCESTTRAIAIHSQS 2337
C++ C++ASR D SYWLS+ EPM +M PI +++ ++SRC+VCE+ +A+HSQ+
Sbjct: 65 CNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGENIRPFISRCAVCEAPAMVMAVHSQT 124
Query: 2338 VTIPSCPGGWEELWVGFSFLMHTDAGSGGGGQSLISPGSCLQDFRPTPFIQCHGVGSCNY 2397
+ IP CP GW LW+G+SF+MHT AG+ G GQ+L SPGSCL++FR PFI+CHG G+CNY
Sbjct: 125 IQIPQCPTGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECHGRGTCNY 184
Query: 2398 YSTASSFWLATLDDRDQWRKPRPQTLKANDLKTRISRCAVCLRR 2441
Y+ A SFWLAT++ + ++KP P TLKA +L+T +SRC VC+RR
Sbjct: 185 YANAYSFWLATIERSEMFKKPTPSTLKAGELRTHVSRCQVCMRR 228
Score = 80.1 bits (196), Expect = 1e-14, Method: Composition-based stats.
Identities = 45/113 (39%), Positives = 61/113 (53%), Gaps = 6/113 (5%)
Query: 2221 LTFHSQTDMEPECPRYTSKLWSGYS-LLHISGDNKAHTQDLGSPGSCLPRFSTMPFLFCS 2279
+ HSQT P+CP S LW GYS ++H S + Q L SPGSCL F + PF+ C
Sbjct: 118 MAVHSQTIQIPQCPTGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECH 177
Query: 2280 LTQTCDYASRGDNSYWLSSTEPMLKTMEPIPS----ADLKKYVSRCSVCESTT 2328
TC+Y + S+WL++ E +P PS +L+ +VSRC VC T
Sbjct: 178 GRGTCNYYANA-YSFWLATIERSEMFKKPTPSTLKAGELRTHVSRCQVCMRRT 229
>pdb|1M3D|C Chain C, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|F Chain F, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|I Chain I, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|L Chain L, Structure Of Type Iv Collagen Nc1 Domains
pdb|1T60|C Chain C, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|F Chain F, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|I Chain I, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|L Chain L, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|O Chain O, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|R Chain R, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|U Chain U, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T60|X Chain X, Crystal Structure Of Type Iv Collagen Nc1 Domain From Bovine
Lens Capsule
pdb|1T61|C Chain C, Crystal Structure Of Collagen Iv Nc1 Domain From Placenta
Basement Membrane
pdb|1T61|F Chain F, Crystal Structure Of Collagen Iv Nc1 Domain From Placenta
Basement Membrane
Length = 227
Score = 283 bits (723), Expect = 1e-75, Method: Composition-based stats.
Identities = 132/226 (58%), Positives = 162/226 (71%), Gaps = 3/226 (1%)
Query: 2216 SRGFFLTFHSQTDMEPECPRYTSKLWSGYSLLHISGDNKAHTQDLGSPGSCLPRFSTMPF 2275
S G+ L HSQTD EP CP +KLWSGYSLL+ G KAH QDLG GSCL RFSTMPF
Sbjct: 2 SIGYLLVKHSQTDQEPMCPVGMNKLWSGYSLLYFEGQEKAHNQDLGLAGSCLARFSTMPF 61
Query: 2276 LFCSLTQTCDYASRGDNSYWLSSTEPMLKTMEPIPSADLKKYVSRCSVCESTTRAIAIHS 2335
L+C+ C YASR D SYWLS+T P+ M P+ D++ Y+SRCSVCE+ AIA+HS
Sbjct: 62 LYCNPGDVCYYASRNDKSYWLSTTAPL--PMMPVAEEDIRPYISRCSVCEAPAVAIAVHS 119
Query: 2336 QSVTIPSCPGGWEELWVGFSFLMHTDAGSGGGGQSLISPGSCLQDFRPTPFIQCHGV-GS 2394
Q V+IP CP GW LW+G+SFLMHT AG GGGQSL+SPGSCL+DFR TPFI+C+G G+
Sbjct: 120 QDVSIPHCPAGWRSLWIGYSFLMHTAAGDEGGGQSLVSPGSCLEDFRATPFIECNGARGT 179
Query: 2395 CNYYSTASSFWLATLDDRDQWRKPRPQTLKANDLKTRISRCAVCLR 2440
C+YY+ SFWL T+ ++ P TLKA ++T ISRC VC++
Sbjct: 180 CHYYANKYSFWLTTIPEQSFQGTPSADTLKAGLIRTHISRCQVCMK 225
>pdb|1LI1|C Chain C, The 1.9-A Crystal Structure Of The Noncollagenous (Nc1)
Domain Of Human Placenta Collagen Iv Shows Stabilization
Via A Novel Type Of Covalent Met-Lys Cross-Link
pdb|1LI1|F Chain F, The 1.9-A Crystal Structure Of The Noncollagenous (Nc1)
Domain Of Human Placenta Collagen Iv Shows Stabilization
Via A Novel Type Of Covalent Met-Lys Cross-Link
Length = 228
Score = 277 bits (709), Expect = 5e-74, Method: Compositional matrix adjust.
Identities = 132/226 (58%), Positives = 162/226 (71%), Gaps = 3/226 (1%)
Query: 2216 SRGFFLTFHSQTDMEPECPRYTSKLWSGYSLLHISGDNKAHTQDLGSPGSCLPRFSTMPF 2275
S G+ L HSQTD EP CP +KLWSGYSLL+ G KAH QDLG GSCL RFSTMPF
Sbjct: 3 SIGYLLVKHSQTDQEPMCPVGMNKLWSGYSLLYFEGQEKAHNQDLGLAGSCLARFSTMPF 62
Query: 2276 LFCSLTQTCDYASRGDNSYWLSSTEPMLKTMEPIPSADLKKYVSRCSVCESTTRAIAIHS 2335
L+C+ C YASR D SYWLS+T P+ M P+ ++K Y+SRCSVCE+ AIA+HS
Sbjct: 63 LYCNPGDVCYYASRNDKSYWLSTTAPL--PMMPVAEDEIKPYISRCSVCEAPAIAIAVHS 120
Query: 2336 QSVTIPSCPGGWEELWVGFSFLMHTDAGSGGGGQSLISPGSCLQDFRPTPFIQCH-GVGS 2394
Q V+IP CP GW LW+G+SFLMHT AG GGGQSL+SPGSCL+DFR TPFI+C+ G G+
Sbjct: 121 QDVSIPHCPAGWRSLWIGYSFLMHTAAGDEGGGQSLVSPGSCLEDFRATPFIECNGGRGT 180
Query: 2395 CNYYSTASSFWLATLDDRDQWRKPRPQTLKANDLKTRISRCAVCLR 2440
C+YY+ SFWL T+ ++ P TLKA ++T ISRC VC++
Sbjct: 181 CHYYANKYSFWLTTIPEQSFQGSPSADTLKAGLIRTHISRCQVCMK 226
>pdb|3HQV|B Chain B, Low Resolution, Molecular Envelope Structure Of Type I
Collagen In Situ Determined By Fiber Diffraction. Single
Type I Collagen Molecule, Rigid Body Refinement
pdb|3HR2|B Chain B, Low Resolution, Molecular Envelope Structure Of Type I
Collagen In Situ Determined By Fiber Diffraction. Single
Type I Collagen Molecule, Post Rigid Body Refinement,
'relaxed'
Length = 1028
Score = 46.2 bits (108), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 44/116 (37%), Positives = 52/116 (44%), Gaps = 6/116 (5%)
Query: 2090 HALFGIAGTNGAKGETGPPGDTGVEGY------PGTPGAKGDRGFIGDTGLPGMDGTPGE 2143
H G AG +G +GE GP G G G G G +GD+G GD G G+ G G
Sbjct: 887 HGSVGPAGKHGNRGEPGPAGSVGPVGAVGPRGPSGPQGIRGDKGEPGDXGARGLPGLKGH 946
Query: 2144 KGFQGEPGDTLAYNLQWTRGRAGEIGPRGDTLAYNLQWTRGRAGEIGPRGPVGFQG 2199
G QG PG + Q G G GPRG GR+G GP GP G +G
Sbjct: 947 NGLQGLPGLAGLHGDQGAPGPVGPAGPRGPAGPSGPIGKDGRSGHPGPVGPAGVRG 1002
Score = 45.1 bits (105), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 39/85 (45%), Positives = 47/85 (55%), Gaps = 3/85 (3%)
Query: 675 GPKGMPGARGDRGPYGLKGERGVPGRPGIDGYPGIKGVKGVQGREGWRGKEGKDGRP--- 731
GP G G RG GP G++G++G PG G G PG+KG G+QG G G G G P
Sbjct: 909 GPVGAVGPRGPSGPQGIRGDKGEPGDXGARGLPGLKGHNGLQGLPGLAGLHGDQGAPGPV 968
Query: 732 GDAGVKGDKGAPGLAGRDGSPGEPG 756
G AG +G G G G+DG G PG
Sbjct: 969 GPAGPRGPAGPSGPIGKDGRSGHPG 993
Score = 42.0 bits (97), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 40/102 (39%), Positives = 46/102 (45%), Gaps = 21/102 (20%)
Query: 1399 GFVGKPGSTGFVGKPGLQGLPGNKGEQGRRGTPGPVGQMGPPGA---------------K 1443
G+ G G TG G PG G G G+ G RG PGP G +GP GA K
Sbjct: 870 GYXGNIGPTGAAGAPGPHGSVGPAGKHGNRGEPGPAGSVGPVGAVGPRGPSGPQGIRGDK 929
Query: 1444 GVIGDYGDAGYPGEDGESAF------SGLQGDKGEPGQTGPM 1479
G GD G G PG G + +GL GD+G PG GP
Sbjct: 930 GEPGDXGARGLPGLKGHNGLQGLPGLAGLHGDQGAPGPVGPA 971
Score = 38.9 bits (89), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 55/148 (37%), Positives = 67/148 (45%), Gaps = 26/148 (17%)
Query: 667 GNISYSFKGPKGMPGARGDRGPYGLKGERGVPGRPGIDGYPGIKGVKGVQGREGWRGKEG 726
GNI + G G PG G GP G G RG PG G G G G +G G +G RG +G
Sbjct: 873 GNIGPT--GAAGAPGPHGSVGPAGKHGNRGEPGPAGSVGPVGAVGPRGPSGPQGIRGDKG 930
Query: 727 KDGRPGDAGVKGDKGAPGLAGRDGSPGEPGSKXXXXXXXXXXXXXXXXXRGIYDPTLDKI 786
+ PGD G +G PGL G +G G PG G++
Sbjct: 931 E---PGDXGARG---LPGLKGHNGLQGLPGLA------------------GLHGDQGAPG 966
Query: 787 EPGVTGPQGPIGPRGEPGEDGYNGKPGP 814
G GP+GP GP G G+DG +G PGP
Sbjct: 967 PVGPAGPRGPAGPSGPIGKDGRSGHPGP 994
Score = 38.5 bits (88), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 31/66 (46%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 1408 GFVGKPGLQGLPGNKGEQGRRGTPGPVGQM---GPPGAKGVIGDYGDAGYPGEDGESAFS 1464
G G GLQGLPG G G +G PGPVG GP G G IG G +G+PG G +
Sbjct: 942 GLKGHNGLQGLPGLAGLHGDQGAPGPVGPAGPRGPAGPSGPIGKDGRSGHPGPVGPAGVR 1001
Query: 1465 GLQGDK 1470
G QG +
Sbjct: 1002 GSQGSQ 1007
Score = 38.1 bits (87), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 43/111 (38%), Positives = 48/111 (43%), Gaps = 3/111 (2%)
Query: 2089 NHALFGIAGTNGAKGETGPPGDTGVEGYPGTPGAKGDRGFIGDTGLPGMDGTPGEKGFQG 2148
N G AG G G GP G G G PG G+ G G +G G G G G+KG
Sbjct: 874 NIGPTGAAGAPGPHGSVGPAGKHGNRGEPGPAGSVGPVGAVGPRGPSGPQGIRGDKG--- 930
Query: 2149 EPGDTLAYNLQWTRGRAGEIGPRGDTLAYNLQWTRGRAGEIGPRGPVGFQG 2199
EPGD A L +G G G G + Q G G GPRGP G G
Sbjct: 931 EPGDXGARGLPGLKGHNGLQGLPGLAGLHGDQGAPGPVGPAGPRGPAGPSG 981
Score = 37.7 bits (86), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 52/149 (34%), Positives = 62/149 (41%), Gaps = 5/149 (3%)
Query: 89 GVKGEAGEAAINGIPGDPGAPGRMGE---KGSRGPDGKMGPPGNKGLDGKHGTQGIEXXX 145
GV G GEA +G G G GR G+ KG RG G +GP G G G HG+ G
Sbjct: 837 GVNGAXGEAGRDGNXGSDGPXGRDGQXGHKGERGYXGNIGPTGAAGAPGPHGSVGPAGKH 896
Query: 146 XXXXXXXXXXXXSRVDIARAVGDQGLQGIEVGLRGDPGEGGINS-KGTKGESGVYGIPGL 204
V G G QGI G +G+PG+ G G KG +G+ G+PGL
Sbjct: 897 GNRGEPGPAGSVGPVGAVGPRGPSGPQGIR-GDKGEPGDXGARGLPGLKGHNGLQGLPGL 955
Query: 205 QXXXXXXXXXXXXXYQGPYGERGPRGQIG 233
GP G GP G IG
Sbjct: 956 AGLHGDQGAPGPVGPAGPRGPAGPSGPIG 984
Score = 37.4 bits (85), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 56/156 (35%), Positives = 69/156 (44%), Gaps = 9/156 (5%)
Query: 670 SYSFKGPKGMPGARGDRGPYGLKGERGVPGRPGIDGYPGIKGVKGVQGREGWRGKEGKDG 729
S +G G+ GA G+ GP G+ G G G G G G+ G G GR+G G +G G
Sbjct: 799 SRGERGQXGIAGALGEXGPLGIAGPXGARGPXGAVGSXGVNGAXGEAGRDGNXGSDGPXG 858
Query: 730 RPGDAGVKGDKGAPGLAGRDGSPGEPGSKXXXXXXXXXXXXXXXXXRGIYDPTLDKIEPG 789
R G G KG++G G G G+ G PG G P G
Sbjct: 859 RDGQXGHKGERGYXGNIGPTGAAGAPGPHGSVGPAGKHGNRGEPGPAGSVGPV------G 912
Query: 790 VTGPQGPIGP---RGEPGEDGYNGKPGPPGLQGRTG 822
GP+GP GP RG+ GE G G G PGL+G G
Sbjct: 913 AVGPRGPSGPQGIRGDKGEPGDXGARGLPGLKGHNG 948
Score = 36.6 bits (83), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 34/92 (36%), Positives = 40/92 (43%)
Query: 2109 GDTGVEGYPGTPGAKGDRGFIGDTGLPGMDGTPGEKGFQGEPGDTLAYNLQWTRGRAGEI 2168
G GV G G G G+ G G G G G GE+G+ G G T A G G
Sbjct: 834 GSXGVNGAXGEAGRDGNXGSDGPXGRDGQXGHKGERGYXGNIGPTGAAGAPGPHGSVGPA 893
Query: 2169 GPRGDTLAYNLQWTRGRAGEIGPRGPVGFQGI 2200
G G+ + G G +GPRGP G QGI
Sbjct: 894 GKHGNRGEPGPAGSVGPVGAVGPRGPSGPQGI 925
Score = 35.0 bits (79), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 31/73 (42%), Positives = 41/73 (56%)
Query: 1405 GSTGFVGKPGLQGLPGNKGEQGRRGTPGPVGQMGPPGAKGVIGDYGDAGYPGEDGESAFS 1464
G+ G G G QG+ G KGEQG G G G GP G G +G G+ G PGE G +
Sbjct: 447 GNNGAQGPXGPQGVQGGKGEQGPAGPXGFQGLXGPSGTAGEVGKXGERGLPGEFGLXGPA 506
Query: 1465 GLQGDKGEPGQTG 1477
G +G++G G++G
Sbjct: 507 GPRGERGPXGESG 519
Score = 33.5 bits (75), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 43/103 (41%), Positives = 49/103 (47%), Gaps = 12/103 (11%)
Query: 2097 GTNGAKGETGPPGDTGVEGYPGTPGAKGDRGFIGDTGLPGMDGTPGEKGFQGEPGDTLAY 2156
G NGA+G GP GV+G G G G GF GL G GT GE G GE G +
Sbjct: 447 GNNGAQGPXGP---QGVQGGKGEQGPAGPXGF---QGLXGPSGTAGEVGKXGERGLPGEF 500
Query: 2157 NLQWTRGRAGEIGPRGDTLAYNLQWTRGRAGEIGPRGPVGFQG 2199
L G GE GP G++ A G +G IG RGP G G
Sbjct: 501 GLXGPAGPRGERGPXGESGAA------GPSGPIGIRGPSGAXG 537
Score = 33.5 bits (75), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 49/135 (36%), Positives = 59/135 (43%), Gaps = 9/135 (6%)
Query: 695 RGVPGRPGIDGYPGIKGVKGVQGREGWRGKEGKDGRPGDAGVKGDKGAPGLAGRDGSPGE 754
RG+ G G G G +G+ G G G G+ G G G AG +G G G G+ GSPGE
Sbjct: 248 RGIXGPVGAAGATGPRGLVGEXGPAGSXGETGNKGEXGSAGAQGPXGPSGEEGKRGSPGE 307
Query: 755 PGSKXXXX------XXXXXXXXXXXXXRGIYDPTLDKIEPGVTGPQGPIGPRGEPGEDGY 808
PGS G+ P ++ G TGP G GP G+ G G
Sbjct: 308 PGSAGPAGPXGLRGSXGSRGLXGADGRAGVMGPPGNR---GSTGPAGVRGPNGDAGRXGE 364
Query: 809 NGKPGPPGLQGRTGE 823
G GP GL G G
Sbjct: 365 XGLMGPRGLXGSXGN 379
Score = 33.1 bits (74), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 39/99 (39%), Positives = 42/99 (42%), Gaps = 9/99 (9%)
Query: 2098 TNGAKGETGPPGDTGVEGYPGTPGAKGDRGFIGDTGLPGMDGTPGEKGFQGEPGDTLAYN 2157
+G G GPPG+ G G G G GD G G+ GL G G G G G G
Sbjct: 331 ADGRAGVMGPPGNRGSTGPAGVRGPNGDAGRXGEXGLMGPRGLXGSXGNVGPAGKEGPVG 390
Query: 2158 LQWTRGRAGEIGPRGDTLAYNLQWTRGRAGEIGPRGPVG 2196
L GR G IGP G RG AG IG GP G
Sbjct: 391 LXGIDGRXGPIGPAG---------PRGEAGNIGFXGPKG 420
Score = 32.7 bits (73), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 29/61 (47%), Positives = 31/61 (50%)
Query: 681 GARGDRGPYGLKGERGVPGRPGIDGYPGIKGVKGVQGREGWRGKEGKDGRPGDAGVKGDK 740
GA G GP GL GE G G G G G G G QG G G+EGK G PG+ G G
Sbjct: 255 GAAGATGPRGLVGEXGPAGSXGETGNKGEXGSAGAQGPXGPSGEEGKRGSPGEPGSAGPA 314
Query: 741 G 741
G
Sbjct: 315 G 315
Score = 32.7 bits (73), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 44/127 (34%), Positives = 54/127 (42%), Gaps = 21/127 (16%)
Query: 2094 GIAGTNGAKGETGPPGDTGVEGYPGTPGAKGDRGFIGDTGLPGMDGTPGEKGFQGEPGDT 2153
GI G GA G TGP G G G G+ G G++G G G G G GE+G +G PG+
Sbjct: 249 GIXGPVGAAGATGPRGLVGEXGPAGSXGETGNKGEXGSAGAQGPXGPSGEEGKRGSPGEP 308
Query: 2154 LAYN---------------LQWTRGRAGEIGPRGDTLAYNLQWTR------GRAGEIGPR 2192
+ L GRAG +GP G+ + R GR GE G
Sbjct: 309 GSAGPAGPXGLRGSXGSRGLXGADGRAGVMGPPGNRGSTGPAGVRGPNGDAGRXGEXGLM 368
Query: 2193 GPVGFQG 2199
GP G G
Sbjct: 369 GPRGLXG 375
Score = 32.3 bits (72), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 43/131 (32%), Positives = 51/131 (38%), Gaps = 37/131 (28%)
Query: 895 GVQGDRGDPGVQESPAHVAHQTLSFGPRTPGGPNRKAFTAMNPLQGPYGAPGDEGRDGLP 954
G G+RG+PG PA + GPR P GP ++G G PGD G GLP
Sbjct: 894 GKHGNRGEPG----PAGSVGPVGAVGPRGPSGPQG--------IRGDKGEPGDXGARGLP 941
Query: 955 GRNGVPGSKGDPATIPKEYLRGDAGYDGLPGEPGTPGDMGLKGEAGDT-------ISSEV 1007
G L+G G GLPG G GD G G G S +
Sbjct: 942 G------------------LKGHNGLQGLPGLAGLHGDQGAPGPVGPAGPRGPAGPSGPI 983
Query: 1008 NMKGEKGYPGP 1018
G G+PGP
Sbjct: 984 GKDGRSGHPGP 994
Score = 31.6 bits (70), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 42/104 (40%), Positives = 47/104 (45%), Gaps = 14/104 (13%)
Query: 451 GSEGLPGLVGPPGAKGFPGQPGRKGEKAKPGG---PQPAGLNFRPPCTILKDFKVLYRDF 507
G G G +GP GA G PG G G K G P PAG ++ V R
Sbjct: 867 GERGYXGNIGPTGAAGAPGPHGSVGPAGKHGNRGEPGPAG-------SVGPVGAVGPR-- 917
Query: 508 QMGLCAHQGSMGALGEVGPKGFQGEPGPKGYAGLAGLPGLNGTH 551
G QG G GE G G +G PG KG+ GL GLPGL G H
Sbjct: 918 --GPSGPQGIRGDKGEPGDXGARGLPGLKGHNGLQGLPGLAGLH 959
Score = 31.6 bits (70), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 31/78 (39%), Positives = 38/78 (48%), Gaps = 9/78 (11%)
Query: 1735 IAATKGDFGEPGMTGLTGEKGWRGDVGWPGRNGTKGLPGAIG------PQGE---PGFPG 1785
+ KG+ G G G G G G G G+ G +GLPG G P+GE G G
Sbjct: 460 VQGGKGEQGPAGPXGFQGLXGPSGTAGEVGKXGERGLPGEFGLXGPAGPRGERGPXGESG 519
Query: 1786 YQGPKGPVGMRGPPGIPG 1803
GP GP+G+RGP G G
Sbjct: 520 AAGPSGPIGIRGPSGAXG 537
>pdb|3HQV|A Chain A, Low Resolution, Molecular Envelope Structure Of Type I
Collagen In Situ Determined By Fiber Diffraction. Single
Type I Collagen Molecule, Rigid Body Refinement
pdb|3HQV|C Chain C, Low Resolution, Molecular Envelope Structure Of Type I
Collagen In Situ Determined By Fiber Diffraction. Single
Type I Collagen Molecule, Rigid Body Refinement
pdb|3HR2|A Chain A, Low Resolution, Molecular Envelope Structure Of Type I
Collagen In Situ Determined By Fiber Diffraction. Single
Type I Collagen Molecule, Post Rigid Body Refinement,
'relaxed'
pdb|3HR2|C Chain C, Low Resolution, Molecular Envelope Structure Of Type I
Collagen In Situ Determined By Fiber Diffraction. Single
Type I Collagen Molecule, Post Rigid Body Refinement,
'relaxed'
Length = 1056
Score = 36.6 bits (83), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 31/56 (55%)
Query: 1423 GEQGRRGTPGPVGQMGPPGAKGVIGDYGDAGYPGEDGESAFSGLQGDKGEPGQTGP 1478
GE+G G GP G G PG +G+ G G G G+ G+ F GL G GE G+ GP
Sbjct: 770 GEKGSXGADGPAGSXGTPGPQGIAGQRGVVGLXGQRGKRGFXGLXGPSGEXGKQGP 825
Score = 36.2 bits (82), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 35/88 (39%), Positives = 39/88 (44%), Gaps = 3/88 (3%)
Query: 2112 GVEGYPGTPGAKGDRGFIGDTGLPGMDGTPGEKGFQGEPGDTLAYNLQWTRGRAGEIGPR 2171
G G G G KGDRG D G G DG+PG+ G +G G G GE GP
Sbjct: 569 GERGAAGLXGPKGDRG---DAGPKGADGSPGKDGVRGLTGPIGPXGPAGAXGDKGEAGPS 625
Query: 2172 GDTLAYNLQWTRGRAGEIGPRGPVGFQG 2199
G + G GE GP GP GF G
Sbjct: 626 GPAGPTGARGAXGDRGEAGPXGPAGFAG 653
>pdb|1X5Z|A Chain A, Solution Structure Of The Fibronectin Type-Iii Domain Of
Human Protein Tyrosine Phosphatase, Receptor Type, D
Isoform 4 Variant
Length = 115
Score = 33.1 bits (74), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 32/72 (44%), Gaps = 13/72 (18%)
Query: 2118 GTPGAKGDRGFIGDTGLPGMDGTPGEKGFQGEPGDTLAYNLQWTRGRAGEIGPRGDTLA- 2176
G+ G+ GD I TG+PG F+ EP + L WT PR DT+A
Sbjct: 1 GSSGSSGDIQVITQTGVPGQP-----LNFKAEPESETSILLSWT-------PPRSDTIAN 48
Query: 2177 YNLQWTRGRAGE 2188
Y L + G GE
Sbjct: 49 YELVYKDGEHGE 60
>pdb|2Q71|A Chain A, Uroporphyrinogen Decarboxylase G168r Single Mutant Enzyme
In Complex With Coproporphyrinogen-Iii
pdb|2Q6Z|A Chain A, Uroporphyrinogen Decarboxylase G168r Single Mutant Apo-
Enzyme
Length = 356
Score = 32.0 bits (71), Expect = 4.4, Method: Composition-based stats.
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 576 GLSGNPWTLPKYLHLRRGQTRRAAAPRFEFQTP--VHRLER 614
G +G PWTL Y+ R G + A A R+ +Q P H+L R
Sbjct: 143 GFAGAPWTLMTYMVERGGSSTMAQAKRWLYQRPQASHQLLR 183
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
0.313 0.142 0.454
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 79,730,668
Number of Sequences: 62578
Number of extensions: 3546783
Number of successful extensions: 12685
Number of sequences better than 100.0: 45
Number of HSP's better than 100.0 without gapping: 42
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 4514
Number of HSP's gapped (non-prelim): 4118
length of query: 2564
length of database: 14,973,337
effective HSP length: 115
effective length of query: 2449
effective length of database: 7,776,867
effective search space: 19045547283
effective search space used: 19045547283
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 60 (27.7 bits)