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= psy10222
(1693 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Xylose
pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Glucose
pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To
6-Bromo-6-Deoxy-D-Glucose
Length = 491
Score = 92.8 bits (229), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 101/451 (22%), Positives = 188/451 (41%), Gaps = 68/451 (15%)
Query: 1285 IACI----LGSFLMEMYGRRLTNLVLCIPFI----------MGWVIISLATEVWVILAG- 1329
I CI LG + +GRR + + + F +G+ I+ V V LAG
Sbjct: 66 IGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGY 125
Query: 1330 -------RFLTGFALGLSSPVALVYIAETTEPKYRGVLSALLCTAVAIGIFTAHLLGTFL 1382
R + G +GL+S ++ +YIAE RG L + A+ G + + F+
Sbjct: 126 VPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFI 185
Query: 1383 ------HWKTTSAVCALF-----PCASFIFAYFT-PESPPWLASKGFTVQAQQAFYWLRG 1430
W T +F P F+ +T PESP WL S+G QA+ + G
Sbjct: 186 ARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMG 245
Query: 1431 HTAESEF--EFKSMLNHAERSTITKSENMTDXXXXXXXXXNILCTEFLKPLAIILVFFFV 1488
+T ++ E K L+H ++ L + + I ++
Sbjct: 246 NTLATQAVQEIKHSLDHGRKTG------------------GRLLMFGVGVIVIGVMLSIF 287
Query: 1489 QQFSGLNTLIFYTVGISKEVSPDVN-EYTATIVIDIVRVVMAFVTCGLLRIFGRRPXXXX 1547
QQF G+N +++Y + K + + TI++ ++ + + + FGR+P
Sbjct: 288 QQFVGINVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQII 347
Query: 1548 XXXXXXXXXXXVASILKFMQGLLPSFMPVILLMFYMVFVSIGLQQLPWMMIGELFPQATR 1607
+ + + Q P + ++ ++FY+ ++ + W+++ E+FP A R
Sbjct: 348 GALGMAIGMFSLGTAF-YTQA--PGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIR 404
Query: 1608 ELGSGISTCFAFLTLFVVVKTGPL------LFLSIGTPETFGLYGCITAFGFVFLYIFLP 1661
I+ +L + V T P+ L ++ +YGC+ +F++ F+P
Sbjct: 405 GKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVP 464
Query: 1662 ETKNKTLQQIEDDFKSKTMEVGTEDEKTAAL 1692
ETK KTL+++E ++ +T + ++TA L
Sbjct: 465 ETKGKTLEELEALWEPET----KKTQQTATL 491
Score = 65.5 bits (158), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 57/288 (19%), Positives = 117/288 (40%), Gaps = 36/288 (12%)
Query: 14 RFLTGLSVGLSSPPSIVYIAESTEPRYRGAILAIVSLAISSGIFISHLLGTFL------- 66
R + G+ VGL+S S +YIAE RG +++ AI G + + + F+
Sbjct: 133 RIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDAS 192
Query: 67 -----HWKTASAVCALFPFISCIFVYSTPESPSWLASKGYSVEAEQAFHWLRGHSAESES 121
W+ A + + + +Y+ PESP WL S+G +AE + G++ +++
Sbjct: 193 WLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLATQA 252
Query: 122 --ELKSMLNHAQKITITKTENMVDKKKKREWKKNILSPEXXXXXXXXXXXXXXXXXSGVN 179
E+K L+H +K L G+N
Sbjct: 253 VQEIKHSLDHGRK------------------TGGRLLMFGVGVIVIGVMLSIFQQFVGIN 294
Query: 180 TVAFYSVGILKNVSPDVN-EYVATMAIDIVRVIMSAVTCGLLRITGRRPLALLSSLGTAF 238
V +Y+ + K + + + T+ + ++ + + + + GR+PL ++ +LG A
Sbjct: 295 VVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAI 354
Query: 239 SLLGLALILKFPQEQLPSFIPVILLMSYIVFVSVGLVPLPWIMTGELL 286
+ L Q P + ++ ++ Y+ ++ P+ W++ E+
Sbjct: 355 GMFSLGTAF---YTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIF 399
Score = 55.5 bits (132), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 36/133 (27%), Positives = 64/133 (48%), Gaps = 14/133 (10%)
Query: 566 RFLTGLSVGLSSPPSIVYIAESTEPRYRGAILAIVSLAISSGIFISHLLGTFL------- 618
R + G+ VGL+S S +YIAE RG +++ AI G + + + F+
Sbjct: 133 RIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDAS 192
Query: 619 -----HWKTASAVCALFPFISCIFVYSTPESPSWLASKGYSVEAEQAFHWLRGHSAESES 673
W+ A + + + +Y+ PESP WL S+G +AE + G++ +++
Sbjct: 193 WLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLATQA 252
Query: 674 --ELKSMLNHAQK 684
E+K L+H +K
Sbjct: 253 VQEIKHSLDHGRK 265
Score = 35.4 bits (80), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 22/112 (19%), Positives = 52/112 (46%), Gaps = 4/112 (3%)
Query: 907 QFSGASTVSFYSVAILQNVSADVN-EYTATMAIDILRVIMSAVTCGLLRITGRRPIAILS 965
QF G + V +Y+ + + + A + T+ + ++ + + + + GR+P+ I+
Sbjct: 289 QFVGINVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIG 348
Query: 966 SLGTAFSLLGLALMLKYPQEELPSFIPVILLMSYIVFVSFGLQPLPWIMAGE 1017
+LG A + L Y Q P + ++ ++ Y+ + P+ W++ E
Sbjct: 349 ALGMAIGMFSLGTAF-YTQA--PGIVALLSMLFYVAAFAMSWGPVCWVLLSE 397
Score = 34.7 bits (78), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 781 IIFVYFTPESPSWLASKGYTVQAEKAFHWLRGHS--DEFDNELKSILDYANS 830
++ +Y PESP WL S+G QAE + G++ + E+K LD+
Sbjct: 214 LMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLATQAVQEIKHSLDHGRK 265
>pdb|2IP4|A Chain A, Crystal Structure Of Glycinamide Ribonucleotide Synthetase
From Thermus Thermophilus Hb8
pdb|2IP4|B Chain B, Crystal Structure Of Glycinamide Ribonucleotide Synthetase
From Thermus Thermophilus Hb8
Length = 417
Score = 33.5 bits (75), Expect = 1.0, Method: Composition-based stats.
Identities = 28/101 (27%), Positives = 42/101 (41%), Gaps = 9/101 (8%)
Query: 1311 IMGWVIISLATEVWVILAGRFLTGFALGLSSPVALVYIAETTEPKYRGVLSALLCTAVAI 1370
I+G ++ L E V+ G G L P L + A +P+ + +L L V +
Sbjct: 243 ILGPLVRGLRAE-GVVYRGVVYAGLXLTREGPKVLEFNARFGDPEAQALLPLLENDLVEL 301
Query: 1371 GIFTAH--LLGTFLHWKTTSAVCALFPCASFIFAYFTPESP 1409
+ A L GT L WK +A C + + PESP
Sbjct: 302 ALRVAEGRLAGTRLSWKEGAAACVVLAAPGY------PESP 336
>pdb|1FRV|B Chain B, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|1FRV|D Chain D, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
Length = 536
Score = 33.1 bits (74), Expect = 1.3, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 408 PKYRGAFLAVSSLAISSGILVSHLLDHLPTVRHLGLVMALVGPLPQRSYLHLG 460
P+Y+G V LA +LV++ H PTV+ + LV+ +G P+ + LG
Sbjct: 360 PRYKGEAFEVGPLA---SVLVAYAKKHEPTVKAVDLVLKTLGVGPEALFSTLG 409
>pdb|1YQ9|H Chain H, Structure Of The Unready Oxidized Form Of [nife]
Hydrogenase
pdb|1YQ9|I Chain I, Structure Of The Unready Oxidized Form Of [nife]
Hydrogenase
Length = 536
Score = 31.6 bits (70), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 408 PKYRGAFLAVSSLAISSGILVSHLLDHLPTVRHLGLVMALVGPLPQRSYLHLG 460
P+Y+G V LA +LV++ H PTV+ + LV+ +G P+ + LG
Sbjct: 360 PRYKGEAFEVGPLA---SVLVAYAKKHEPTVKAVDLVLKTLGVGPEALFSTLG 409
>pdb|2FRV|L Chain L, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|2FRV|B Chain B, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|2FRV|D Chain D, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|2FRV|F Chain F, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|2FRV|H Chain H, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
pdb|2FRV|J Chain J, Crystal Structure Of The Oxidized Form Of Ni-Fe
Hydrogenase
Length = 536
Score = 31.6 bits (70), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 408 PKYRGAFLAVSSLAISSGILVSHLLDHLPTVRHLGLVMALVGPLPQRSYLHLG 460
P+Y+G V LA +LV++ H PTV+ + LV+ +G P+ + LG
Sbjct: 360 PRYKGEAFEVGPLA---SVLVAYAKKHEPTVKAVDLVLKTLGVGPEALFSTLG 409
>pdb|1WOO|A Chain A, Crystal Structure Of T-Protein Of The Glycine Cleavage
System
pdb|1WOP|A Chain A, Crystal Structure Of T-Protein Of The Glycine Cleavage
System
pdb|1WOR|A Chain A, Crystal Structure Of T-Protein Of The Glycine Cleavage
System
pdb|1WOS|A Chain A, Crystal Structure Of T-Protein Of The Glycine Cleavage
System
Length = 364
Score = 31.2 bits (69), Expect = 4.6, Method: Composition-based stats.
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 828 ANSAEKAFHWLRGHSDEFDNELKSIMD 854
A + EK F+W++ HS FD E+ +I D
Sbjct: 113 AANIEKDFNWIKSHSKNFDVEVSNISD 139
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
0.325 0.138 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 43,778,566
Number of Sequences: 62578
Number of extensions: 1634210
Number of successful extensions: 4646
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 4625
Number of HSP's gapped (non-prelim): 20
length of query: 1693
length of database: 14,973,337
effective HSP length: 112
effective length of query: 1581
effective length of database: 7,964,601
effective search space: 12592034181
effective search space used: 12592034181
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.9 bits)