RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6101
(341 letters)
>2lm4_A Succinate dehydrogenase assembly factor 2, mitoch; structural
genomics, northeast structural genomics consortiu
PSI-biology; NMR {Saccharomyces cerevisiae}
Length = 109
Score = 113 bits (285), Expect = 1e-31
Identities = 51/98 (52%), Positives = 74/98 (75%), Gaps = 6/98 (6%)
Query: 235 ERVGEPLELRKARLLYQSRKRGMLENGLLLSTFAAKYLDTMNEDLLKQYDQLINLPSNDW 294
+R EPL+ ++ARL+YQSRKRG+LE LLLS FAAKYL MNE+ L++YD L+N DW
Sbjct: 13 KRTNEPLDKKRARLIYQSRKRGILETDLLLSGFAAKYLKKMNEEELEEYDSLLNE--LDW 70
Query: 295 DIYYWATG---VRPIPLQF-NNEVMKLLQDHTKNKDRQ 328
DIYYWAT P+P ++ N++++K LQ+ ++NK+++
Sbjct: 71 DIYYWATKNFKTSPLPDKWANSKLLKQLQEFSENKEKE 108
Score = 60.2 bits (146), Expect = 8e-12
Identities = 30/84 (35%), Positives = 50/84 (59%), Gaps = 12/84 (14%)
Query: 43 RSRGGGRGCRLGD--FRHWLSN--SGMNEDLLKQYDQLINLPSNDWDIYYWATG---VRP 95
+SR RG D + + MNE+ L++YD L+N DWDIYYWAT P
Sbjct: 29 QSRK--RGILETDLLLSGFAAKYLKKMNEEELEEYDSLLNE--LDWDIYYWATKNFKTSP 84
Query: 96 IPLQF-NNEVMKLLQDHTKNKDRQ 118
+P ++ N++++K LQ+ ++NK+++
Sbjct: 85 LPDKWANSKLLKQLQEFSENKEKE 108
>1puz_A Conserved hypothetical protein; NMA1147, MR19, structural genomics,
PSI, protein structure initiative; NMR {Neisseria
meningitidis} SCOP: a.218.1.1
Length = 82
Score = 88.5 bits (220), Expect = 2e-22
Identities = 13/78 (16%), Positives = 37/78 (47%), Gaps = 3/78 (3%)
Query: 242 ELRKARLLYQSRKRGMLENGLLLSTFAAKYLDTMNEDLLKQYDQLINLPSNDWDIYYWAT 301
++ K ++ +Q+R RG+LE L+ F K + +++ L ++ +++ D ++
Sbjct: 6 DIAKRKIRFQTR-RGLLELDLIFGRFMEKEFEHLSDKELSEFSEILEF--QDQELLALIN 62
Query: 302 GVRPIPLQFNNEVMKLLQ 319
G +++ ++
Sbjct: 63 GHSETDKGHLIPMLEKIR 80
Score = 47.3 bits (113), Expect = 2e-07
Identities = 8/74 (10%), Positives = 27/74 (36%), Gaps = 15/74 (20%)
Query: 43 RSRGGGRGCR-----LGDF--RHWLSNSGMNEDLLKQYDQLINLPSNDWDIYYWATGVRP 95
++R RG G F + + +++ L ++ +++ D ++ G
Sbjct: 15 QTR---RGLLELDLIFGRFMEKEF---EHLSDKELSEFSEILEF--QDQELLALINGHSE 66
Query: 96 IPLQFNNEVMKLLQ 109
+++ ++
Sbjct: 67 TDKGHLIPMLEKIR 80
>1x6i_A Hypothetical protein YGFY; structural genomics, transcriptional
regulation, structure 2 function project, S2F, unknown
function; 1.20A {Escherichia coli} PDB: 1x6j_A
Length = 91
Score = 87.4 bits (217), Expect = 8e-22
Identities = 17/84 (20%), Positives = 38/84 (45%), Gaps = 3/84 (3%)
Query: 242 ELRKARLLYQSRKRGMLENGLLLSTFAAKYLDTMNEDLLKQYDQLINLPSNDWDIYYWAT 301
KAR+ + R RGM E + + F D++++D + + +L+ +D D++ W
Sbjct: 6 INNKARIHWACR-RGMRELDISIMPFFEHEYDSLSDDEKRIFIRLLEC--DDPDLFNWLM 62
Query: 302 GVRPIPLQFNNEVMKLLQDHTKNK 325
+++L+Q + +
Sbjct: 63 NHGKPADAELEMMVRLIQTRNRER 86
Score = 50.0 bits (120), Expect = 2e-08
Identities = 12/77 (15%), Positives = 30/77 (38%), Gaps = 9/77 (11%)
Query: 43 RSRGGGRGCRLGD--FRHWLSN--SGMNEDLLKQYDQLINLPSNDWDIYYWATGVRPIPL 98
R RG R D + + +++D + + +L+ +D D++ W
Sbjct: 15 ACR---RGMRELDISIMPFFEHEYDSLSDDEKRIFIRLLEC--DDPDLFNWLMNHGKPAD 69
Query: 99 QFNNEVMKLLQDHTKNK 115
+++L+Q + +
Sbjct: 70 AELEMMVRLIQTRNRER 86
>2jr5_A UPF0350 protein VC_2471; structure, structural genomics, PSI,
protein structure initiative, northeast structural
genomics consortium, NESG; NMR {Vibrio cholerae}
Length = 94
Score = 87.1 bits (216), Expect = 1e-21
Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 3/86 (3%)
Query: 242 ELRKARLLYQSRKRGMLENGLLLSTFAAKYLDTMNEDLLKQYDQLINLPSNDWDIYYWAT 301
+KAR+ + R RGMLE +++ F + D++ E + L+ +D D++ W
Sbjct: 4 AEQKARIKWACR-RGMLELDVVIMPFFEECFDSLTESEQDDFVALLES--DDPDLFAWVM 60
Query: 302 GVRPIPLQFNNEVMKLLQDHTKNKDR 327
G ++ + H +K R
Sbjct: 61 GHGRCENLGLAAMVDKIVAHNLSKVR 86
Score = 50.1 bits (120), Expect = 2e-08
Identities = 13/79 (16%), Positives = 24/79 (30%), Gaps = 9/79 (11%)
Query: 43 RSRGGGRGCRLGD--FRHWLSN--SGMNEDLLKQYDQLINLPSNDWDIYYWATGVRPIPL 98
R RG D + + E + L+ +D D++ W G
Sbjct: 13 ACR---RGMLELDVVIMPFFEECFDSLTESEQDDFVALLES--DDPDLFAWVMGHGRCEN 67
Query: 99 QFNNEVMKLLQDHTKNKDR 117
++ + H +K R
Sbjct: 68 LGLAAMVDKIVAHNLSKVR 86
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 54.5 bits (130), Expect = 3e-08
Identities = 48/373 (12%), Positives = 104/373 (27%), Gaps = 128/373 (34%)
Query: 23 EQHTNLMKPDLSKVQSQP---LDRSRGGGRGCRLGDFRHWLSNSGMNEDLLKQYDQLINL 79
+ + L + L +++ +D G G G + W++ D+ Y +
Sbjct: 135 QPYLKL-RQALLELRPAKNVLID----GVLGS--G--KTWVAL-----DVCLSYKVQCKM 180
Query: 80 PSNDWDIYYWAT-----GVRPIPLQFNNEVMKLLQDHTKNKDRQARLRQP--DLYETLLT 132
I+ W + + ++ + T D + ++ + L
Sbjct: 181 DFK---IF-WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRR 236
Query: 133 LQHLGIKFYGSFGIRSRALL-LDRRYCW----LSHFDL-CHGILISSDSNLS-------- 178
L K Y LL L + F+L C +L + ++
Sbjct: 237 LLKS--KPY------ENCLLVLLN--VQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATT 286
Query: 179 WNVDLEQQSPVYENVEEE----------------------PVLTSLVFCG---------- 206
++ L+ S E + P S++
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSII--AESIRDGLATW 344
Query: 207 -----------SQIVKNSVRSMSKE----------IFPPSQEPEIPA-------YQERVG 238
+ I+++S+ + +FPPS IP +
Sbjct: 345 DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAH--IPTILLSLIWFDVIKS 402
Query: 239 EPL----ELRKARLLYQSRKRGMLE-NGLLLSTFA-AKYLDTMNEDLLKQYDQLINLPSN 292
+ + +L K L+ + K + + L + ++ ++ Y+ S+
Sbjct: 403 DVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSD 462
Query: 293 D-----WDIY-YW 299
D D Y Y
Sbjct: 463 DLIPPYLDQYFYS 475
Score = 46.0 bits (108), Expect = 1e-05
Identities = 60/395 (15%), Positives = 105/395 (26%), Gaps = 125/395 (31%)
Query: 67 EDLLKQ------YDQLINLPSND-------WDI-------------------YYW-ATGV 93
+D+ K D +I W + Y + + +
Sbjct: 39 QDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPI 98
Query: 94 RPIPLQ-------FNNEVMKLLQDHTKNKDRQARLRQP--DLYETLLTLQ-HLGIKFYGS 143
+ Q + + +L D+ QP L + LL L+ + G
Sbjct: 99 KTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGV 158
Query: 144 FGI----------RSRALL--LDRRYCWLS-------------HFDLCHGI------LIS 172
G S + +D + WL+ L + I
Sbjct: 159 LGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD 218
Query: 173 SDSNLSWNVDLEQ-------QSPVYE-------NVEEEPVLTSLVFCGSQIV-----KNS 213
SN+ + Q +S YE NV+ + +I+ K
Sbjct: 219 HSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNL-SCKILLTTRFKQV 277
Query: 214 VRSMS-KEIFPPSQEPEIPAYQERVGEPLELRKARLLYQSRKRGMLE-NGLLLSTFAAKY 271
+S S + + L L+ Q R +L N LS A
Sbjct: 278 TDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESI 337
Query: 272 LDTMNE-DLLKQY--DQLI--------NLPSNDWDIYYWATGVRP----IPLQF------ 310
D + D K D+L L ++ + V P IP
Sbjct: 338 RDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWF 397
Query: 311 ---NNEVMKLLQD-HTK---NKDR-QARLRQPDLY 337
++VM ++ H K ++ + P +Y
Sbjct: 398 DVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIY 432
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 47.4 bits (112), Expect = 5e-06
Identities = 63/352 (17%), Positives = 99/352 (28%), Gaps = 136/352 (38%)
Query: 8 RSQHAKPPSQAQSACEQHTNLMKPDLSKVQSQPLDRSRGGGRGCRLGDFRHWLSNSGMNE 67
R + + LS++ LD + +G + WL N
Sbjct: 174 RDLYQTYHVLVGDLIKFSAET----LSELIRTTLDAEKVFTQGL---NILEWLEN----- 221
Query: 68 DLLKQYDQLINLPSNDWDIYYWATGVRPI--PLQFNNEVMKLLQDHTKNKDRQARLRQPD 125
PSN D Y + PI PL ++Q L
Sbjct: 222 ------------PSNTPDKDYLLSI--PISCPLIG------VIQ-----------LAH-- 248
Query: 126 LYETLLTLQHLGI-------KFYGSFGIRSRALLLDRRYCWLSHFDLCHGILIS-SDSNL 177
Y ++T + LG G+ G S+ L+ + I+ +DS
Sbjct: 249 -Y--VVTAKLLGFTPGELRSYLKGATG-HSQGLVT--------------AVAIAETDSWE 290
Query: 178 SWNVDLEQQSPVYENVEEEPVLTSLVFCGSQIVKNSVRSMSKEIFPPSQ-EPEIPAYQER 236
S+ + +V + +T L F G VR E +P + P I
Sbjct: 291 SF----------FVSVRK--AITVLFFIG-------VR--CYEAYPNTSLPPSILEDSLE 329
Query: 237 VGE----PLELRKARLLYQSRKRGMLE-NGLLLSTFAAKYLDTMNEDLLKQYDQ----LI 287
E P ML + L Y++ N L Q L+
Sbjct: 330 NNEGVPSP----------------MLSISNLTQEQ-VQDYVNKTNSH-LPAGKQVEISLV 371
Query: 288 NLPSNDWDIYYWATGVRPIPLQ-FNNEVMKLLQDHTKNKDRQARL----RQP 334
N N +G P L N + K + Q+R+ R+
Sbjct: 372 NGAKN-----LVVSG-PPQSLYGLNLTLRKA---KAPSGLDQSRIPFSERKL 414
Score = 43.5 bits (102), Expect = 8e-05
Identities = 46/231 (19%), Positives = 69/231 (29%), Gaps = 90/231 (38%)
Query: 145 GIRSRALLLDRRYCWLSHFDLCHGILISSDSNLSWNVDLEQQSPVYENVEEEPVLTSLVF 204
+R L L SH L H +L+ T+ F
Sbjct: 3 AYSTRPLTL-------SHGSLEHVLLVP---------------------------TASFF 28
Query: 205 CGSQIVKNSVRSMSKEIFPPS-QEP-EIPAYQERVGEPLELRKARLL-YQSRKRGMLENG 261
SQ+ +E F EP E A + P EL + L Y S + G
Sbjct: 29 IASQL---------QEQFNKILPEPTEGFAADDEPTTPAEL-VGKFLGYVSSLVEPSKVG 78
Query: 262 -------LLLSTFAAKYLDTMNEDL------LKQYDQLINLPSNDW-DIYYWATGV--RP 305
L L+ F YL+ D+ L Q + + + + Y A + RP
Sbjct: 79 QFDQVLNLCLTEFENCYLE--GNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRP 136
Query: 306 IPLQFNNEVMKLLQDHTKNKDRQAR-----------------LRQPDLYET 339
+ N+ L + + A+ LR DLY+T
Sbjct: 137 FDKKSNS---ALFRAV---GEGNAQLVAIFGGQGNTDDYFEELR--DLYQT 179
Score = 30.0 bits (67), Expect = 1.4
Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 17/71 (23%)
Query: 25 HTNLMKPDLSKVQSQPLDRSRGGGRGCRLG----------DFRHWLSNSGMNEDLLKQYD 74
H++L+ P + L ++ + D R LS S ++E ++ D
Sbjct: 428 HSHLLVPASDLINKD-LVKNNVSFNAKDIQIPVYDTFDGSDLRV-LSGS-ISERIV---D 481
Query: 75 QLINLPSNDWD 85
+I LP W+
Sbjct: 482 CIIRLP-VKWE 491
>2p22_B Vacuolar protein sorting-associated protein 28; endosome,
trafficking complex, VPS23, VPS28, VPS37, MVB12; 2.70A
{Saccharomyces cerevisiae}
Length = 118
Score = 26.8 bits (59), Expect = 4.5
Identities = 11/43 (25%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 94 RPIPLQFNNEVMKLLQDHTKNKDRQARLRQPDLYETLLTLQHL 136
+ I F++EV L + +KD++ ++Y ++TL H+
Sbjct: 12 QDISQLFHDEV-PLFDNSITSKDKEVIETLSEIYSIVITLDHV 53
>2f6m_B Vacuolar protein sorting-associated protein VPS28; endosomes,
trafficking complex, vacuole protei sorting, ESCRT
protein complexes; HET: DDQ; 2.10A {Saccharomyces
cerevisiae} SCOP: a.2.17.2 PDB: 2f66_B
Length = 109
Score = 26.8 bits (59), Expect = 5.2
Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 92 GVRPIPLQFNNEVMKLLQDHTKNKDRQARLRQPDLYETLLTLQHL 136
G I F++EV L + +KD++ ++Y ++TL H+
Sbjct: 1 GAMDISQLFHDEV-PLFDNSITSKDKEVIETLSEIYSIVITLDHV 44
>1bnd_A BDNF, brain derived neurotrophic factor; complex (growth
factor-growth factor) complex; 2.30A {Homo sapiens}
SCOP: g.17.1.3 PDB: 1b8m_A
Length = 119
Score = 26.6 bits (58), Expect = 6.0
Identities = 8/19 (42%), Positives = 8/19 (42%)
Query: 43 RSRGGGRGCRLGDFRHWLS 61
GCR D RHW S
Sbjct: 60 PMGYTKEGCRGIDKRHWNS 78
>1n4k_A Inositol 1,4,5-trisphosphate receptor type 1; IP3 receptor,
IP3-binding core, calcium channel,protein- ligand
complex, B-trefoil fold; HET: I3P; 2.20A {Mus musculus}
SCOP: a.118.22.1 b.42.6.1
Length = 381
Score = 27.6 bits (60), Expect = 6.9
Identities = 24/123 (19%), Positives = 48/123 (39%), Gaps = 14/123 (11%)
Query: 53 LGDFRHWLSNSGMNEDLLKQYDQLINLPSNDWDIYYWATGVRPIPLQFNNEVMKLLQDHT 112
LG L + ++ + +L+ D+ Y+ TG N+ L +
Sbjct: 230 LGSIAGKLEKGTITQNERRSVTKLLE------DLVYFVTG------GTNSGQDVLEVVFS 277
Query: 113 K-NKDRQARLRQPDLYETLLTLQHLGIKFYGSFGIRSRALLLDRRY-CWLSHFDLCHGIL 170
K N++RQ +R+ ++ + + L G + L D+R+ + LC+ +L
Sbjct: 278 KPNRERQKLMREQNILKQIFKLLQAPFTDCGDGPMLRLEELGDQRHAPFRHICRLCYRVL 337
Query: 171 ISS 173
S
Sbjct: 338 RHS 340
>2qmc_A GGT, gamma-glutamyltranspeptidase; NTN-hydrolase, transferase; HET:
GTB; 1.55A {Helicobacter pylori} PDB: 2qm6_A* 3fnm_A*
2nqo_A
Length = 377
Score = 27.2 bits (61), Expect = 8.1
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 120 RLRQPDLYETLLTLQHLGIK-FY 141
Q DL +TL ++ LG K FY
Sbjct: 208 LFVQKDLAKTLNQIKTLGAKGFY 230
>2caz_B Vacuolar protein sorting-associated protein VPS28; protein
transport, ESCRT, MVB, multivesicular bodies, endosome,
lysosome, PH domain, protein sorting; 3.6A
{Saccharomyces cerevisiae} SCOP: a.2.17.2
Length = 155
Score = 26.6 bits (58), Expect = 9.0
Identities = 11/43 (25%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 94 RPIPLQFNNEVMKLLQDHTKNKDRQARLRQPDLYETLLTLQHL 136
+ I F++EV L + +KD++ ++Y ++TL H+
Sbjct: 20 QDISQLFHDEV-PLFDNSITSKDKEVIETLSEIYSIVITLDHV 61
>1ou5_A TRNA CCA-adding enzyme, tRNA-nucleotidyltransferase; polymerase,
translation; 3.40A {Homo sapiens} SCOP: a.173.1.1
d.218.1.4
Length = 448
Score = 27.1 bits (60), Expect = 9.1
Identities = 8/38 (21%), Positives = 13/38 (34%), Gaps = 9/38 (23%)
Query: 74 DQLINLPSNDWDIYYWATGVRPIPLQFNNEVMKLLQDH 111
D L + D D AT P ++ ++ Q
Sbjct: 82 DLLNGVKPQDIDF---ATTATP------TQMKEMFQSA 110
Score = 27.1 bits (60), Expect = 9.1
Identities = 8/38 (21%), Positives = 13/38 (34%), Gaps = 9/38 (23%)
Query: 284 DQLINLPSNDWDIYYWATGVRPIPLQFNNEVMKLLQDH 321
D L + D D AT P ++ ++ Q
Sbjct: 82 DLLNGVKPQDIDF---ATTATP------TQMKEMFQSA 110
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.318 0.135 0.411
Gapped
Lambda K H
0.267 0.0439 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,160,529
Number of extensions: 299428
Number of successful extensions: 642
Number of sequences better than 10.0: 1
Number of HSP's gapped: 626
Number of HSP's successfully gapped: 27
Length of query: 341
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 247
Effective length of database: 4,077,219
Effective search space: 1007073093
Effective search space used: 1007073093
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)