RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10331
(183 letters)
>2ot3_A RAB5 GDP/GTP exchange factor; rabex-5, VPS9 domain, vesicular
traffic, protein transport; 2.10A {Homo sapiens} SCOP:
a.222.1.1 PDB: 1txu_A
Length = 274
Score = 159 bits (403), Expect = 4e-49
Identities = 87/183 (47%), Positives = 118/183 (64%), Gaps = 4/183 (2%)
Query: 1 MQNFYQTFAKRMENHKLYADVSAQDRELLLDYVEKYSMISLYPLLFCPPFTSDEDQDLEI 60
Q+FY A+RM+ V + E ++D +EKY M LY +FCP T DE +DL I
Sbjct: 59 AQDFYHNVAERMQTRG---KVPPERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKDLAI 115
Query: 61 QERIRQLKWVNAKHLDCGIEETNATVRDLVYNSMTKLLEMDSVRAPQDKLACVVACCRDI 120
Q+RIR L+WV + L + E V D+V ++T ++EMDS R P+DKLAC+ C + I
Sbjct: 116 QKRIRALRWVTPQMLCVPVNEDIPEVSDMVVKAITDIIEMDSKRVPRDKLACITKCSKHI 175
Query: 121 FLL-LQSSVGPASADEFLPALIFLVLKMNPARLKSNIHFVTRFCNANRLMSGEAGYFFTN 179
F + PASAD+FLP LI++VLK NP RL+SNI ++TRFCN +RLM+GE GY+FTN
Sbjct: 176 FNAIKITKNEPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTN 235
Query: 180 LVS 182
L
Sbjct: 236 LCC 238
>2efe_A Similarity to vacuolar protein sorting-associated VPS9; GEF,
GTPase, VPS9, nucleotide, transport protein; HET: GNH;
2.08A {Arabidopsis thaliana} PDB: 2efd_A 2efc_A* 2efh_A*
Length = 267
Score = 132 bits (334), Expect = 6e-39
Identities = 54/187 (28%), Positives = 95/187 (50%), Gaps = 9/187 (4%)
Query: 1 MQNFYQTFAKRMENHKLYADVSAQDRELLLDYVEKYSMISLYPLLFCPPFTSDEDQDLEI 60
+Q F+ H L++ S ++ + D +EKY M L+ +F +
Sbjct: 52 VQEFFSKMEAAFRAHPLWSGCSEEELDSAGDGLEKYVMTKLFTRVFASNTEEVIADEKLF 111
Query: 61 QERIRQLKWVNAKHLDCGIEETNATVRDLVYNSMTKLLEMDSVRAPQDKLACVVACCRDI 120
Q+ ++++ ++LD N + +L +++ +AP+DKL C++ CC+ I
Sbjct: 112 QKMSLVQQFISPENLDIQPTFQN---ESSWLLAQKELQKINMYKAPRDKLVCILNCCKVI 168
Query: 121 FLLLQ-----SSVGPASADEFLPALIFLVLKMNPARLKSNIHFVTRFCNANRLMSGEAGY 175
LL S+ ADEFLP LI++ +K NP +L SN+ ++ R+ ++L GEA Y
Sbjct: 169 NNLLLNASIASNENAPGADEFLPVLIYVTIKANPPQLHSNLLYIQRYRRESKL-VGEAAY 227
Query: 176 FFTNLVS 182
FFTN++S
Sbjct: 228 FFTNILS 234
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 34.9 bits (79), Expect = 0.005
Identities = 9/19 (47%), Positives = 12/19 (63%), Gaps = 2/19 (10%)
Query: 6 QTFAKRMENH-KLYADVSA 23
Q K+++ KLYAD SA
Sbjct: 20 QAL-KKLQASLKLYADDSA 37
Score = 31.5 bits (70), Expect = 0.082
Identities = 8/20 (40%), Positives = 10/20 (50%), Gaps = 7/20 (35%)
Query: 124 LQSSV---GPASADEFLPAL 140
LQ+S+ SA PAL
Sbjct: 25 LQASLKLYADDSA----PAL 40
>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 = 33.7 bits (76), Expect = 0.027
Identities = 31/222 (13%), Positives = 70/222 (31%), Gaps = 61/222 (27%)
Query: 1 MQNFYQTFAKRMENHK--------LYADVSAQDRELLLDYVEKYSMISLYPLLFCPPFTS 52
+ + + + ++ DV D ++++ + KYS++ P S
Sbjct: 371 YRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQP---KESTIS 427
Query: 53 DEDQDLEIQERIRQLKWVNAKHLDCGIEETNATVRDLVYNSMTKLLEMDSVRAPQDK--- 109
LE++ ++ ++ +D YN D + D+
Sbjct: 428 IPSIYLELKVKLENEYALHRSIVDH-------------YNIPKTFDSDDLIPPYLDQYFY 474
Query: 110 ------LACV-----VACCRDIFL---LLQSSV--------GPASADEFLPALIF---LV 144
L + + R +FL L+ + S L L F +
Sbjct: 475 SHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYI 534
Query: 145 LKMNP---ARLKSNIHFVTRFCNANRLMSGEAGYFFTNLVSI 183
+P + + + F+ + N L+ + +T+L+ I
Sbjct: 535 CDNDPKYERLVNAILDFLPK-IEEN-LICSK----YTDLLRI 570
Score = 27.1 bits (59), Expect = 3.7
Identities = 12/73 (16%), Positives = 32/73 (43%), Gaps = 6/73 (8%)
Query: 2 QNFYQTFAKRM--ENHK-LYADVSAQDRELLLD---YVEKYSMISLYPLLFCPPFTSDED 55
+ Q F + + N+K L + + + R+ + Y+E+ + +F S
Sbjct: 76 EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQ 135
Query: 56 QDLEIQERIRQLK 68
L++++ + +L+
Sbjct: 136 PYLKLRQALLELR 148
>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 = 31.9 bits (72), Expect = 0.13
Identities = 27/143 (18%), Positives = 43/143 (30%), Gaps = 58/143 (40%)
Query: 42 YPLLFCPPFTSDEDQDLEIQE-------RIRQLKWVNAKHLDCGIEETNATV---RDL-- 89
YP PP S + LE E I L + + + +TN+ + + +
Sbjct: 314 YPNTSLPP--SILEDSLENNEGVPSPMLSISNL---TQEQVQDYVNKTNSHLPAGKQVEI 368
Query: 90 -VYNSMTKLLEMDSVRAPQDKLACVVACCRDIFLLLQSSVGPASADEFLPALIFLVLKM- 147
+ N + VV+ GP + L L + K
Sbjct: 369 SLVNG------------AK---NLVVS-------------GPPQS---LYGLNLTLRKAK 397
Query: 148 NPARL-KSNIHF-------VTRF 162
P+ L +S I F RF
Sbjct: 398 APSGLDQSRIPFSERKLKFSNRF 420
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 29.1 bits (65), Expect = 1.1
Identities = 24/109 (22%), Positives = 35/109 (32%), Gaps = 29/109 (26%)
Query: 2 QNFYQTFAKRMENHKLYADV-----SAQDRELLLDYV---EKYSMISLYP-LLFCPPFT- 51
Q+ Y + + L V S QD E L++++ EK + + PF
Sbjct: 520 QSIYAKYGAK--GSTLIV-VPFNQGSKQDVEALIEFIYDTEKNGGLGWDLDAII--PFAA 574
Query: 52 --------SDEDQDLEIQERI------RQLKWVNAKHLDCGIEETNATV 86
D E RI R + V + GIE A V
Sbjct: 575 IPEQGIELEHIDSKSEFAHRIMLTNILRMMGCVKKQKSARGIETRPAQV 623
>1hp1_A 5'-nucleotidase; metallophosphatase, dinuclear, metalloenzyme,
hydrolase, domain movement; HET: ATP; 1.70A {Escherichia
coli} SCOP: d.114.1.1 d.159.1.2 PDB: 1ush_A 2ush_A
1hpu_A* 1ho5_A* 1oi8_A 1oid_A 1oie_A
Length = 516
Score = 26.9 bits (60), Expect = 4.7
Identities = 9/36 (25%), Positives = 14/36 (38%), Gaps = 4/36 (11%)
Query: 5 YQTFAKRMENHKLYADVSAQDRELLLDYVEKYSMIS 40
Y N Y + D E+L Y++K S +
Sbjct: 472 YPRLD----NKPGYVNTGFIDAEVLKAYIQKSSPLD 503
>3fzy_A RTX toxin RTXA; RTXA toxin, CPD, cysteine protease domain,
PRE-cleavage form IDP00167, structural genomics; HET:
IHP; 1.95A {Vibrio cholerae} PDB: 3eeb_A* 3gcd_A*
Length = 234
Score = 26.7 bits (58), Expect = 5.1
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 2 QNFYQTFAKRMENHKLYADVSAQDRELLLD 31
+ F F M+ + L DVS + EL +D
Sbjct: 174 KGFGHQFINAMDANGLRVDVSVRSSELAVD 203
>1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family,
transferase-D complex; HET: DNA MSE ADI; 1.70A
{Sulfolobus solfataricus} SCOP: d.240.1.1 e.8.1.7 PDB:
1jxl_A* 1n48_A* 1n56_A* 1ryr_A* 1rys_A* 1s0m_A* 1s0n_A*
1s0o_A* 1s10_A* 1s97_A* 1s9f_A* 2ia6_A* 2ibk_A* 2r8g_A*
2r8h_A* 2r8i_A* 2rdj_A* 3fds_A* 3m9m_B* 3m9n_B* ...
Length = 352
Score = 26.4 bits (59), Expect = 6.5
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 14 NHKLYADVSAQDRELLLDYVEKYSMISL 41
++Y VS++ LL +Y EK + S+
Sbjct: 77 RKEVYQQVSSRIMNLLREYSEKIEIASI 104
>3i4j_A Aminotransferase, class III; structural GENOMICS,NYSGXRC, target
11246C, pyridoxal phosphate, PSI-2, protein structure
initiative; 1.70A {Deinococcus radiodurans}
Length = 430
Score = 26.0 bits (58), Expect = 8.4
Identities = 4/23 (17%), Positives = 8/23 (34%)
Query: 44 LLFCPPFTSDEDQDLEIQERIRQ 66
LL PP + + + +
Sbjct: 401 LLLGPPLSITAAEVDGLLALLAG 423
>4a6r_A Omega transaminase; transferase, PLP-binding enzyme, transaminase
fold type I; HET: TA8; 1.35A {Chromobacterium violaceum}
PDB: 4a6t_A* 4a6u_A 4a72_A* 4ah3_A*
Length = 459
Score = 26.0 bits (58), Expect = 8.5
Identities = 3/23 (13%), Positives = 8/23 (34%)
Query: 44 LLFCPPFTSDEDQDLEIQERIRQ 66
++ PP + E+ +
Sbjct: 422 IVSAPPLVMTRAEVDEMLAVAER 444
>3nui_A Pyruvate transaminase; amino transferase, transferase; 2.00A
{Vibrio fluvialis}
Length = 478
Score = 26.0 bits (58), Expect = 8.6
Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 5/38 (13%)
Query: 44 LLFCPPFTSDEDQDLEIQERIRQ-----LKWVNAKHLD 76
++ CPPF E Q E+ +++ + V A L+
Sbjct: 435 VVLCPPFILTEAQMDEMFDKLEKALDKVFAEVAAAALE 472
>3hmu_A Aminotransferase, class III; structural genomics, pyridoxal
phosphate, PSI-2, protein structure initiative; 2.10A
{Silicibacter pomeroyi}
Length = 472
Score = 26.0 bits (58), Expect = 9.2
Identities = 6/23 (26%), Positives = 11/23 (47%)
Query: 44 LLFCPPFTSDEDQDLEIQERIRQ 66
++ PP + E+ RIR+
Sbjct: 425 MIISPPLVITPAEIDEMFVRIRK 447
>3gju_A Putative aminotransferase; pyridoxal phosphate, PLP-dependent
transferase-like fold, ST genomics, joint center for
structural genomics, JCSG; HET: MSE LLP PLP; 1.55A
{Mesorhizobium loti} PDB: 3fcr_A*
Length = 460
Score = 25.6 bits (57), Expect = 10.0
Identities = 5/23 (21%), Positives = 8/23 (34%)
Query: 44 LLFCPPFTSDEDQDLEIQERIRQ 66
L F PP +Q + +
Sbjct: 429 LGFAPPLCLTREQADIVVSKTAD 451
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
0.325 0.137 0.407
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,658,226
Number of extensions: 143615
Number of successful extensions: 425
Number of sequences better than 10.0: 1
Number of HSP's gapped: 417
Number of HSP's successfully gapped: 22
Length of query: 183
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 95
Effective length of database: 4,244,745
Effective search space: 403250775
Effective search space used: 403250775
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (24.5 bits)