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= 008020
(581 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XUT|A Chain A, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter.
pdb|2XUT|B Chain B, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter.
pdb|2XUT|C Chain C, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter
Length = 524
Score = 86.7 bits (213), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 114/484 (23%), Positives = 195/484 (40%), Gaps = 65/484 (13%)
Query: 19 PADRSKTGGWVPAALSLGIEICERLSTMGIAVNLVTYLGGTM------HLPSATSANIVT 72
P D K +P ++ E CER S G+ L +L + L A + ++
Sbjct: 4 PVDAPKWPRQIPYIIA--SEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFH 61
Query: 73 DFMGTSFLLCLLGGFLADSFLGRYRTIAIFATVQTFGTGLLAISTKQPQLRPPPCQATDI 132
F+ + LLGG++AD F G+Y TI + + G LAI Q
Sbjct: 62 SFVIGVYFFPLLGGWIADRFFGKYNTILWLSLIYCVGHAFLAIFEHSVQ----------- 110
Query: 133 TKCQHASGIQMGVLYISLYLIALGTGGLKSSVSGFGTDQFDEKDEKEKTQMAYFFSRFFF 192
Y L+LIALG+GG+K VS F DQFD+ + K Q A F F+F
Sbjct: 111 ------------GFYTGLFLIALGSGGIKPLVSSFMGDQFDQSN-KSLAQKA--FDMFYF 155
Query: 193 VISTGTLMAVTVLVYIQDEVGRSWGYGICSICMFTAILIFLSGTRRYRY-----KKCSG- 246
I+ G+ A + + G + +GI + MF A + F G +RY + K G
Sbjct: 156 TINFGSFFASLSMPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGF 215
Query: 247 SPIVH---ICQXXXXXXXXXXXELPSSTASLYE--DYPEESRIQHTYQFRCLDKASVVTN 301
P++ + + L ++ Y + P + L V
Sbjct: 216 LPVIRSALLTKVEGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLVMGFVGAG 275
Query: 302 TDYSEDGAFVSNPWTLCPVTRVEEVKMVIRLLPIWATTILFWSTYAQMITFSVEQATTMQ 361
+ A S+P V+ V+ V+R+L ++A FWS + Q + + QA M
Sbjct: 276 ASLQLERARKSHP-----DAAVDGVRSVLRILVLFALVTPFWSLFDQKASTWILQANDMV 330
Query: 362 RSIGNFKIPAASLTVFFVAAILITLGAYDRLIIPLLKKRKGKPGFSNLQLIAIGLFLSAL 421
+ + PA + +++ L ++ ++ +R G ++L A+ + +
Sbjct: 331 KP--QWFEPAMMQAL--NPLLVMLLIPFNNFVLYPAIERMG------VKLTALRKMGAGI 380
Query: 422 GMASASVVEVKRLAVAKANGTTGTTLPISVFYLIPQFFLVGSGEGFMYTGQLDFFITQSP 481
+ S + V + + G+ +S+F+ I + L+ GE + L+F +Q+P
Sbjct: 381 AITGLSWIVVGTIQLMMDGGSA-----LSIFWQILPYALLTFGEVLVSATGLEFAYSQAP 435
Query: 482 KGMK 485
K MK
Sbjct: 436 KAMK 439
>pdb|4APS|A Chain A, Crystal Structure Of A Pot Family Peptide Transporter In
An Inward Open Conformation.
pdb|4APS|B Chain B, Crystal Structure Of A Pot Family Peptide Transporter In
An Inward Open Conformation
Length = 491
Score = 60.5 bits (145), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 59/225 (26%), Positives = 98/225 (43%), Gaps = 35/225 (15%)
Query: 21 DRSKTGGWVPAALS--LGIEICERLSTMGIAVNLVTYLG-----GTMHLPSATSANIVTD 73
D+ KT P LS E+ ER S G+ L+ Y+ G +H+ AT+A+I+
Sbjct: 3 DKGKTFFGQPLGLSTLFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAI 62
Query: 74 FMGTSFLLCLLGGFLADSFLGRYRTIAIFATVQTFGTGLLAISTKQPQLRPPPCQATDIT 133
+ +L +GGF+AD +G + + G +LA+ P A+
Sbjct: 63 YASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIVLAL----------PFGAS--- 109
Query: 134 KCQHASGIQMGVLYISLYLIALGTGGLKSSVSGFGTDQFDEKDEKEKTQMAYFFSRFFFV 193
L+ S+ LI +GTG LK +VS +DE D + FS F F
Sbjct: 110 -----------ALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAG----FSIFVFG 154
Query: 194 ISTGTLMAVTVLVYIQDEVGRSWGYGICSICMFTAILIFLSGTRR 238
I+ G +A ++ Q+ G + + +I MF +L++ G ++
Sbjct: 155 INLGAFIAPLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFGGKK 199
>pdb|1WX0|A Chain A, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|B Chain B, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|C Chain C, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|D Chain D, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|E Chain E, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|F Chain F, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|G Chain G, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|H Chain H, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|I Chain I, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|J Chain J, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
Length = 223
Score = 33.5 bits (75), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 39/87 (44%), Gaps = 8/87 (9%)
Query: 36 GIEICERLSTMGIAVNLVTYLGGTMHLPSATS-ANIVTDFMGTSFLLCLLGGFLADSFLG 94
G++ C+RLS GI VN+ L +A + A+ V+ F+G + GG L
Sbjct: 99 GLKACKRLSAEGIKVNMTLIFSANQALLAARAGASYVSPFLGRVDDISWDGGEL------ 152
Query: 95 RYRTIAIFATVQTFGTGLLAISTKQPQ 121
R I VQ ++A S + P+
Sbjct: 153 -LREIVEMIQVQDLPVKVIAASIRHPR 178
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
0.324 0.137 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,815,707
Number of Sequences: 62578
Number of extensions: 613432
Number of successful extensions: 1258
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1250
Number of HSP's gapped (non-prelim): 6
length of query: 581
length of database: 14,973,337
effective HSP length: 104
effective length of query: 477
effective length of database: 8,465,225
effective search space: 4037912325
effective search space used: 4037912325
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 54 (25.4 bits)