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 composition-based statistics:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,
Eugene V. Koonin, and Stephen F. Altschul (2001),
"Improving the accuracy of PSI-BLAST protein database searches with
composition-based statistics and other refinements", Nucleic Acids Res. 29:2994-3005.
Query= SelTryp; hypothetical protein [Trypanosoma brucei TREU927]
PARTIALLY FROM XP_844760.1
(259 letters)
Database: genome.fa
35 sequences; 31,379,198 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
gi|154340161|ref|NC_009319.1| Leishmania braziliensis MHOM/BR/75... 109 2e-24
gi|154342106|ref|NC_009322.1| Leishmania braziliensis MHOM/BR/75... 30 1.6
gi|154344351|ref|NC_009325.1| Leishmania braziliensis MHOM/BR/75... 28 8.5
>gi|154340161|ref|NC_009319.1| Leishmania braziliensis MHOM/BR/75/M2904
chromosome 27
Length = 1217395
Score = 109 bits (272), Expect = 2e-24, Method: Composition-based stats.
Identities = 61/155 (39%), Positives = 91/155 (58%)
Frame = +1
Query: 95 TVQHEVRVEYCSGUGYRRHYEEVAESLLRSLPPELREQQKGKKPFIKFVGVVYSVGAFRE 154
+V H++ + YC+G GY +++E++ + L R LP ++ VG Y R
Sbjct: 122362 SVVHKLEILYCTG*GYAKYFEDMKQQLQRVLP---------NAGDVQIVGGTYPTPPARA 122514
Query: 155 FIGNILSTGFLASIAISFFAPFLRGALPPHIAEWIEQHRGMVVGAGFMMNMVASSLLQSG 214
+ ST FLAS+ ++ L LPP +I Q RGM+VG GF++NM+ SSL Q+G
Sbjct: 122515 LAAKVCSTAFLASLGMALAGGQL-AFLPPAALNFIVQQRGMLVGTGFLLNMIGSSLTQTG 122691
Query: 215 AFEVYLNGSLIYSKLETGAVPTAETLADHILRQII 249
AFEV L+G LI+SKL+ GAVPT E + IL++ +
Sbjct: 122692 AFEVTLDGELIFSKLQAGAVPTVEVMRRIILQKTL 122796
Score = 58.9 bits (141), Expect = 3e-09, Method: Composition-based stats.
Identities = 45/156 (28%), Positives = 78/156 (50%), Gaps = 4/156 (2%)
Frame = +2
Query: 98 HEVRVEYCSGUGYRRHYEEVAESLLRSLPPELREQQKGKKPFI---KFVGVVYSVGAFRE 154
HEV + GY +EE L EL+E + P + +G V + R
Sbjct: 120077 HEVLAHHNEANGYGSEFEE--------LRKELQESEAVSLPNLADLDIIGQVSPISPNRV 120232
Query: 155 FIGNILSTGFLASIAISFFAPFLRGALPPHIAEWIEQHRGMVVGAGFMMNMVASSLLQSG 214
+ L F A++ ++F ++ +P + Q R +++ ++++++ + L S
Sbjct: 120233 LVSKALQGAFFATLGVAFMGDQIK-FIPESARAVLLQRRSLIISGSLLLSVLSRAALPSN 120409
Query: 215 AFEVYLNGSLIYSKLETGA-VPTAETLADHILRQII 249
AFEV+L+G LIYS L+TG VPTAE L++ +L Q +
Sbjct: 120410 AFEVFLDGELIYSALDTGGRVPTAELLSNLLLEQTL 120517
Score = 47.8 bits (112), Expect = 8e-06, Method: Composition-based stats.
Identities = 36/82 (43%), Positives = 44/82 (53%), Gaps = 3/82 (3%)
Frame = +1
Query: 8 ISFSLALLIAAFLAANAGSATNADNEATDYSSHRYKYLEMLKEADLKQMLHEKGEA---F 64
I SLALL F A A SA + + Y YL ML E DL+Q+LHEK
Sbjct: 121831 IVVSLALLFV-FAACRANSAHEV-QPTQEGNKDPYAYLGMLDEVDLQQILHEKTHGQVQV 122004
Query: 65 HHLRSKRELILAVLKLEKREEA 86
RSK EL+ AV K+E+RE+A
Sbjct: 122005 SAFRSKEELVAAVRKIEEREDA 122070
>gi|154342106|ref|NC_009322.1| Leishmania braziliensis MHOM/BR/75/M2904
chromosome 30
Length = 1359875
Score = 30.0 bits (66), Expect = 1.6, Method: Composition-based stats.
Identities = 15/41 (36%), Positives = 21/41 (51%)
Frame = +1
Query: 1 MRNRFVRISFSLALLIAAFLAANAGSATNADNEATDYSSHR 41
+R R VRI+ + L I LA N+GSA + +HR
Sbjct: 514636 LRIRIVRITVIMVLFIYRLLAVNSGSAVPKGHRCCAICTHR 514758
Score = 29.3 bits (64), Expect = 2.7, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 23/42 (54%)
Frame = +3
Query: 83 REEALRKARVTDTVQHEVRVEYCSGUGYRRHYEEVAESLLRS 124
R A+R++ D+ EVR C G+RR ++ +LLR+
Sbjct: 624681 RSVAIRRSTTADSPSMEVRARVCCVCGHRRTAAQMRCTLLRT 624806
>gi|154344351|ref|NC_009325.1| Leishmania braziliensis MHOM/BR/75/M2904
chromosome 33
Length = 1504429
Score = 27.7 bits (60), Expect = 8.5, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Frame = -2
Query: 87 LRKARVTDTVQHEVRVEYCSGUGYR-RHYEEVAESLLRSLPPELREQQKG 135
LR A ++DT +HE V C G +R + + + +L L EL+ + G
Sbjct: 755490 LRGAHISDTQRHEPHVAECDGEQHRVVCFPSIQQCILERLLGELKLTEGG 755341
Database: genome.fa
Posted date: Feb 19, 2009 11:18 PM
Number of letters in database: 31,379,198
Number of sequences in database: 35
Lambda K H
0.312 0.131 0.377
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 35
Number of Hits to DB: 47,123,283
Number of extensions: 727040
Number of successful extensions: 5850
Number of sequences better than 10.0: 35
Number of HSP's gapped: 5826
Number of HSP's successfully gapped: 310
Length of database: 10,459,732
Neighboring words threshold: 13
Window for multiple hits: 40
X1: 15 ( 6.7 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (20.9 bits)
S2: 53 (25.0 bits)