Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
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.
Query= Dr_sW_023_B12
(303 letters)
Database: Non-redundant SwissProt sequences
184,735 sequences; 68,354,980 total letters
Score E
Sequences producing significant alignments: (bits) Value
sp|P31634|GAG_SIVMS Gag polyprotein [Contains: Core protein... 37 0.019
sp|P24106|GAG_HV2CA Gag polyprotein (Pr55Gag) [Contains: Ma... 35 0.071
sp|P24107|POL_HV2CA Gag-Pol polyprotein (Pr160Gag-Pol) [Con... 35 0.071
sp|Q8N3Z6|ZCHC7_HUMAN Zinc finger CCHC domain containing pr... 33 0.16
sp|P17756|GAG_HV2D1 Gag polyprotein (Pr55Gag) [Contains: Ma... 31 0.78
sp|Q74119|GAG_HV2KR Gag polyprotein (Pr55Gag) [Contains: Ma... 31 0.78
sp|Q74120|POL_HV2KR Gag-Pol polyprotein (Pr160Gag-Pol) [Con... 31 0.78
sp|P17757|POL_HV2D1 Gag-Pol polyprotein (Pr160Gag-Pol) [Con... 31 0.78
sp|P20874|GAG_HV2ST Gag polyprotein (Pr55Gag) [Contains: Ma... 31 1.0
sp|P20876|POL_HV2ST Gag-Pol polyprotein (Pr160Gag-Pol) [Con... 31 1.0
>sp|P31634|GAG_SIVMS Gag polyprotein [Contains: Core protein p17; Core protein p24]
Length = 510
Score = 36.6 bits (83), Expect = 0.019
Identities = 16/36 (44%), Positives = 18/36 (50%)
Frame = +2
Query: 11 PGPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 118
PGP F Q + TV C NC K GH +QC R
Sbjct: 375 PGPLPFAAAQQQGRRTVKCWNCGKEGHTAKQCKAPR 410
>sp|P24106|GAG_HV2CA Gag polyprotein (Pr55Gag) [Contains: Matrix protein p17 (MA);
Capsid protein p24 (CA); Spacer peptide p2; Nucleocapsid
protein p7 (NC); Spacer peptide p1; Protein p6]
Length = 521
Score = 34.7 bits (78), Expect = 0.071
Identities = 14/35 (40%), Positives = 18/35 (51%)
Frame = +2
Query: 14 GPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 118
GPP ++Q + T+ C NC K GH QC R
Sbjct: 374 GPPPIPFAAAQQRRTIKCWNCGKEGHSARQCRAPR 408
>sp|P24107|POL_HV2CA Gag-Pol polyprotein (Pr160Gag-Pol) [Contains: Matrix protein p17
(MA); Capsid protein p24 (CA); p2 spacer peptide;
Nucleocapsid protein* (NC*); Transframe peptide (TF) (p6
pol); Protease (Retropepsin) (PR); Reverse
transcriptase/ribonuclease H (p66 RT); p51 RT; p15;
Integrase (IN)]
Length = 1462
Score = 34.7 bits (78), Expect = 0.071
Identities = 14/35 (40%), Positives = 18/35 (51%)
Frame = +2
Query: 14 GPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 118
GPP ++Q + T+ C NC K GH QC R
Sbjct: 374 GPPPIPFAAAQQRRTIKCWNCGKEGHSARQCRAPR 408
>sp|Q8N3Z6|ZCHC7_HUMAN Zinc finger CCHC domain containing protein 7
Length = 542
Score = 33.5 bits (75), Expect = 0.16
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Frame = +2
Query: 2 TVTPGPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNRMRSKFLGPPPIMEIIKF--DH 175
T PGPP + S+ C +CA+ GH+ +C + P P+ I + D
Sbjct: 328 TTKPGPPKKPKTPSRPSALAYCYHCAQKGHYGHECPEREV----YDPSPVSPFICYYDDK 383
Query: 176 FDIYQ 190
++I +
Sbjct: 384 YEIQE 388
Score = 30.0 bits (66), Expect = 1.7
Identities = 12/26 (46%), Positives = 16/26 (61%)
Frame = +2
Query: 29 QRFSSQNKTTVCCANCAKNGHFTEQC 106
QR+ S NK +C NC K GH ++ C
Sbjct: 231 QRYYSANKNIIC-RNCDKRGHLSKNC 255
>sp|P17756|GAG_HV2D1 Gag polyprotein (Pr55Gag) [Contains: Matrix protein p17 (MA);
Capsid protein p24 (CA); Spacer peptide p2; Nucleocapsid
protein p7 (NC); Spacer peptide p1; Protein p6]
Length = 521
Score = 31.2 bits (69), Expect = 0.78
Identities = 14/38 (36%), Positives = 20/38 (52%)
Frame = +2
Query: 5 VTPGPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 118
+TP P F ++Q + + C NC K GH +QC R
Sbjct: 373 LTPAPIPFA--AAQQRRAIRCWNCGKEGHSAKQCRAPR 408
>sp|Q74119|GAG_HV2KR Gag polyprotein (Pr55Gag) [Contains: Matrix protein p17 (MA);
Capsid protein p24 (CA); Spacer peptide p2; Nucleocapsid
protein p7 (NC); Spacer peptide p1; Protein p6]
Length = 521
Score = 31.2 bits (69), Expect = 0.78
Identities = 14/38 (36%), Positives = 20/38 (52%)
Frame = +2
Query: 5 VTPGPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 118
+ P P F ++Q + T+ C NC K+GH QC R
Sbjct: 373 LAPAPIPFA--AAQQRRTIKCWNCGKDGHSARQCRAPR 408
>sp|Q74120|POL_HV2KR Gag-Pol polyprotein (Pr160Gag-Pol) [Contains: Matrix protein p17
(MA); Capsid protein p24 (CA); p2 spacer peptide;
Nucleocapsid protein* (NC*); Transframe peptide (TF) (p6
pol); Protease (Retropepsin) (PR); Reverse
transcriptase/ribonuclease H (p66 RT); p51 RT; p15;
Integrase (IN)]
Length = 1463
Score = 31.2 bits (69), Expect = 0.78
Identities = 14/38 (36%), Positives = 20/38 (52%)
Frame = +2
Query: 5 VTPGPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 118
+ P P F ++Q + T+ C NC K+GH QC R
Sbjct: 373 LAPAPIPFA--AAQQRRTIKCWNCGKDGHSARQCRAPR 408
>sp|P17757|POL_HV2D1 Gag-Pol polyprotein (Pr160Gag-Pol) [Contains: Matrix protein p17
(MA); Capsid protein p24 (CA); p2 spacer peptide;
Nucleocapsid protein* (NC*); Transframe peptide (TF) (p6
pol); Protease (Retropepsin) (PR); Reverse
transcriptase/ribonuclease H (p66 RT); p51 RT; p15;
Integrase (IN)]
Length = 1462
Score = 31.2 bits (69), Expect = 0.78
Identities = 14/38 (36%), Positives = 20/38 (52%)
Frame = +2
Query: 5 VTPGPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 118
+TP P F ++Q + + C NC K GH +QC R
Sbjct: 373 LTPAPIPFA--AAQQRRAIRCWNCGKEGHSAKQCRAPR 408
>sp|P20874|GAG_HV2ST Gag polyprotein (Pr55Gag) [Contains: Matrix protein p17 (MA);
Capsid protein p24 (CA); Spacer peptide p2; Nucleocapsid
protein p7 (NC); Spacer peptide p1; Protein p6]
Length = 521
Score = 30.8 bits (68), Expect = 1.0
Identities = 14/38 (36%), Positives = 19/38 (50%)
Frame = +2
Query: 5 VTPGPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 118
+ P P F ++Q + T+ C NC K GH QC R
Sbjct: 373 MAPAPIPFA--AAQQRRTIKCWNCGKEGHSARQCRAPR 408
>sp|P20876|POL_HV2ST Gag-Pol polyprotein (Pr160Gag-Pol) [Contains: Matrix protein p17
(MA); Capsid protein p24 (CA); p2 spacer peptide;
Nucleocapsid protein* (NC*); Transframe peptide (TF) (p6
pol); Protease (Retropepsin) (PR); Reverse
transcriptase/ribonuclease H (p66 RT); p51 RT; p15;
Integrase (IN)]
Length = 1463
Score = 30.8 bits (68), Expect = 1.0
Identities = 14/38 (36%), Positives = 19/38 (50%)
Frame = +2
Query: 5 VTPGPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 118
+ P P F ++Q + T+ C NC K GH QC R
Sbjct: 373 MAPAPIPFA--AAQQRRTIKCWNCGKEGHSARQCRAPR 408
Database: Non-redundant SwissProt sequences
Posted date: Dec 6, 2005 7:40 AM
Number of letters in database: 68,354,980
Number of sequences in database: 184,735
Database: swissprot.01
Posted date: Dec 6, 2005 8:18 AM
Number of letters in database: 66,202,850
Number of sequences in database: 184,431
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 37,876,673
Number of Sequences: 369166
Number of extensions: 672381
Number of successful extensions: 1792
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 1647
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 1792
length of database: 68,354,980
effective HSP length: 69
effective length of database: 55,608,265
effective search space used: 1723856215
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)