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_011_C24
(867 letters)
Database: Non-redundant SwissProt sequences
184,735 sequences; 68,354,980 total letters
Score E
Sequences producing significant alignments: (bits) Value
sp|Q8N3Z6|ZCHC7_HUMAN Zinc finger CCHC domain containing pr... 49 2e-05
sp|P31634|GAG_SIVMS Gag polyprotein [Contains: Core protein... 37 0.071
sp|P24106|GAG_HV2CA Gag polyprotein (Pr55Gag) [Contains: Ma... 35 0.35
sp|P24107|POL_HV2CA Gag-Pol polyprotein (Pr160Gag-Pol) [Con... 35 0.35
sp|P40507|YIH9_YEAST Hypothetical 41.6 kDa protein in SDS3-... 33 1.0
sp|P51763|RCEM_CHRVI Reaction center protein M chain (Photo... 33 1.3
sp|P17756|GAG_HV2D1 Gag polyprotein (Pr55Gag) [Contains: Ma... 32 1.7
sp|Q74119|GAG_HV2KR Gag polyprotein (Pr55Gag) [Contains: Ma... 32 1.7
sp|Q74120|POL_HV2KR Gag-Pol polyprotein (Pr160Gag-Pol) [Con... 32 1.7
sp|P17757|POL_HV2D1 Gag-Pol polyprotein (Pr160Gag-Pol) [Con... 32 1.7
>sp|Q8N3Z6|ZCHC7_HUMAN Zinc finger CCHC domain containing protein 7
Length = 542
Score = 48.5 bits (114), Expect = 2e-05
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Frame = +2
Query: 485 CPDVWRQYKYTVTPGPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNRMRSKFLGPPPI 664
C ++WRQY T PGPP + S+ C +CA+ GH+ +C + P P+
Sbjct: 318 CTEIWRQYHLTTKPGPPKKPKTPSRPSALAYCYHCAQKGHYGHECPEREV----YDPSPV 373
Query: 665 MEIIKF--DHFDIYQ 703
I + D ++I +
Sbjct: 374 SPFICYYDDKYEIQE 388
Score = 31.2 bits (69), Expect = 3.9
Identities = 17/43 (39%), Positives = 22/43 (51%)
Frame = +2
Query: 491 DVWRQYKYTVTPGPPVFQRFSSQNKTTVCCANCAKNGHFTEQC 619
D+ Q TPG QR+ S NK +C NC K GH ++ C
Sbjct: 215 DIEAQIANNRTPGRWT-QRYYSANKNIIC-RNCDKRGHLSKNC 255
>sp|P31634|GAG_SIVMS Gag polyprotein [Contains: Core protein p17; Core protein p24]
Length = 510
Score = 37.0 bits (84), Expect = 0.071
Identities = 17/41 (41%), Positives = 19/41 (46%)
Frame = +2
Query: 509 KYTVTPGPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 631
K PGP F Q + TV C NC K GH +QC R
Sbjct: 370 KEAFQPGPLPFAAAQQQGRRTVKCWNCGKEGHTAKQCKAPR 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 = 0.35
Identities = 14/35 (40%), Positives = 18/35 (51%)
Frame = +2
Query: 527 GPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 631
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 = 0.35
Identities = 14/35 (40%), Positives = 18/35 (51%)
Frame = +2
Query: 527 GPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 631
GPP ++Q + T+ C NC K GH QC R
Sbjct: 374 GPPPIPFAAAQQRRTIKCWNCGKEGHSARQCRAPR 408
>sp|P40507|YIH9_YEAST Hypothetical 41.6 kDa protein in SDS3-THS1 intergenic region
Length = 360
Score = 33.1 bits (74), Expect = 1.0
Identities = 18/52 (34%), Positives = 20/52 (38%), Gaps = 3/52 (5%)
Frame = +2
Query: 485 CPDVWRQYKYTV---TPGPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 631
CP +WR Y G FQ TV C NC GHF + C R
Sbjct: 149 CPSIWRSYLLKTKDANQGDFDFQ--------TVFCYNCGNAGHFGDDCAERR 192
>sp|P51763|RCEM_CHRVI Reaction center protein M chain (Photosynthetic reaction center M
subunit)
Length = 325
Score = 32.7 bits (73), Expect = 1.3
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Frame = -3
Query: 586 ICTTNCGFILTGKSLENWWSW--RHGIFILSPNIWTNLKNY 470
+ T G +LTG +ENW+ W +HG+ P + T + Y
Sbjct: 277 VITAGIGILLTGTVVENWYLWAIKHGVAPAYPEVVTAVDPY 317
>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 = 32.3 bits (72), Expect = 1.7
Identities = 15/41 (36%), Positives = 21/41 (51%)
Frame = +2
Query: 509 KYTVTPGPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 631
K +TP P F ++Q + + C NC K GH +QC R
Sbjct: 370 KEALTPAPIPFA--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 = 32.3 bits (72), Expect = 1.7
Identities = 15/41 (36%), Positives = 21/41 (51%)
Frame = +2
Query: 509 KYTVTPGPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 631
K + P P F ++Q + T+ C NC K+GH QC R
Sbjct: 370 KEALAPAPIPFA--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 = 32.3 bits (72), Expect = 1.7
Identities = 15/41 (36%), Positives = 21/41 (51%)
Frame = +2
Query: 509 KYTVTPGPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 631
K + P P F ++Q + T+ C NC K+GH QC R
Sbjct: 370 KEALAPAPIPFA--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 = 32.3 bits (72), Expect = 1.7
Identities = 15/41 (36%), Positives = 21/41 (51%)
Frame = +2
Query: 509 KYTVTPGPPVFQRFSSQNKTTVCCANCAKNGHFTEQCTRNR 631
K +TP P F ++Q + + C NC K GH +QC R
Sbjct: 370 KEALTPAPIPFA--AAQQRRAIRCWNCGKEGHSAKQCRAPR 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: 94,078,051
Number of Sequences: 369166
Number of extensions: 1852030
Number of successful extensions: 4219
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 3997
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): 4218
length of database: 68,354,980
effective HSP length: 110
effective length of database: 48,034,130
effective search space used: 8550075140
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)