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_026_H03
(365 letters)
Database: Non-redundant SwissProt sequences
184,735 sequences; 68,354,980 total letters
Score E
Sequences producing significant alignments: (bits) Value
sp|P04052|RPB1_DROME DNA-directed RNA polymerase II largest... 34 0.092
sp|Q61140|BCA1_MOUSE CRK-associated substrate (p130cas) (Br... 34 0.12
sp|P16356|RPB1_CAEEL DNA-directed RNA polymerase II largest... 33 0.21
sp|P35074|RPB1_CAEBR DNA-directed RNA polymerase II largest... 32 0.46
sp|O74252|STEA_EMENI Transcription factor SteA 31 0.78
sp|P08775|RPB1_MOUSE DNA-directed RNA polymerase II largest... 31 1.0
sp|P14248|RPB1_PLAFD DNA-directed RNA polymerase II largest... 31 1.0
sp|Q01705|NOTC1_MOUSE Neurogenic locus notch homolog protei... 30 1.7
sp|P24928|RPB1_HUMAN DNA-directed RNA polymerase II largest... 30 2.3
sp|P11414|RPB1_CRIGR DNA-directed RNA polymerase II largest... 30 2.3
>sp|P04052|RPB1_DROME DNA-directed RNA polymerase II largest subunit
Length = 1887
Score = 34.3 bits (77), Expect = 0.092
Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 6/84 (7%)
Frame = +2
Query: 2 PSGPKYSVGQYLHYDKSKEGPGPADYKVGSP------DLFLTASPKYTMGSGAQMPDSRL 163
P+ P YS H ++ P + Y SP ++ +S KY+ S P +R
Sbjct: 1793 PTSPLYSPSSPQHSPSNQYSPTGSTYSATSPRYSPNMSIYSPSSTKYSPTSPTYTPTARN 1852
Query: 164 LTPSPAHYKHEMVTSHLPGSPAFT 235
+P+ Y + + P SPA++
Sbjct: 1853 YSPTSPMYSPTAPSHYSPTSPAYS 1876
Score = 28.1 bits (61), Expect = 6.6
Identities = 25/62 (40%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Frame = +2
Query: 2 PSGPKYSVGQYLHYDKSKEGPGPADYKVGSPDLFLTASPKYTMGSGAQMPDSRLLTP-SP 178
P+ P YS YD S PG Y GSP + ASPKY+ P S L +P SP
Sbjct: 1756 PTSPTYSPPSP-SYDGS---PGSPQYTPGSPQ-YSPASPKYS-------PTSPLYSPSSP 1803
Query: 179 AH 184
H
Sbjct: 1804 QH 1805
>sp|Q61140|BCA1_MOUSE CRK-associated substrate (p130cas) (Breast cancer anti-estrogen
resistance 1 protein)
Length = 874
Score = 33.9 bits (76), Expect = 0.12
Identities = 25/91 (27%), Positives = 38/91 (41%), Gaps = 2/91 (2%)
Frame = +2
Query: 41 YDKSKEGPGPADYKVGSPDLFLTASPKYTMGSGAQMPDSRLLTPS-PAHYKHEMVTSHLP 217
YDK GPGP G P P G A +P + +P P Y+ + +L
Sbjct: 67 YDKKPAGPGP-----GPPATPPQPQPSLPQGVHAPVPPASQYSPMLPTAYQPQSDNVYLV 121
Query: 218 GSPAFT-MGIIHSPYKGEHFREPPIED*NIF 307
+P+ T G+ +P F+ PP + + F
Sbjct: 122 PTPSKTQQGLYQAPGPNPQFQSPPAKQTSTF 152
>sp|P16356|RPB1_CAEEL DNA-directed RNA polymerase II largest subunit
Length = 1852
Score = 33.1 bits (74), Expect = 0.21
Identities = 28/101 (27%), Positives = 38/101 (37%), Gaps = 1/101 (0%)
Frame = +2
Query: 2 PSGPKYSVGQYLHYDKSKEGPGPADYKVGSPDLFLTASPKYTMGSGAQMPDSRLLTPSPA 181
PS P Y+ + S G Y SP + SP YT S P S TPSP+
Sbjct: 1753 PSSPTYTPSSPTYNPTSPRGFSSPQYSPTSPT-YSPTSPSYTPSSPQYSPTSPTYTPSPS 1811
Query: 182 HYKHEMVTSHLPGSPAFT-MGIIHSPYKGEHFREPPIED*N 301
+ + P SP ++ +SP + P D N
Sbjct: 1812 E-QPGTSAQYSPTSPTYSPSSPTYSPASPSYSPSSPTYDPN 1851
Score = 29.6 bits (65), Expect = 2.3
Identities = 19/62 (30%), Positives = 23/62 (37%)
Frame = +2
Query: 2 PSGPKYSVGQYLHYDKSKEGPGPADYKVGSPDLFLTASPKYTMGSGAQMPDSRLLTPSPA 181
P+ P Y G K P Y SP + SP+Y+ S P S TPS
Sbjct: 1705 PTSPSYESGGGYSPSSPKYSPSSPTYSPTSPS-YSPTSPQYSPTSPQYSPSSPTYTPSSP 1763
Query: 182 HY 187
Y
Sbjct: 1764 TY 1765
>sp|P35074|RPB1_CAEBR DNA-directed RNA polymerase II largest subunit
Length = 1853
Score = 32.0 bits (71), Expect = 0.46
Identities = 23/78 (29%), Positives = 30/78 (38%)
Frame = +2
Query: 2 PSGPKYSVGQYLHYDKSKEGPGPADYKVGSPDLFLTASPKYTMGSGAQMPDSRLLTPSPA 181
PS P Y+ + S Y SP + SP YT S P S TPSPA
Sbjct: 1754 PSSPTYTPSSPTYNPTSPRAFSSPQYSPTSPT-YSPTSPSYTPSSPQYSPTSPTYTPSPA 1812
Query: 182 HYKHEMVTSHLPGSPAFT 235
+ + P SP ++
Sbjct: 1813 D-QPGTSNQYSPSSPTYS 1829
>sp|O74252|STEA_EMENI Transcription factor SteA
Length = 692
Score = 31.2 bits (69), Expect = 0.78
Identities = 24/65 (36%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Frame = +2
Query: 59 GPGPADYKVGSPDLFLTASPKYTMGSG----AQMPDSRLLT---PSPAHYKHEMVTSHLP 217
GP PA Y TA P+ + GSG +P S L + P+PA H V S L
Sbjct: 346 GPEPA-YIANEDTGLYTAIPEMSTGSGFNPMMHLPPSNLASAHFPTPARTFHSNVYSVLE 404
Query: 218 GSPAF 232
GSP +
Sbjct: 405 GSPTY 409
>sp|P08775|RPB1_MOUSE DNA-directed RNA polymerase II largest subunit (RPB1)
Length = 1970
Score = 30.8 bits (68), Expect = 1.0
Identities = 24/79 (30%), Positives = 33/79 (41%), Gaps = 1/79 (1%)
Frame = +2
Query: 2 PSGPKYSVGQYLHYDKS-KEGPGPADYKVGSPDLFLTASPKYTMGSGAQMPDSRLLTPSP 178
PS P YS + S K P Y SP+ + ASPKY+ S P S +P+
Sbjct: 1820 PSSPSYSPSSPSYSPTSPKYTPTSPSYSPSSPE-YTPASPKYSPTSPKYSPTSPKYSPTS 1878
Query: 179 AHYKHEMVTSHLPGSPAFT 235
Y + P SP ++
Sbjct: 1879 PTYS-PTTPKYSPTSPTYS 1896
Score = 29.6 bits (65), Expect = 2.3
Identities = 23/79 (29%), Positives = 32/79 (40%), Gaps = 1/79 (1%)
Frame = +2
Query: 2 PSGPKYSVGQYLHYDKSKE-GPGPADYKVGSPDLFLTASPKYTMGSGAQMPDSRLLTPSP 178
P+ P YS + +S P Y SP + SPKYT S + P S TP+
Sbjct: 1799 PTSPSYSPSSPRYTPQSPTYTPSSPSYSPSSPS-YSPTSPKYTPTSPSYSPSSPEYTPAS 1857
Query: 179 AHYKHEMVTSHLPGSPAFT 235
Y + P SP ++
Sbjct: 1858 PKYS-PTSPKYSPTSPKYS 1875
Score = 29.3 bits (64), Expect = 3.0
Identities = 23/78 (29%), Positives = 32/78 (41%)
Frame = +2
Query: 2 PSGPKYSVGQYLHYDKSKEGPGPADYKVGSPDLFLTASPKYTMGSGAQMPDSRLLTPSPA 181
P+ PKYS K P Y SP + +PKY+ S P S + TP+
Sbjct: 1855 PASPKYSP------TSPKYSPTSPKYSPTSPT-YSPTTPKYSPTSPTYSPTSPVYTPTSP 1907
Query: 182 HYKHEMVTSHLPGSPAFT 235
Y T + P SP ++
Sbjct: 1908 KYSPTSPT-YSPTSPKYS 1924
>sp|P14248|RPB1_PLAFD DNA-directed RNA polymerase II largest subunit
Length = 2452
Score = 30.8 bits (68), Expect = 1.0
Identities = 30/90 (33%), Positives = 40/90 (44%), Gaps = 5/90 (5%)
Frame = +2
Query: 2 PSGPKYSVGQYLHYDKS-KEGPGPADYKVGSPDLFLTASPKYT---MGSGAQMPDSRLLT 169
P+ PKYS + S K P Y SP ASP Y+ + S P S +
Sbjct: 2320 PTSPKYSPTSPKYSPTSPKYSPTSPKYSPTSPVAQNIASPNYSPYSITSPKFSPTSPAYS 2379
Query: 170 -PSPAHYKHEMVTSHLPGSPAFTMGIIHSP 256
SP + K +V +H P SPA+ I+ SP
Sbjct: 2380 ISSPVYDKSGVVNAHQPMSPAY---ILQSP 2406
>sp|Q01705|NOTC1_MOUSE Neurogenic locus notch homolog protein 1 precursor (Notch 1) (Motch
A) (mT14) (p300) [Contains: Notch 1 extracellular
truncation; Notch 1 intracellular domain]
Length = 2531
Score = 30.0 bits (66), Expect = 1.7
Identities = 15/32 (46%), Positives = 16/32 (50%)
Frame = +2
Query: 155 SRLLTPSPAHYKHEMVTSHLPGSPAFTMGIIH 250
S L PSP M SHLPG P +GI H
Sbjct: 2205 SHPLLPSPFQQSPSMPLSHLPGMPDTHLGISH 2236
>sp|P24928|RPB1_HUMAN DNA-directed RNA polymerase II largest subunit (RPB1)
Length = 1970
Score = 29.6 bits (65), Expect = 2.3
Identities = 23/79 (29%), Positives = 32/79 (40%), Gaps = 1/79 (1%)
Frame = +2
Query: 2 PSGPKYSVGQYLHYDKSKE-GPGPADYKVGSPDLFLTASPKYTMGSGAQMPDSRLLTPSP 178
P+ P YS + +S P Y SP + SPKYT S + P S TP+
Sbjct: 1799 PTSPSYSPSSPRYTPQSPTYTPSSPSYSPSSPS-YSPTSPKYTPTSPSYSPSSPEYTPTS 1857
Query: 179 AHYKHEMVTSHLPGSPAFT 235
Y + P SP ++
Sbjct: 1858 PKYS-PTSPKYSPTSPKYS 1875
Score = 29.3 bits (64), Expect = 3.0
Identities = 23/78 (29%), Positives = 32/78 (41%)
Frame = +2
Query: 2 PSGPKYSVGQYLHYDKSKEGPGPADYKVGSPDLFLTASPKYTMGSGAQMPDSRLLTPSPA 181
P+ PKYS K P Y SP + +PKY+ S P S + TP+
Sbjct: 1855 PTSPKYSP------TSPKYSPTSPKYSPTSPT-YSPTTPKYSPTSPTYSPTSPVYTPTSP 1907
Query: 182 HYKHEMVTSHLPGSPAFT 235
Y T + P SP ++
Sbjct: 1908 KYSPTSPT-YSPTSPKYS 1924
>sp|P11414|RPB1_CRIGR DNA-directed RNA polymerase II largest subunit (RPB1)
Length = 467
Score = 29.6 bits (65), Expect = 2.3
Identities = 23/79 (29%), Positives = 32/79 (40%), Gaps = 1/79 (1%)
Frame = +2
Query: 2 PSGPKYSVGQYLHYDKSKE-GPGPADYKVGSPDLFLTASPKYTMGSGAQMPDSRLLTPSP 178
P+ P YS + +S P Y SP + SPKYT S + P S TP+
Sbjct: 296 PTSPSYSPSSPRYTPQSPTYTPSSPSYSPSSPS-YSPTSPKYTPTSPSYSPSSPEYTPTS 354
Query: 179 AHYKHEMVTSHLPGSPAFT 235
Y + P SP ++
Sbjct: 355 PKYS-PTSPKYSPTSPKYS 372
Score = 29.3 bits (64), Expect = 3.0
Identities = 23/78 (29%), Positives = 32/78 (41%)
Frame = +2
Query: 2 PSGPKYSVGQYLHYDKSKEGPGPADYKVGSPDLFLTASPKYTMGSGAQMPDSRLLTPSPA 181
P+ PKYS K P Y SP + +PKY+ S P S + TP+
Sbjct: 352 PTSPKYSP------TSPKYSPTSPKYSPTSPT-YSPTTPKYSPTSPTYSPTSPVYTPTSP 404
Query: 182 HYKHEMVTSHLPGSPAFT 235
Y T + P SP ++
Sbjct: 405 KYSPTSPT-YSPTSPKYS 421
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: 46,432,319
Number of Sequences: 369166
Number of extensions: 1007395
Number of successful extensions: 1965
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 1884
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): 1952
length of database: 68,354,980
effective HSP length: 88
effective length of database: 52,098,300
effective search space used: 1719243900
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)