BLASTP 2.2.23 [Feb-03-2010]
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.
Reference for compositional score matrix adjustment:
Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala,
Aleksandr Morgulis, Alejandro A. Schäffer, and Yi-Kuo Yu (2005) "Protein database
searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= Os12g0560400 Os12g0560400|AK062352
(104 letters)
Database: rap3
52,214 sequences; 17,035,801 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Os12g0560400 Similar to DNA-directed RNA polymerase II 14.5... 220 2e-58
Os03g0102200 Similar to DNA-directed RNA polymerase II 14.5... 185 6e-48
Os07g0615800 DNA-directed RNA polymerase, subunit C11/M/9 f... 139 6e-34
>Os12g0560400 Similar to DNA-directed RNA polymerase II 14.5 kDa polypeptide (EC
2.7.7.6) (RPB9) (RPB14.5)
Length = 104
Score = 220 bits (561), Expect = 2e-58, Method: Compositional matrix adjust.
Identities = 104/104 (100%), Positives = 104/104 (100%)
Query: 1 NNILYPKEDRDQKILLYACRNCDHQEVADNNCVYRNVVHHSAGEFTQVLQDVAGDPTLPR 60
NNILYPKEDRDQKILLYACRNCDHQEVADNNCVYRNVVHHSAGEFTQVLQDVAGDPTLPR
Sbjct: 1 NNILYPKEDRDQKILLYACRNCDHQEVADNNCVYRNVVHHSAGEFTQVLQDVAGDPTLPR 60
Query: 61 TKAVRCAVCGHGEAVFFQATARGEEGMTLFFVCCNPSCGHRWRE 104
TKAVRCAVCGHGEAVFFQATARGEEGMTLFFVCCNPSCGHRWRE
Sbjct: 61 TKAVRCAVCGHGEAVFFQATARGEEGMTLFFVCCNPSCGHRWRE 104
>Os03g0102200 Similar to DNA-directed RNA polymerase II 14.5 kDa polypeptide (EC
2.7.7.6) (RPB9) (RPB14.5)
Length = 114
Score = 185 bits (470), Expect = 6e-48, Method: Compositional matrix adjust.
Identities = 83/104 (79%), Positives = 95/104 (91%)
Query: 1 NNILYPKEDRDQKILLYACRNCDHQEVADNNCVYRNVVHHSAGEFTQVLQDVAGDPTLPR 60
NNILYPKE++D+++LL+ACRNC+HQEV+++ CVYRN V H+AGE TQVLQDVA DPTLPR
Sbjct: 11 NNILYPKEEKDRRLLLFACRNCEHQEVSESKCVYRNEVAHAAGERTQVLQDVASDPTLPR 70
Query: 61 TKAVRCAVCGHGEAVFFQATARGEEGMTLFFVCCNPSCGHRWRE 104
TK VRCA CGHGEAVFFQATARGEEGMTLFFVCCN +C HRWRE
Sbjct: 71 TKTVRCAACGHGEAVFFQATARGEEGMTLFFVCCNLTCAHRWRE 114
>Os07g0615800 DNA-directed RNA polymerase, subunit C11/M/9 family protein
Length = 117
Score = 139 bits (349), Expect = 6e-34, Method: Compositional matrix adjust.
Identities = 57/100 (57%), Positives = 78/100 (78%)
Query: 1 NNILYPKEDRDQKILLYACRNCDHQEVADNNCVYRNVVHHSAGEFTQVLQDVAGDPTLPR 60
+N+LYP+ED++ LLYAC +C+HQE A + CVY+ V+ AGE +L+D A DPTLPR
Sbjct: 13 SNMLYPREDKETHTLLYACNSCEHQEPATDTCVYKRVLRKPAGEPKDILKDAATDPTLPR 72
Query: 61 TKAVRCAVCGHGEAVFFQATARGEEGMTLFFVCCNPSCGH 100
T++++C CGH EA FFQA +GE+G+TL+F+CCNPSCGH
Sbjct: 73 TRSIKCYNCGHPEAAFFQAPTKGEKGLTLYFICCNPSCGH 112
Database: rap3
Posted date: Nov 19, 2010 6:03 PM
Number of letters in database: 17,035,801
Number of sequences in database: 52,214
Lambda K H
0.325 0.138 0.462
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 52214
Number of Hits to DB: 3,894,586
Number of extensions: 138146
Number of successful extensions: 598
Number of sequences better than 1.0e-10: 3
Number of HSP's gapped: 598
Number of HSP's successfully gapped: 3
Length of query: 104
Length of database: 17,035,801
Length adjustment: 72
Effective length of query: 32
Effective length of database: 13,276,393
Effective search space: 424844576
Effective search space used: 424844576
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 149 (62.0 bits)