BLASTP 2.2.26 [Sep-21-2011]
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 compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 009860
(523 letters)
Database: swissprot
539,616 sequences; 191,569,459 total letters
Searching..................................................done
>sp|B0S733|REN3A_DANRE Regulator of nonsense transcripts 3A OS=Danio rerio GN=upf3a PE=2
SV=2
Length = 452
Score = 87.4 bits (215), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 57/166 (34%), Positives = 95/166 (57%), Gaps = 14/166 (8%)
Query: 8 TKVVIRHLPPSLSQNDLLALFRDHFND--RYNWFCFRPGKSSYKHQRYSRAYVELKKPAG 65
+KVVIR LPPSLS++ L ++H + +++F F P S +SRAY+ K P
Sbjct: 43 SKVVIRRLPPSLSKDQL----QEHLSPLPSFDYFEFFPADQSLYPHLFSRAYINFKNPED 98
Query: 66 VFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSRE-GTIFKDPDYLEFLKV 124
+ F + +G+VF++ KG ++ A+VE+AP Q+V K +K + GTI +DP+Y FL+
Sbjct: 99 IIIFRDRFDGYVFIDNKGQEYPAVVEFAPFQKVSKKKLKKKDAKAGTIEEDPEYRRFLEN 158
Query: 125 IAKPAE-NLPSAEIQLERKEAELSGAPKETLV--VTPLMEYVRQKR 167
+ E ++ + E L E+ +E + TPL+EY++ K+
Sbjct: 159 YSCDEEKSMANPETLL----GEIEAKTRELIAKRTTPLLEYIKNKK 200
>sp|Q9BZI7|REN3B_HUMAN Regulator of nonsense transcripts 3B OS=Homo sapiens GN=UPF3B PE=1
SV=1
Length = 483
Score = 79.0 bits (193), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 54/166 (32%), Positives = 91/166 (54%), Gaps = 14/166 (8%)
Query: 8 TKVVIRHLPPSLSQNDLLALFRDHFND--RYNWFCFRPGKSSYKHQRYSRAYVELKKPAG 65
+KVVIR LPP+L++ L ++H +++F F +S Y+RAY+ K
Sbjct: 51 SKVVIRRLPPTLTKEQL----QEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQED 106
Query: 66 VFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSRE-GTIFKDPDYLEFLKV 124
+ F + +G+VF++ KG ++ AIVE+AP Q+ K ++K + GTI DP+Y +FL+
Sbjct: 107 IILFRDRFDGYVFLDNKGQEYPAIVEFAPFQKAAKKKTKKRDTKVGTIDDDPEYRKFLES 166
Query: 125 IAKPAENLPSA-EIQLERKEAELSGAPKETLV--VTPLMEYVRQKR 167
A E + S E LE E+ +E + TPL+ +++ K+
Sbjct: 167 YATDNEKMTSTPETLLE----EIEAKNRELIAKKTTPLLSFLKNKQ 208
>sp|Q9H1J1|REN3A_HUMAN Regulator of nonsense transcripts 3A OS=Homo sapiens GN=UPF3A PE=1
SV=1
Length = 476
Score = 76.6 bits (187), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 54/164 (32%), Positives = 86/164 (52%), Gaps = 10/164 (6%)
Query: 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVF 67
+KVVIR LPP L++ L R Y F F S Y H YSRAY+ + P +
Sbjct: 68 SKVVIRRLPPGLTKEQLEEQLRPLPAHDYFEF-FAADLSLYPHL-YSRAYINFRNPDDIL 125
Query: 68 EFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSRE-GTIFKDPDYLEFLKVIA 126
F + +G++F++ KG ++ A+VE+AP Q++ K RK + G+I DP+Y +FL+
Sbjct: 126 LFRDRFDGYIFLDSKGLEYPAVVEFAPFQKIAKKKLRKKDAKTGSIEDDPEYKKFLETYC 185
Query: 127 KPAENLPS-AEIQLERKEAELSGAPKETLV--VTPLMEYVRQKR 167
E + E L E+ +E + TPL+EY++ ++
Sbjct: 186 VEEEKTSANPETLL----GEMEAKTRELIARRTTPLLEYIKNRK 225
>sp|Q10267|UPF3_SCHPO Nonsense-mediated mRNA decay protein 3 OS=Schizosaccharomyces pombe
(strain 972 / ATCC 24843) GN=upf3 PE=3 SV=1
Length = 278
Score = 71.6 bits (174), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 47/163 (28%), Positives = 83/163 (50%), Gaps = 15/163 (9%)
Query: 9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSY--KHQRYSRAYVELKKPAGV 66
KV++ +LPP+L + L + F W F GK++ + + S AY++ + V
Sbjct: 13 KVLVFNLPPTLPEQVFLQSI-NSFLPHVEWHRFSKGKATVGTRSELLSFAYLKFQSATAV 71
Query: 67 FEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLEFLKVIA 126
EF + GH F+++K ++AIV AP Q++P + DS EG++ +DP + EF KV
Sbjct: 72 QEFFRVYQGHTFIDKKNNTYRAIVTIAPYQKIPPSKVKADSLEGSLEQDPKFQEF-KVQR 130
Query: 127 KPAENLPSAEIQLERKEAELSGAPKETLVVTPLMEYVRQKRAA 169
+ S + +E+ + TPL++Y+ +K+ A
Sbjct: 131 ESYSQTASNDDVIEKLQTS-----------TPLLQYLAEKKNA 162
>sp|P48412|UPF3_YEAST Nonsense-mediated mRNA decay protein 3 OS=Saccharomyces cerevisiae
(strain ATCC 204508 / S288c) GN=UPF3 PE=1 SV=1
Length = 387
Score = 45.4 bits (106), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 36/138 (26%), Positives = 65/138 (47%), Gaps = 15/138 (10%)
Query: 9 KVVIRHLPPSLSQNDLLALFRDHFND-----------RYNWFCFRPGKSS---YKHQRYS 54
K+VIR LPP+L+ ++ A+ RD+ ND +Y+ +CF G S +K+ YS
Sbjct: 87 KLVIRLLPPNLTADEFFAILRDNNNDDGDKQDIQGKLKYSDWCFFEGHYSSKVFKNSTYS 146
Query: 55 RAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKD-SREGTIF 113
R + + + A + F++ K ++ +P + S+KD + GTI
Sbjct: 147 RCNFLFDNLSDLEKCANFIKTCKFIDNKDNITIPDMKLSPYVKKFTQTSKKDAALVGTIE 206
Query: 114 KDPDYLEFLKVIAKPAEN 131
+D + F+ + + EN
Sbjct: 207 EDEIFKTFMNSMKQLNEN 224
>sp|Q8MCM4|MATK_TRIRP Maturase K OS=Trifolium repens GN=matK PE=3 SV=1
Length = 506
Score = 35.4 bits (80), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 31/120 (25%), Positives = 46/120 (38%), Gaps = 22/120 (18%)
Query: 11 VIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSS-------------YKHQRYSRAY 57
++R+ + LL LF HF NW CF P K S + H Y Y
Sbjct: 163 ILRYWVKDVPFFHLLRLFLSHFC---NWNCFIPTKKSISTFSKRNPRLFLFLHNFYVCEY 219
Query: 58 VELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPD 117
+F F + H+ + F+ I YA + + + FS+ S FKDP+
Sbjct: 220 ------ESIFLFLRNKSSHLRLKSFSVFFERIFFYAKRKHLVEVFSKDFSYTLPFFKDPN 273
>sp|Q8MCL9|MATK_TRITL Maturase K OS=Trifolium thalii GN=matK PE=3 SV=1
Length = 506
Score = 35.4 bits (80), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 31/120 (25%), Positives = 46/120 (38%), Gaps = 22/120 (18%)
Query: 11 VIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSS-------------YKHQRYSRAY 57
++R+ + LL LF HF NW CF P K S + H Y Y
Sbjct: 163 ILRYWVKDVPFFHLLRLFLYHFC---NWNCFIPTKKSISTFSKRNPRLFLFLHNFYVCEY 219
Query: 58 VELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPD 117
+F F + H+ + F+ I YA + + + FS+ S FKDP+
Sbjct: 220 ------ESIFLFLRNKSSHLRLKSFSVFFERIFFYAKREHLVEVFSKDFSYTLPFFKDPN 273
>sp|Q46IC6|THIG_PROMT Thiazole synthase OS=Prochlorococcus marinus (strain NATL2A)
GN=thiG PE=3 SV=1
Length = 268
Score = 35.0 bits (79), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 38/140 (27%), Positives = 60/140 (42%), Gaps = 18/140 (12%)
Query: 159 LMEYVRQKR-------AAESGAQESLAVGRVGRRSRAASASKTSSTTTKRGSEKKKYILK 211
LME + KR A S A+E++ + R+GR + +T++ KKY+L
Sbjct: 61 LMESIDWKRIWMLPNTAGCSNAEEAIRIARLGRELAKLAGQETNNFVKLEVIPDKKYLLP 120
Query: 212 D---SAKNARRKDKSTFTVVAKREDQPASSSGKETSASETICGVEGSVGIPLTSDTGKK- 267
D + K A + K FTV+ P + E E C +G P+ S G +
Sbjct: 121 DPIGTLKAAEQLVKEGFTVLPYINSDPLIAKQLE----EIGCATVMPLGSPIGSAQGIRN 176
Query: 268 --KILLLKGKEREIPHVPDA 285
I ++ + R IP + DA
Sbjct: 177 AANIAMIIAESR-IPIIIDA 195
>sp|G5EBZ4|LE418_CAEEL Protein let-418 OS=Caenorhabditis elegans GN=let-418 PE=1 SV=1
Length = 1829
Score = 34.3 bits (77), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 446 VTRGEMKDDMSYGSKTV---DIAAPTSGGSHRHNGRRAATNITKDDGCINMIEGKSSKRR 502
+++ E+ D + +G++ + D+ A GS + AA I DD ++ + +S+K
Sbjct: 1087 MSKTELDDVLRWGTEELFSEDLDAAEGEGSEKKGA--AAQEIVWDDAAVDALLDRSNKEE 1144
Query: 503 GAAGSGGNEKQVW 515
AG G EK W
Sbjct: 1145 TPAGEDGEEKAEW 1157
>sp|Q6GLY8|SGK1B_XENLA Serine/threonine-protein kinase Sgk1-B OS=Xenopus laevis GN=sgk1-b
PE=2 SV=1
Length = 434
Score = 32.3 bits (72), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 53/121 (43%), Gaps = 24/121 (19%)
Query: 309 QRREAGGRLIRKILLNN----ETRQTQSVTGVQPQQKMQNLNQENGKPLP--------GP 356
QRR I+KI N+ + + QS+ + P Q+ + LN EN P P GP
Sbjct: 32 QRRMGLNEFIQKIATNSSYSCKPSEVQSILNISPPQESELLN-ENSSPPPSHSQQINLGP 90
Query: 357 TSSPNGHVTNNDSPIFSFDGN--------TKRSSDDRF-ARKVLHGSGAVSEKQEKRTRN 407
+S+P H +D G + +D++F A KVL + +K+EK +
Sbjct: 91 SSNP--HAKPSDFQFLKIIGKGSFGKVLLARHKADEKFYAVKVLQKKAILKKKEEKHIMS 148
Query: 408 K 408
+
Sbjct: 149 E 149
>sp|Q9RVW0|RPOC_DEIRA DNA-directed RNA polymerase subunit beta' OS=Deinococcus
radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 /
LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
GN=rpoC PE=3 SV=1
Length = 1546
Score = 32.3 bits (72), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 43/105 (40%), Gaps = 8/105 (7%)
Query: 270 LLLKGKEREIPHVPDALLDKQRESSPVKNSASPTVPKQIQRREAG--GRLIRKILLNNET 327
++++ ++R + DAL+D R SPV N S + + G GR + +L
Sbjct: 582 MIIRNEKRMLQEAVDALIDNGRRGSPVTNPGSDRSLRSLTDLLGGKQGRFRQNLLGKRVD 641
Query: 328 RQTQSVTGVQPQQKMQN------LNQENGKPLPGPTSSPNGHVTN 366
+SV V PQ K+ + E KP G VTN
Sbjct: 642 YSGRSVIVVGPQLKLHQCGVPKRMALELFKPFLFKVLEEKGEVTN 686
>sp|Q1J0P7|RPOC_DEIGD DNA-directed RNA polymerase subunit beta' OS=Deinococcus
geothermalis (strain DSM 11300) GN=rpoC PE=3 SV=1
Length = 1537
Score = 32.3 bits (72), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 43/105 (40%), Gaps = 8/105 (7%)
Query: 270 LLLKGKEREIPHVPDALLDKQRESSPVKNSASPTVPKQIQRREAG--GRLIRKILLNNET 327
++++ ++R + DAL+D R SPV N S + + G GR + +L
Sbjct: 572 MIIRNEKRMLQEAVDALIDNGRRGSPVTNPGSDRSLRSLTDLLGGKQGRFRQNLLGKRVD 631
Query: 328 RQTQSVTGVQPQQKMQN------LNQENGKPLPGPTSSPNGHVTN 366
+SV V PQ K+ + E KP G VTN
Sbjct: 632 YSGRSVIVVGPQLKLHQCGVPKRMALELFKPFLFKVLEEKGEVTN 676
Database: swissprot
Posted date: Mar 23, 2013 2:32 AM
Number of letters in database: 191,569,459
Number of sequences in database: 539,616
Lambda K H
0.310 0.127 0.355
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 194,326,715
Number of Sequences: 539616
Number of extensions: 8439752
Number of successful extensions: 21267
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 172
Number of HSP's that attempted gapping in prelim test: 21080
Number of HSP's gapped (non-prelim): 336
length of query: 523
length of database: 191,569,459
effective HSP length: 122
effective length of query: 401
effective length of database: 125,736,307
effective search space: 50420259107
effective search space used: 50420259107
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 64 (29.3 bits)