ProDom output appended by default
Note: comments marked by "## COMMENT: "
NOTE: all other PredictProtein output deleted from this file!
The following information has been received by the server:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
________________________________________________________________________________
return concise
phdacc
test seq from phd people
run prodom
# 1ppt.pir ( 1ppt.hssp from: 1 to: 36 )
MPPRWASLLL LACSLLLLAV PPGTAGPSQP TYPGDDAPVE DLIRFYNDLQ
QYLNVVTRHR YGRRSSSRVL CEEPMGAAGC
________________________________________________________________________________
--- ------------------------------------------------------------
--- Results from running BLAST against PRODOM domains
---
--- PLEASE quote:
--- F Corpet, J Gouzy, D Kahn (1998). The ProDom database
--- of protein domain families. Nucleic Ac Res 26:323-326.
---
--- BEGIN of BLASTP output
BLASTP 1.4.7 [16-Oct-94] [Build 12:52:03 Oct 30 1994]
Reference: Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers,
and David J. Lipman (1990). Basic local alignment search tool. J. Mol. Biol.
215:403-10.
Query= prot , (#) ppOld, 1ppt.pir ( 1ppt.hssp from: 1 to: 36 ) t1
(80 letters)
Database: prodom_99_2
157,167 sequences; 18,560,502 total letters.
Searching..................................................done
Smallest
Sum
High Probability
Sequences producing High-scoring Segment Pairs: Score P(N) N
PD001267 p99.2 (53) PAHO(22) PYY(13) NEUY(12) // AMIDAT... 112 2.6e-11 1
PD041507 p99.2 (2) F13A(1) O08619(1) // FACTOR COAGULAT... 46 0.0013 2
PD123104 p99.2 (1) O00634_HUMAN // NETRIN2 LIKE PROTEIN 59 0.025 1
>PD001267 p99.2 (53) PAHO(22) PYY(13) NEUY(12) // AMIDATION HORMONE PANCREAS
PANCREATIC POLYPEPTIDE PP NEUROPEPTIDE PRECURSOR SIGNAL CLEAVAGE
Length = 36
Score = 112 (52.3 bits), Expect = 2.6e-11, P = 2.6e-11
Identities = 18/35 (51%), Positives = 27/35 (77%)
Query: 27 PSQPTYPGDDAPVEDLIRFYNDLQQYLNVVTRHRY 61
P +P YPGDDA E+L ++Y +L+ Y+N++TR RY
Sbjct: 2 PPEPEYPGDDATPEELAQYYAELRHYINLITRPRY 36
>PD041507 p99.2 (2) F13A(1) O08619(1) // FACTOR COAGULATION XIII A CHAIN
PRECURSOR PROTEIN GLUTAMINE GAMMAGLUTAMYLTRANSFERASE TRANSGLUTAMINASE
Length = 62
Score = 46 (21.5 bits), Expect = 0.0013, Sum P(2) = 0.0013
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 23 GTAGPSQPTYPGDDAPVEDL 42
G P+ GDD P EDL
Sbjct: 12 GAIPPNNSNAAGDDLPTEDL 31
Score = 40 (18.7 bits), Expect = 0.0013, Sum P(2) = 0.0013
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 48 DLQQYLNVVTRHRYGRR 64
+LQ YLNV H + R
Sbjct: 40 NLQDYLNVTAVHLFKER 56
>PD123104 p99.2 (1) O00634_HUMAN // NETRIN2 LIKE PROTEIN
Length = 39
Score = 59 (27.5 bits), Expect = 0.025, P = 0.025
Identities = 13/36 (36%), Positives = 16/36 (44%)
Query: 3 PRWASLLLLACSLLLLAVPPGTAGPSQPTYPGDDAP 38
P W LLL L A+ PG P+ P + AP
Sbjct: 2 PGWPWGLLLTAGTLFAALSPGPPAPADPCHDEGGAP 37
Parameters:
E=0.1
B=500
V=500
-ctxfactor=1.00
Query ----- As Used ----- ----- Computed ----
Frame MatID Matrix name Lambda K H Lambda K H
+0 0 BLOSUM62 0.324 0.140 0.445 same same same
Query
Frame MatID Length Eff.Length E S W T X E2 S2
+0 0 80 80 0.10 66 3 11 22 0.19 29
Statistics:
Query Expected Observed HSPs HSPs
Frame MatID High Score High Score Reportable Reported
+0 0 56 (26.1 bits) 112 (52.3 bits) 4 4
Query Neighborhd Word Excluded Failed Successful Overlaps
Frame MatID Words Hits Hits Extensions Extensions Excluded
+0 0 2192 3580518 944662 2615876 19978 198
Database: prodom_99_2
Release date: unknown
Posted date: 10:12 PM EDT Jul 29, 1999
# of letters in database: 18,560,502
# of sequences in database: 157,167
# of database sequences satisfying E: 3
No. of states in DFA: 516 (51 KB)
Total size of DFA: 76 KB (128 KB)
Time to generate neighborhood: 0.01u 0.00s 0.01t Real: 00:00:00
Time to search database: 5.13u 0.05s 5.18t Real: 00:00:05
Total cpu time: 5.15u 0.07s 5.22t Real: 00:00:05
--- END of BLASTP output
--- ------------------------------------------------------------
---
--- Again: these results were obtained based on the domain data-
--- base collected by Daniel Kahn and his coworkers in Toulouse.
---
--- PLEASE quote:
--- F Corpet, J Gouzy, D Kahn (1998). The ProDom database
--- of protein domain families. Nucleic Ac Res 26:323-326.
---
________________________________________________________________________________
Prodom links:
--- ------------------------------------------------------------ --- --- Again: these results were obtained based on the domain data- --- base collected by Daniel Kahn and his coworkers in Toulouse. --- --- PLEASE quote: --- F Corpet, J Gouzy, D Kahn (1998). The ProDom database --- of protein domain families. Nucleic Ac Res 26:323-326. --- --- The general WWW page is on: ---- --------------------------------------- --- http://www.toulouse.inra.fr/prodom.html ---- --------------------------------------- --- --- For WWW graphic interfaces to PRODOM, in particular for your --- protein family, follow the following links (each line is ONE --- single link for your protein!!): --- http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD001267 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD001267 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD001267 ==> graphical output of all proteins having domain PD001267 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD041507 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD041507 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD041507 ==> graphical output of all proteins having domain PD041507 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD123104 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD123104 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD123104 ==> graphical output of all proteins having domain PD123104 --- --- NOTE: if you want to use the link, make sure the entire line --- is pasted as URL into your browser! --- --- END of PRODOM --- ------------------------------------------------------------