SS   BBB      A      SS   EEEE
                S  S  B  B    A A    S  S  E
                S     B B    A   A   S     E
                 S    BB     AAAAA    S    EEE
                  S   B B    A   A     S   E
                   S  B  B   A   A      S  E
               S   S  B  B   A   A  S   S  E
                SSS   BBB    A   A   SSS   EEEEE 

Please send comments to sbase-comment@icgeb.trieste.it. or
contact us by the phone/fax numbers given in the HELP file. Thanks.

containing the word HELP alone in the first line of the message body, or
via the World Wide Web at http://www.icgeb.trieste.it/sbase/mailserv.html

The SBASE e-mail server performs a search with your query against the
SBASE library of protein domain sequences, version 4.0, using the BLAST
algorithm, and the search results are returned in this message.

Evaluation of the output:
=========================

The output file contains the BLAST search results organized as follows:

1. Graphic representation of homologies showing where the individual domain homologies are in the query. In order to get this you need to specify the HSPCRUNCH option in the input file. If you use this option, a statistical filtering of your alignments was also performed using the default HSPCRUNCH parameters. If no statistically significant alignments are found, you can find "The HSPcrunch filter produced no output" message in the output file. This picture has more than 80 characters per line; to make a nice printout, print this part of your output from a PC or MAC as a "landscape" (lines parallel with the longer side of the paper). If you specified the NOPICTURE option together with HSPCRUNCH, a list of the accepted alignments in N to C-terminal order is provided instead of the graphic representation.
2. List of the best scoring domain entries. As SBASE entries are named by domain names (function, structure, etc.), this list already may give information on the expected domain composition.
3. List of alignments.If you included the ANNOTATIONS YES option in the input file, for each SBASE entry you can find the complete annotation of the domain followed by one (or several) alignments with (different parts of) the query. If one domain is found several times in your query, you may find several alignments with the same or related entries at different parts of the query. Please note that it depends on the score parameter whether or not you see all the alignments. Do not use very low cutoff values because that results in prohibitively long output files. (For the time being, we have set the default cutoff to 35 and the minimum cutoff to 30).
4. Run statistics. This is usually not essential for the evaluation of the results; you can get a complete description of these and other blast parameters by sending a HELP message to blast.ncbi.nlm.nih.gov

Important: Failure to see a homology with a known domain may be due to several reasons: i) The domain type is not (yet) included in the SBASE domain library; ii) The threshold score parameter was set too high for the domain to be detected; iii) A different scoring matrix may be necessary in order to detect the alignment with the domain type in question. In the present version of the SBASE server we support the PAM120, PAM40, PAM250 and BLOSUM62 matrices.

Paper to reference in reporting results:
=========================================
Sandor Pongor, Zsolt Hatsagi, Kirill Degtyarenko, Peter Fabian, Vesna
Skerl, Hedvig Hegyi, Janos Murvai & Valeria Bevilacqua: "The SBASE protein
domain library, release 3.0: a collection of annotated protein sequence
segments" Nucleic Acids Research 22 3610-3615 (1994)

Papers to reference regarding the algorithms used by the server program:
========================================================================

BLAST:

Stephen F. Altschul, Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990) Basic local alignment search tool J. Mol. Biol. 215:403-410. HSPcrunch: Sonnhammer, E. L. L and Durbin, R. (1994). A workbench for Large Scale Sequence Homology Analysis. Comput. Applic. Biosci, 10:301-307.

 
 The HSPcrunch filter produced no output.
 You may wish to change the parameters, which were:
 bias_ratio:0.75         coverage limit:10
 
============================================================
Query=  >gi|140963|sp|P28321|YKJ4_YEAST
        (313 letters)
 
Database:  /usr6/home/hatsagi/DATA/sbase4.seq
           61,103 sequences; 3,275,945 total letters.
Searching..................................................done
 
                                                                     Smallest
                                                                     Poisson
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N
TRY2_ANOGA-20-50   PROPEP, TRYPSIN 2 PRECURSOR (EC 34214)       55  0.19      1
FIMB_YEAST-395-639 ACTIN-BINDING, FIMBRIN (ABP67)               54  0.96      1
TRPC_BRELA-1-261   IGPS, INDOLE-3-GLYCEROL PHOSPHATE SYNT...    52  0.998     1
DPO1_ECOLI-521-928 DNA POLYMERASE DOMAINS, DNA POLYMERASE...    52  0.999     1
DPO1_ECOLI-324-928 KLENOW, DNA POLYMERASE I (EC 2777)           52  0.999     1
RIB1_HUMAN-24-438  ER-LUMINAL, RIBOPHORIN I PRECURSOR           45  0.99998   2
NODL_DROME-19-653  EGF-REPEAT, NEUROGENIC LOCUS DELTA PRO...    50  0.999999  1
MGR5_RAT-616-636   TRANSMEMBRANE, METABOTROPIC GLUTAMATE ...    40  1.000000  1
RIB1_RAT-23-437    ER-LUMINAL, RIBOPHORIN I PRECURSOR           48  1.000000  2
 
 
 
>TRY2_ANOGA-20-50 PROPEP, TRYPSIN 2 PRECURSOR (EC 34214)
            Length = 31
 
 Score = 55 (27.0 bits), Expect = 0.22, P = 0.19
 Identities = 8/18 (44%), Positives = 16/18 (88%)
 
Query:   165 QIIAPLLAKFLPRVRIDT 182
             +++ PLL++FLPR++ D+
Sbjct:    10 HLVHPLLPRFLPRLHRDS 27
 
 
>FIMB_YEAST-395-639 ACTIN-BINDING, FIMBRIN (ABP67)
            Length = 245
 
 Score = 54 (26.5 bits), Expect = 3.2, P = 0.96
 Identities = 9/22 (40%), Positives = 15/22 (68%)
 
Query:    24 KFGYMFWPVQNGTNEVRGRVLL 45
 K G + W V +  NEVR+R+++
Sbjct:   216 KLGALIWLVPEDINEVRARLII 237
 
 
>TRPC_BRELA-1-261 IGPS, INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE (EC 4114
            Length = 261
 
 Score = 52 (25.5 bits), Expect = 6.5, P = 1.0
 Identities = 9/23 (39%), Positives = 16/23 (69%)
 
Query:   251 DTINDPKGSEKFIQDCPSADKEL 273
             D++N+ +G+ +FI +C SA   L
Sbjct:    45 DSLNQGRGGARFIMECKSASPSL 67
 
 
>DPO1_ECOLI-521-928 DNA POLYMERASE DOMAINS, DNA POLYMERASE I (EC 2777)
            Length = 408
 
 Score = 52 (25.5 bits), Expect = 6.7, P = 1.0
 Identities = 7/15 (46%), Positives = 12/15 (80%)
 
Query:    50 GEYTKIQFRLMDHLS 64
             ++Y+ I+ R+M HLS
Sbjct:   184 ADYSQIELRIMAHLS 198
 
 
>DPO1_ECOLI-324-928 KLENOW, DNA POLYMERASE I (EC 2777)
            Length = 605
 
 Score = 52 (25.5 bits), Expect = 6.9, P = 1.0
 Identities = 7/15 (46%), Positives = 12/15 (80%)
 
Query:    50 GEYTKIQFRLMDHLS 64
             ++Y+ I+ R+M HLS
Sbjct:   381 ADYSQIELRIMAHLS 395
 
 
>RIB1_HUMAN-24-438 ER-LUMINAL, RIBOPHORIN I PRECURSOR
            Length = 415
 
 Score = 45 (22.1 bits), Expect = 75., P = 1.0
 Identities = 9/23 (39%), Positives = 13/23 (56%)

Query:     5 PYKVQTTVPELQYENFDGAKFGY 27
             PY  Q T +E Q+  F+G  + Y
Sbjct:   118 PYPTQITQSEKQFVVFEGNHYFY 140
 
 Score = 39 (19.1 bits), Expect = 11., Poisson P(2) = 1.0
 Identities = 5/12 (41%), Positives = 9/12 (75%)
 
Query:   209 YGSFRQIHDFMQ 220
             YG+FR++  + Q
Sbjct:   177 YGPFRDVPAYSQ 188
 
 
>NODL_DROME-19-653 EGF-REPEAT, NEUROGENIC LOCUS DELTA PROTEIN PRECURSOR
            Length = 635
 
 Score = 50 (24.6 bits), Expect = 14., P = 1.0
 Identities = 9/26 (34%), Positives = 19/26 (73%)
 
Query:    66 NGYESFTFDQRGAGVTSPGRSKGVTD 91
             ++Y+S TFD +  G T+ +R+ G+++
Sbjct:   549 ESYDSVTFDAHQYGATTQARADGLAN 574
 
 
>MGR5_RAT-616-636 TRANSMEMBRANE, METABOTROPIC GLUTAMATE RECEPTOR 5 PRECU
            Length = 21
 
 Score = 40 (19.6 bits), Expect = 21., P = 1.0
 Identities = 6/9 (66%), Positives = 7/9 (77%)
 
Query:   126 GGICLNYAC 134
             +GICL Y C
Sbjct:     7 AGICLGYLC 15
 
 
>RIB1_RAT-23-437 ER-LUMINAL, RIBOPHORIN I PRECURSOR
            Length = 415
 
 Score = 48 (23.6 bits), Expect = 27., P = 1.0
 Identities = 13/36 (36%), Positives = 17/36 (47%)
 
Query:     5 PYKVQTTVPELQYENFDGAKFGYMFWPVQNGTNEVR 40
             PY  Q T +E Q+  F+G  + Y   P    T  VR
Sbjct:   117 PYPTQITQSEKQFVVFEGNHYFYSPYPTKTQTMRVR 152
 
 Score = 38 (18.7 bits), Expect = 21., Poisson P(2) = 1.0
 Identities = 5/12 (41%), Positives = 9/12 (75%)
 
Query:   209 YGSFRQIHDFMQ 220
             YG+F++I  + Q
Sbjct:   176 YGPFKDIPAYSQ 187
 
 
Parameters:
  E = 25., S = 49 (24.1 bits),  E2 = 0.14, S2 = 34
  W = 3, T = 12 (5.9 bits), X = 21 (10.3 bits)
  M = PAM120
  H = 0, V = 500, B = 250
  -gapdecayrate 0.5 (the default)
 
Statistics:
  Lambda = 0.340 nats/unit score, Lambda/ln2 = 0.491 bits/unit score
  K = 0.187, H = 0.951 bits/position
  Expected/Observed high score = 55 (27.0 bits) / 55 (27.0 bits)
  # of letters in query:  313
  # of neighborhood words in query:  6582
  # of exact words scoring below T:  1
  Database:  /usr6/home/hatsagi/DATA/sbase4.seq
  # of letters in database:  3,275,945
  # of word hits against database:  1,534,031
  # of failed hit extensions:  1,275,963
  # of excluded hits:  258,048
  # of successful extensions:  20
  # of overlapping HSPs discarded:  9
  # of HSPs reportable:  11
  # of sequences in database:  61,103
  # of database sequences with at least one HSP:  9
No. of states in DFA:  545 (54 KB)
Total size of DFA:  123 KB (128 KB)
Time to generate neighborhood:  0.03u 0.06s 0.10t  Real: 00:00:00
Time to search database:  11.56u 8.20s 19.76t  Real: 00:00:20
Total cpu time:  11.68u 8.43s 20.11t  Real: 00:00:21
Further info:
=============
Server functions:   Peter Fabian
                    
                    Tel: +39-40-3757330
 
 
Server software:    Zsolt Hatsagi 
                     
                    Tel: +39-40-3757342
 
General info:       Sandor Pongor
                    
                    Tel: +39-40-3757300
 
FAX:                +39-40-226-555
 
Mail:               International Centre for Genetic Engineering
                    and Biotechnology
                    AREA Science Park, Padriciano 99
                    34012 Trieste, Italy