my URL is
$ curl -s "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=PUT&PROGRAM=blastn&DATABASE=nr&QUERY_BELIEVE_DEFLINE=false&ENTREZ_QUERY=gyra%20%5Bgene%5D%20AND%20AL123456.3%20AND%20txid83332%20%5BORGN%5D&QUERY=%3EPMID%2019846642%20Forward%0AATGTTCGATTCCGGCTTCC%0A%3EPMID%2019846642%20Reverse%0AGGGCTTCGGTGTACCTCAT%0A"
with QUERY_BELIEVE_DEFLINE=false : there is no gi on your fasta line:
it returns
(...)
<!--QBlastInfoBegin
RID = 59MF46VT01R
RTOE = 20
QBlastInfoEnd
-->
(...)
I fetched the result with:
curl -s "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&RID=59MF46VT01R&FORMAT_TYPE=Text"
BLASTN 2.2.28+
Reference: Stephen F. Altschul, 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.
RID: 59MF46VT01R
Database: Nucleotide collection (nt)
20,069,287 sequences; 50,671,056,400 total letters
Query= PMID 19846642 Forward
Length=19
Score E
Sequences producing significant alignments: (Bits) Value
emb|AL123456.3| Mycobacterium tuberculosis H37Rv complete genome 35.6 3e-04
ALIGNMENTS
>emb|AL123456.3| Mycobacterium tuberculosis H37Rv complete genome
Length=4411532
Features in this part of subject sequence:
DNA gyrase (subunit A) GyrA (DNA topoisomerase (ATP-hydro...
Score = 35.6 bits (38), Expect = 3e-04
Identities = 19/19 (100%), Gaps = 0/19 (0%)
Strand=Plus/Plus
Query 1 ATGTTCGATTCCGGCTTCC 19
|||||||||||||||||||
Sbjct 7476 ATGTTCGATTCCGGCTTCC 7494
Features in this part of subject sequence:
Probable medium chain fatty-acid-CoA ligase FadD14 (fatty...
Score = 26.5 bits (28), Expect = 0.14
Identities = 14/14 (100%), Gaps = 0/14 (0%)
Strand=Plus/Plus
Query 3 GTTCGATTCCGGCT 16
||||||||||||||
Sbjct 1181898 GTTCGATTCCGGCT 1181911
Features in this part of subject sequence:
Probable arsenic-transport integral membrane protein ArsB1
Score = 26.5 bits (28), Expect = 0.14
Identities = 14/14 (100%), Gaps = 0/14 (0%)
Strand=Plus/Minus
Query 5 TCGATTCCGGCTTC 18
||||||||||||||
Sbjct 3002143 TCGATTCCGGCTTC 3002130
Features in this part of subject sequence:
Possible lipid transfer protein or keto acyl-CoA thiolase...
Score = 26.5 bits (28), Expect = 0.14
Identities = 14/14 (100%), Gaps = 0/14 (0%)
Strand=Plus/Minus
Query 1 ATGTTCGATTCCGG 14
||||||||||||||
Sbjct 3959155 ATGTTCGATTCCGG 3959142
Features in this part of subject sequence:
Glutamine synthetase GlnA1 (glutamine synthase) (GS-I)
Score = 24.7 bits (26), Expect = 0.48
Identities = 13/13 (100%), Gaps = 0/13 (0%)
Strand=Plus/Plus
Query 6 CGATTCCGGCTTC 18
|||||||||||||
Sbjct 2487721 CGATTCCGGCTTC 2487733
Features in this part of subject sequence:
Probable sugar-transport integral membrane protein ABC tr...
Score = 24.7 bits (26), Expect = 0.48
Identities = 13/13 (100%), Gaps = 0/13 (0%)
Strand=Plus/Plus
Query 6 CGATTCCGGCTTC 18
|||||||||||||
Sbjct 2589020 CGATTCCGGCTTC 2589032
Features in this part of subject sequence:
Probable epoxide hydrolase EphC (epoxide hydratase)
Score = 22.9 bits (24), Expect = 1.7
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Plus
Query 4 TTCGATTCCGGC 15
||||||||||||
Sbjct 1247372 TTCGATTCCGGC 1247383
Features in this part of subject sequence:
Probable Fmu protein (sun protein)
Score = 22.9 bits (24), Expect = 1.7
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Minus
(...)
Query= PMID 19846642 Reverse
Length=19
Score E
Sequences producing significant alignments: (Bits) Value
emb|AL123456.3| Mycobacterium tuberculosis H37Rv complete genome 35.6 3e-04
ALIGNMENTS
>emb|AL123456.3| Mycobacterium tuberculosis H37Rv complete genome
Length=4411532
Features in this part of subject sequence:
DNA gyrase (subunit A) GyrA (DNA topoisomerase (ATP-hydro...
Score = 35.6 bits (38), Expect = 3e-04
Identities = 19/19 (100%), Gaps = 0/19 (0%)
Strand=Plus/Minus
Query 1 GGGCTTCGGTGTACCTCAT 19
|||||||||||||||||||
Sbjct 7698 GGGCTTCGGTGTACCTCAT 7680
Features in this part of subject sequence:
Conserved hypothetical protein
Score = 26.5 bits (28), Expect = 0.14
Identities = 14/14 (100%), Gaps = 0/14 (0%)
Strand=Plus/Minus
Query 3 GCTTCGGTGTACCT 16
||||||||||||||
Sbjct 1029956 GCTTCGGTGTACCT 1029943
Lambda K H
0.634 0.408 0.912
Gapped
Lambda K H
0.625 0.410 0.780
Matrix: blastn matrix:2 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Sequences: 1
Number of Hits to DB: 0
Number of extensions: 0
Number of successful extensions: 0
Number of sequences better than 10: 0
Number of HSP's better than 10 without gapping: 0
Number of HSP's gapped: 0
Number of HSP's successfully gapped: 0
Length of database: 4411534
A: 0
X1: 22 (20.1 bits)
X2: 33 (29.8 bits)
X3: 110 (99.2 bits)
S1: 22 (21.1 bits)
Thanks ! I apparently did not realize what the definition line really is ! I thought it was basically a comment line but it can apparently be used as part of the algorithm.