Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate 350970 BT1442 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI ptt file)
Query= reanno::Marino:GFF3099 (404 letters) >FitnessBrowser__Btheta:350970 Length = 804 Score = 149 bits (376), Expect = 3e-40 Identities = 119/383 (31%), Positives = 196/383 (51%), Gaps = 29/383 (7%) Query: 28 RGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLS-NVMTNEPALR 86 R +G+ I ++GR I+ G++HP L A DQ +K+ H+ +T++PA+ Sbjct: 410 RADGATITLEDGRTLIEGMSSWWCAVHGYNHPVLNQAAKDQLDKMSHVMFGGLTHDPAIE 469 Query: 87 LAKTLCDLT--FAERVFFANSGAEANEAAFKLARRYAWEHHGK-EKNEIISFKNSFHGRT 143 L K L L +++F+A+SG+ A E A K+A +Y W GK +KN ++ ++ +HG T Sbjct: 470 LGKLLLPLVPPSMQKIFYADSGSVAVEVALKMAVQY-WYAAGKPDKNNFVTIRSGYHGDT 528 Query: 144 LFTVSVG----------GQPKYLEGFEPAPGGIHHAEFNDLESV--KKLISK--EKTCAI 189 +SV G + F PAP E+N E + ++ I K ++ A+ Sbjct: 529 WNAMSVCDPVTGMHSLFGSSLPVRYFVPAPSSRFDGEWNPDEIIPLRETIEKHSKELAAL 588 Query: 190 VVEPI-QGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGVVPD 248 ++EPI QG GG+ +L+ LC E+D LL+FDE+ +G GR+G +A++ GV PD Sbjct: 589 ILEPIVQGAGGMWFYHPQYLREAEKLCKEHDILLIFDEIATGFGRTGKLFAWEHAGVEPD 648 Query: 249 ILSSAKGLGGGF-PVAAMLTTAKVAASLG-----VGTHGSTYGGNALACAVAQRVVDTVS 302 I+ K L GG+ ++A+L + ++A ++ HG T+ GN LACAVA V + Sbjct: 649 IMCIGKALTGGYMTLSAVLASNQIADTISNHAPKAFMHGPTFMGNPLACAVACASVRLLL 708 Query: 303 QPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAGLE 362 + VK +L++ + ++ +VR G +G + TE+ A +E Sbjct: 709 DSGWAENVKRIEAQLKEELAP-ARKFPQVADVRILG-AIGVIQTERSVSMAY-MQRRFVE 765 Query: 363 EGVMVLVAGANVIRLAPSLIIPE 385 EG+ V G V + P +I PE Sbjct: 766 EGIWVRPFGKLVYLMPPFIISPE 788 Lambda K H 0.318 0.137 0.406 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 675 Number of extensions: 33 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 404 Length of database: 804 Length adjustment: 36 Effective length of query: 368 Effective length of database: 768 Effective search space: 282624 Effective search space used: 282624 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory