Align Ornithine aminotransferase; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate 350970 BT1442 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI ptt file)
Query= SwissProt::Q6CWC1 (437 letters) >FitnessBrowser__Btheta:350970 Length = 804 Score = 161 bits (408), Expect = 6e-44 Identities = 123/417 (29%), Positives = 208/417 (49%), Gaps = 25/417 (5%) Query: 16 EYEQEYSAHNY----HPLPVV-FSRASGAHVWDPEGKEYLDFLSAYSAVNQGHCHPHIIQ 70 ++++E+ H Y PLPV RA GA + +G+ ++ +S++ G+ HP + Q Sbjct: 386 QFDREHLWHPYTSTTDPLPVYKVKRADGATITLEDGRTLIEGMSSWWCAVHGYNHPVLNQ 445 Query: 71 ALVDQASKLT-LSSRAFSNDCFASFSKFVTEFF--GYESVLPMNTGAEAVESALKLARRW 127 A DQ K++ + ++D K + + + ++G+ AVE ALK+A ++ Sbjct: 446 AAKDQLDKMSHVMFGGLTHDPAIELGKLLLPLVPPSMQKIFYADSGSVAVEVALKMAVQY 505 Query: 128 GYMVKKIQPNEAIILGARGNFHGRTFGAISLSTDEEDSRMNFGPFLE-NVTAKIPGGSDD 186 Y K N + + R +HG T+ A+S+ FG L P D Sbjct: 506 WYAAGKPDKNNFVTI--RSGYHGDTWNAMSVCDPVTGMHSLFGSSLPVRYFVPAPSSRFD 563 Query: 187 EFIRYGEIDDYKRAFESHGDKICAVIVEPI-QGEAGIVVPRADFLTDLQELCKKHQVLLI 245 EI + E H ++ A+I+EPI QG G+ +L + ++LCK+H +LLI Sbjct: 564 GEWNPDEIIPLRETIEKHSKELAALILEPIVQGAGGMWFYHPQYLREAEKLCKEHDILLI 623 Query: 246 CDEIQTGIARTGKLLCYEHSPNCKPDIILLGKAISGGVLPVSCVLSSREIMDCFTPGS-- 303 DEI TG RTGKL +EH+ +PDI+ +GKA++GG + +S VL+S +I D + + Sbjct: 624 FDEIATGFGRTGKLFAWEHA-GVEPDIMCIGKALTGGYMTLSAVLASNQIADTISNHAPK 682 Query: 304 ---HGSTYGGNPLASRVAIAALEVVQNENLVERSARLGKFLQDELVKLQHESNGVISEVR 360 HG T+ GNPLA VA A++ ++ + E R+ L++EL + +++VR Sbjct: 683 AFMHGPTFMGNPLACAVACASVRLLLDSGWAENVKRIEAQLKEELAPARKFPQ--VADVR 740 Query: 361 GKGLLTAIVINPEKANGRTAWDLCLLMKDQGVLAKPTHEHIIRLAPPLVISEEDLLK 417 G + VI E++ + ++G+ +P + ++ L PP +IS E L K Sbjct: 741 ILGAIG--VIQTERSVSMAYMQRRFV--EEGIWVRPFGK-LVYLMPPFIISPEQLSK 792 Lambda K H 0.318 0.136 0.400 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: 732 Number of extensions: 43 Number of successful extensions: 6 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: 437 Length of database: 804 Length adjustment: 37 Effective length of query: 400 Effective length of database: 767 Effective search space: 306800 Effective search space used: 306800 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