Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate GFF919 PGA1_c09350 aminotransferase class-III
Query= BRENDA::Q98TS5 (439 letters) >FitnessBrowser__Phaeo:GFF919 Length = 450 Score = 157 bits (396), Expect = 8e-43 Identities = 125/414 (30%), Positives = 204/414 (49%), Gaps = 54/414 (13%) Query: 60 VALERGKGVYVWDVEGRRYFDFLSAYSAVNQGHCHPKILDALKSQADKLTLTSRAFYNDV 119 + LERG+G+YV+D +GR+Y + L+ + G+ + +++DA+ Q KL T F Sbjct: 17 LCLERGEGIYVFDSDGRKYIEGLAGLWCTSLGYSNTEVMDAITEQLHKLPFT-HTFGGKT 75 Query: 120 LGEYEEYITKIFGYNKVLPM-----NTGVEGGETACKLARKWAYTVKGIPKYKAQIIFAA 174 ++ K+ V N+G + +T K+ R + + G P+ K +II Sbjct: 76 HQPIQDLADKLAAMVPVEDAYIFFGNSGSDANDTHYKMLRYY-FNAIGKPE-KRKIITRE 133 Query: 175 GNFWGRTMSAISSSTDPSSYEGFGPFMPGFKII----PY-------NDLPA--LERALQ- 220 + G T++A S ++ P++ F + I+ P+ N+ A +ER LQ Sbjct: 134 RGYHGVTVAAGSLTSLPANLAHFDAPLEALSILRADSPHYYTARQGNETEAQFVERILQN 193 Query: 221 --------DPN-VAAFMVEPIQGEAGVIVPDEGYLTGVRQLCTAHNVLFIADEVQTGLAR 271 DP+ +AA +VEPI G +GVIVP +GY G++ L + +L ADEV G R Sbjct: 194 LEDQIISEDPDTIAAMIVEPITGASGVIVPPDGYYEGLQALLRKYGILIWADEVICGFGR 253 Query: 272 TGKMLAVDHENVRPDLVILGKALSGGVYPVSAVLCDD---EVML--TIKPG--EHGSTYG 324 TG + PDL+ K LS +P+SA + E M+ T + G HG TY Sbjct: 254 TGADFGCTTMGITPDLMTFAKQLSSAYFPISASVIPGWMYEAMVDQTNEVGVFGHGYTYS 313 Query: 325 GNPLGCRVAMASLEVIEEEKLAENANXMGELLRAELMK--TPSDIVTAVRGKGLLNAIVI 382 G+P C A+ +LE+ E + L ++A +G L+ +L + T +V VRGKGL+ A+ + Sbjct: 314 GHPAACAAALKTLEIYERDNLFDHAAEVGSYLQTQLREIFTDHPLVGEVRGKGLIAALEL 373 Query: 383 KQSK-----------DCDAWKVCLRLRDNGLLAKPTHGDIIRLAPPLTIKEDEI 425 +K A ++C +DNGL+ + G+ + L PPL I +E+ Sbjct: 374 VSNKTTGASFDKGRAGATAQRLC---QDNGLILRAVAGNAVALCPPLIITREEV 424 Lambda K H 0.318 0.136 0.404 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: 498 Number of extensions: 26 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: 439 Length of database: 450 Length adjustment: 32 Effective length of query: 407 Effective length of database: 418 Effective search space: 170126 Effective search space used: 170126 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: 51 (24.3 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