Align Ornithine aminotransferase; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate PP_4108 PP_4108 putative 4-aminobutyrate aminotransferase
Query= SwissProt::Q6CWC1 (437 letters) >FitnessBrowser__Putida:PP_4108 Length = 416 Score = 167 bits (422), Expect = 7e-46 Identities = 127/419 (30%), Positives = 209/419 (49%), Gaps = 37/419 (8%) Query: 30 PVVFSRASGAHVWDPEGKEYLDFLSAYSAVNQGHCHPHIIQALVDQASKLT-LSSRAFSN 88 P+ S A VWD +GK Y+DF+ +N GHC+P +++A+ QA++LT + A + Sbjct: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 Query: 89 DCFASFSKFVTEFFGYESVLP---MNTGAEAVESALKLARRWGYMVKKIQPNEAIILGAR 145 + + + +++F L N+GAEA E+ALK+AR + I+ Sbjct: 75 GPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG--------ATGKRAIIAFD 126 Query: 146 GNFHGRTFGAISLSTDEEDSRMNFGPFLENVTAKIPGGSDDEFIRYGE-IDDYKRAF--E 202 G FHGRT ++L+ + G L +P S D + + + R F E Sbjct: 127 GGFHGRTLATLNLNGKVAPYKQRVGE-LPGPVYHLPYPSADTGVTCEQALKAMDRLFSVE 185 Query: 203 SHGDKICAVIVEPIQGEAGIVVPRADFLTDLQELCKKHQVLLICDEIQTGIARTGKLLCY 262 + + A I EP+QGE G + F L+ C + +L+I DEIQ+G RTG+ + Sbjct: 186 LAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAF 245 Query: 263 EHSPNCKPDIILLGKAISGGVLPVSCVLSSREIMDCFTPGSHGSTYGGNPLASRVAIAAL 322 +PD++LL K+I+GG +P+ V+ +E+M G G TY GNP++ A+A+L Sbjct: 246 PRL-GIEPDLLLLAKSIAGG-MPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL 303 Query: 323 EVVQNENLVERSARLGKFLQDELVKLQHE---SNGV---ISEVRGKGLLTAIVINPEKAN 376 + +ENL R Q++ + ++E ++G+ I + G G + I A+ Sbjct: 304 AQMTDENLATWGER-----QEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEF--ANAD 356 Query: 377 GRTA-WDLCLLM---KDQGVLAKPTHE--HIIRLAPPLVISEEDLLKGVDSIRVSLSKL 429 G A L +M + +G+L P+ + HIIRL PL I E L +G+D + L++L Sbjct: 357 GSPAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 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: 387 Number of extensions: 14 Number of successful extensions: 7 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: 416 Length adjustment: 32 Effective length of query: 405 Effective length of database: 384 Effective search space: 155520 Effective search space used: 155520 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