Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate Synpcc7942_0031 Synpcc7942_0031 aminotransferase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__SynE:Synpcc7942_0031 Length = 424 Score = 159 bits (403), Expect = 1e-43 Identities = 135/421 (32%), Positives = 195/421 (46%), Gaps = 36/421 (8%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 P+ + G+ A + DG+ ID + V GH + +VEAI QA L H F H Sbjct: 20 PLKVVSGKGARLTLADGRELIDCISSWWVNLHGHAHLRIVEAIAQQAATLEHVIFAGFSH 79 Query: 75 GPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGA-----TGKRAIIAFDGGF 129 P L +L + +P +++G+ A E ALK+A + I+AFDG + Sbjct: 80 EPAERLAMELCKILPEKLTRV-FFSDNGSTAVEVALKMALQYWHNLDQPRSRILAFDGAY 138 Query: 130 HGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVE--LA 187 HG T +++ G+ + + +L V LPYP G +A +A + +VE LA Sbjct: 139 HGDTFGAMSV-GERSLFNAPFEKLLFSVEFLPYPETWWGDETVEAKEAA-AIAAVEQALA 196 Query: 188 VEDVAAFIFEP-VQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFP 246 DVAA I EP VQG GG P F Q L G L+I DE+ +GFGRTG FA Sbjct: 197 AGDVAAVIIEPLVQGAGGMRMARPQFLQQLAARVQAAGSLLIADEVMTGFGRTGAWFACQ 256 Query: 247 RLGIEPDLLLLAKSIAGG-MPLGAVVGRKELMAALPKGG------LGGTYSGNPISCAAA 299 R GI+PDL+ L+K + GG +PL V + + G G +Y+ NP+ CAAA Sbjct: 257 RAGIQPDLICLSKGLTGGFLPLSITVATEVIYDTFCSGNPDHTFYHGHSYTANPLGCAAA 316 Query: 300 LASLAQMTDENLATWGERQEQAIVSRYERWKASGLS-----PYIGRLTGVGAMRGIEFAN 354 +ASL + D +AIV E GL P + R G + + + Sbjct: 317 IASLELLLD----------SEAIVQGLEDAHLPGLELLAQHPKVTRPRLTGGIAACDLVS 366 Query: 355 ADGSPAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414 G +V +AA ARGLLL P G +++ LL P + L++ + L E Sbjct: 367 DRGGYLDPIGLRVRQAAIARGLLLRPLG---NVLYLLPPYCLTPTELQDIYAAIADLLDE 423 Query: 415 L 415 + Sbjct: 424 I 424 Lambda K H 0.320 0.137 0.402 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: 454 Number of extensions: 28 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: 416 Length of database: 424 Length adjustment: 32 Effective length of query: 384 Effective length of database: 392 Effective search space: 150528 Effective search space used: 150528 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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