Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate Synpcc7942_0943 Synpcc7942_0943 acetylornithine aminotransferase
Query= SwissProt::Q94AL9 (477 letters) >FitnessBrowser__SynE:Synpcc7942_0943 Length = 422 Score = 172 bits (435), Expect = 3e-47 Identities = 125/396 (31%), Positives = 192/396 (48%), Gaps = 31/396 (7%) Query: 78 RKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYL 137 R PL + G+ ++D GR YLD AGIA GH HP++V+ + +QI++L H + LY Sbjct: 33 RFPLALERGEGCRVWDTQGRSYLDFVAGIATCTLGHAHPELVDAISDQIRKLHHVSNLYY 92 Query: 138 NHAIADFSEALASKLPGDLKVVFFTNSGTEANELALMMAKLYTGC------QDIVAVRNG 191 + L + D VFF NSG EANE A+ +A+ + I+ + Sbjct: 93 IPEQGQLAAWLTANSCADR--VFFCNSGAEANEAAIKLARKHGNTVLEAENPIILTAQAS 150 Query: 192 YHGNAAATMGATGQSMWKFNVVQNSVHHALNP--DPYRGVFGSDGEKYAKDLQDLIQYGT 249 +HG A + ATGQ + H P +R V +D L +L G Sbjct: 151 FHGRTLAAVTATGQPKY---------HKGFQPLVQGFRYVPYNDLAALEATLAELDAAGE 201 Query: 250 TGHIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEA 309 T +A + E +QG GG+ Y A + L I DEVQ G R+G WG+E Sbjct: 202 T--VAAILLEPLQGEGGVNPGDRAYFQAVRQLCDQRRMLLILDEVQVGMGRSGQLWGYEN 259 Query: 310 HNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIE 369 + PD T+AKG+G G P+GA++ +L + +TFGGN ++ AGLA+ V+E Sbjct: 260 LGIEPDAFTVAKGLGGGVPIGALLVKAS-CNILQAGEHASTFGGNPLACRAGLAIAQVME 318 Query: 370 KEKLQENAAMVGSYLKEKLTQLKEKH-EIIGDVRGRGLMLGVELVSDRKLKTPATAETLH 428 +++L N G L+ L +L +++ ++ VRG GL+ G+ L +D + TP + Sbjct: 319 RDQLLANVQARGEQLRAGLQELVDRYPNLLAGVRGWGLINGLVLRNDPNV-TP-----IA 372 Query: 429 IMDQMKELGVLIGKGGYFGNVFRITPPLCFTKDDAD 464 ++ E G+L+ G V R PPL + + D Sbjct: 373 LVKAAIEQGLLLVPAG--AEVVRFVPPLIVSAAEID 406 Lambda K H 0.320 0.136 0.403 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: 417 Number of extensions: 22 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: 477 Length of database: 422 Length adjustment: 33 Effective length of query: 444 Effective length of database: 389 Effective search space: 172716 Effective search space used: 172716 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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