Align acetylornithine aminotransferase (EC 2.6.1.11); succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate WP_010441737.1 G7G_RS0112345 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= reanno::Marino:GFF3099 (404 letters) >NCBI__GCF_000192475.1:WP_010441737.1 Length = 424 Score = 165 bits (417), Expect = 3e-45 Identities = 128/417 (30%), Positives = 206/417 (49%), Gaps = 47/417 (11%) Query: 18 NYAPGSIIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLSN 77 N+ PG +I RGEGSR+WD++G E++D G LGH HP ++GA+ +Q K ++ Sbjct: 25 NFDPGIVI-ARGEGSRVWDEDGNEYVDYLIGSGPMLLGHGHPEIIGAVLEQLPK--GMTF 81 Query: 78 VMTNEPALRLAKTLCD-LTFAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFK 136 N + LA+ + + + E+V F SG EA+ A +LAR Y G++K ++ F+ Sbjct: 82 FANNAKGIELAEAIVEAVPCCEQVRFVASGGEADMYAIRLARAYT----GRDK--VLKFE 135 Query: 137 NSFHGRTL-FTVSVGGQ-----PKYLEGFEPAPGGIHH----AEFNDLESVKKLISKEK- 185 +HG + +S+ + P+ + P G+ A FNDL +V+ L+ + K Sbjct: 136 GGYHGMSAEAQMSLAPEVRINFPQAIPDSAGIPQGVADQMLIAPFNDLTAVEALLDENKD 195 Query: 186 TCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGV 245 AI+VEP+Q ++P +LQGLRDLCD+ LL+FDE+ +G R + A + YGV Sbjct: 196 VAAIIVEPLQ---RIIPALPGYLQGLRDLCDKYSVLLIFDEIVTGF-RLAYGGAQERYGV 251 Query: 246 VPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGS--------TYGGNALACAVAQRV 297 PDI + K +GGGFP+AA+ ++ T G+ T GN +A A + Sbjct: 252 TPDICTLGKIIGGGFPLAAIGANTEIMQHFDKSTVGANKWLMQLGTLSGNPIAAAAGLKT 311 Query: 298 VDTVSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLT----------E 347 +D + + + ++A KL+ + + + ++ G L T + Sbjct: 312 MDILRREGSYERLRAIGKKLQDMQSEELSKADIPHQICGDETLFDIFFTASVCRDYRTAK 371 Query: 348 KWQGKAKDFLNAGLEEGVMVLVAGANVIRLAPSLIIPEPDIELALERFEAAVKKLTA 404 K + NA L + AG +L PSL I E D+EL +AAV+ + A Sbjct: 372 HDDPKRNEAYNATLRHHGIFKSAG----KLYPSLAISEMDLELTKNAVQAAVRSIHA 424 Lambda K H 0.318 0.137 0.406 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: 467 Number of extensions: 32 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: 404 Length of database: 424 Length adjustment: 31 Effective length of query: 373 Effective length of database: 393 Effective search space: 146589 Effective search space used: 146589 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: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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