Align acetylornithine aminotransferase (EC 2.6.1.11); succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate WP_010965684.1 CA_RS12260 aspartate aminotransferase family protein
Query= reanno::Marino:GFF3099 (404 letters) >NCBI__GCF_000008765.1:WP_010965684.1 Length = 387 Score = 340 bits (872), Expect = 4e-98 Identities = 175/374 (46%), Positives = 246/374 (65%), Gaps = 6/374 (1%) Query: 28 RGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLSNVMTNEPALRL 87 +GEG++++D++G E+ID G+AV CLGH +P +V A+ +Q+ K+ H+SN NE A+ L Sbjct: 19 KGEGTKLYDKDGNEYIDFVSGVAVNCLGHCNPSIVKAIEEQSSKLMHVSNYYWNENAMEL 78 Query: 88 AKTLCDLTFAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHGRTLFTV 147 + LC + ++VF NSG EA EA KLAR+YA H + K EII NSFHGRT+ + Sbjct: 79 TEILCKNSEFDKVFMCNSGTEAIEAGLKLARKYALLHGDENKKEIIYMDNSFHGRTMGAL 138 Query: 148 SVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKLISKEKTCAIVVEPIQGEGGVMPGDQAF 207 SV GQPKY E F+P G + +FNDL+ +K+ IS KT A++VEPIQGEGG++P + + Sbjct: 139 SVTGQPKYQESFKPLIGAVKSVKFNDLDDIKQKIS-SKTAAVIVEPIQGEGGIIPAKKEY 197 Query: 208 LQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGVVPDILSSAKGLGGGFPVAAMLT 267 L+ LRDLCDEN+ALL+FDEVQ G+GR G +AYQ + VVPDI+ AK LGGGFP+ AML Sbjct: 198 LKLLRDLCDENNALLIFDEVQCGMGRVGSLFAYQKFEVVPDIVCIAKALGGGFPIGAMLA 257 Query: 268 TAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPEILK-GVKARSDKLRKGMMDIGE 326 VA+S G HG+TYGGN LACAVA V+ + ++++ V +S L +M + E Sbjct: 258 KESVASSFVPGDHGNTYGGNPLACAVAIAVLKELVDKKVVEINVNEKSKYLFDKLMTLKE 317 Query: 327 RYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAGLEEGVMVLVAGANVIRLAPSLIIPEP 386 +Y V +VRG GLL+G + K +N E ++++ AG NV+R P L + Sbjct: 318 KYKVINDVRGMGLLIGVEVA----CDVKKIINKCFESKLLLITAGKNVVRFLPPLNVSFE 373 Query: 387 DIELALERFEAAVK 400 +I+ AL FE ++K Sbjct: 374 EIDKALGIFEESIK 387 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: 426 Number of extensions: 23 Number of successful extensions: 4 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: 387 Length adjustment: 31 Effective length of query: 373 Effective length of database: 356 Effective search space: 132788 Effective search space used: 132788 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 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