Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_010965684.1 CA_RS12260 aspartate aminotransferase family protein
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >NCBI__GCF_000008765.1:WP_010965684.1 Length = 387 Score = 347 bits (890), Expect = e-100 Identities = 179/373 (47%), Positives = 240/373 (64%), Gaps = 5/373 (1%) Query: 27 RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNGYTNEPVLRL 86 +GEG++L+D+ G EYIDF G+AVN LGH +P +VKA+ EQ+ K H N Y NE + L Sbjct: 19 KGEGTKLYDKDGNEYIDFVSGVAVNCLGHCNPSIVKAIEEQSSKLMHVSNYYWNENAMEL 78 Query: 87 AKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRTLFTV 146 + L + D+VF CNSG EA EA LKLARKYA K I+ N+FHGRT+ + Sbjct: 79 TEILCKNSEFDKVFMCNSGTEAIEAGLKLARKYALLHGDENKKEIIYMDNSFHGRTMGAL 138 Query: 147 SAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDDNTCAVIVEPMQGEGGVVPADADFL 206 S GQP Y + F PL ++ +NDLD K I T AVIVEP+QGEGG++PA ++L Sbjct: 139 SVTGQPKYQESFKPLIGAVKSVKFNDLDDIKQKISSKTAAVIVEPIQGEGGIIPAKKEYL 198 Query: 207 RGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKALGGGFPIGALLAS 266 + LR+LCD +NALLIFDEVQ G+GR G L+AY + V PD++ AKALGGGFPIGA+LA Sbjct: 199 KLLRDLCDENNALLIFDEVQCGMGRVGSLFAYQKFEVVPDIVCIAKALGGGFPIGAMLAK 258 Query: 267 ERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLN-GVKQRHQWFCERLNAINAR 325 E AS G HG TYGGNPLACAVA V + ++V+ V ++ ++ ++L + + Sbjct: 259 ESVASSFVPGDHGNTYGGNPLACAVAIAVLKELVDKKVVEINVNEKSKYLFDKLMTLKEK 318 Query: 326 YGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLMILIAGANVVRFAPALIISEDE 385 Y + ++RG+GLLIG E A K I N+ E L+++ AG NVVRF P L +S +E Sbjct: 319 YKVINDVRGMGLLIGV----EVACDVKKIINKCFESKLLLITAGKNVVRFLPPLNVSFEE 374 Query: 386 VNSGLDRFELACK 398 ++ L FE + K Sbjct: 375 IDKALGIFEESIK 387 Lambda K H 0.321 0.137 0.412 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: 437 Number of extensions: 15 Number of successful extensions: 3 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: 406 Length of database: 387 Length adjustment: 31 Effective length of query: 375 Effective length of database: 356 Effective search space: 133500 Effective search space used: 133500 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 Jul 25 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