Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_090442076.1 BLS63_RS07545 diaminobutyrate--2-oxoglutarate transaminase
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >NCBI__GCF_900100495.1:WP_090442076.1 Length = 459 Score = 172 bits (437), Expect = 1e-47 Identities = 133/423 (31%), Positives = 194/423 (45%), Gaps = 58/423 (13%) Query: 27 RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTE--QAGKFWHTGNGYT--NEP 82 + EG + D +G Y+D G ALGH HP +V +L + +G HT + T + Sbjct: 43 KAEGVWVTDVEGNTYLDCLAGAGTLALGHNHPEVVASLNDFLASGMPMHTLDLTTPLKDA 102 Query: 83 VLRLAKQLIDATFADRVF-FCN-SGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHG 140 L+ D FC SGA+A EAALKLA+ + +S I++F +HG Sbjct: 103 FSETLLHLLPGNGRDYCLQFCGPSGADAVEAALKLAKTV------TGRSNILSFSGGYHG 156 Query: 141 RTLFTVSAGGQPAYSQDFAPLPPQIQHAIY---------------------------NDL 173 T ++ G A L P +Q Y D+ Sbjct: 157 MTHGALAVTGNAAPKNAIHTLMPGVQFLPYPHEYRCPLGIGGEAGVQALMHYFTQFIEDV 216 Query: 174 DSAKALIDDNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTG 233 +S +L AVI+E +QGEGGV PA + +LR +RE+ H LLI DEVQ G RTG Sbjct: 217 ESGVSL----PAAVILEAVQGEGGVNPAPSGWLRSIREVTRKHGILLILDEVQAGFARTG 272 Query: 234 ELYAYMHYGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAG 293 +++A+ H G+ PD++ +KA+GGG P+ ALL +R G H T+ GN +A A Sbjct: 273 KMFAFEHAGIEPDIIVMSKAVGGGLPM-ALLGIKRQFDAWAPGAHTGTFRGNQMAMAAGM 331 Query: 294 EVFATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEY------ 347 + + + ++R W ++L + RY ++RG GL++G + DE Sbjct: 332 TTLEVLQRQALTAQAERRGNWLKQQLTLLQQRYPALGQVRGRGLMLGIEIVDERQRPDGL 391 Query: 348 ------AGKAKAISNQAAEEGLMILIAG--ANVVRFAPALIISEDEVNSGLDRFELACKR 399 A A AI GL++ G NVVR P LII E++ + RFE A Sbjct: 392 HSYPMDARLAAAIQQHCFSHGLLLERGGRNGNVVRLLPPLIIDEEQCALLIARFEQALIA 451 Query: 400 FLA 402 LA Sbjct: 452 ALA 454 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: 475 Number of extensions: 29 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: 406 Length of database: 459 Length adjustment: 32 Effective length of query: 374 Effective length of database: 427 Effective search space: 159698 Effective search space used: 159698 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 Sep 24 2021. The underlying query database was built on Sep 17 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