Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.-; EC 2.6.1.118 (characterized, see rationale)
to candidate WP_083763404.1 AMB_RS01605 aspartate aminotransferase family protein
Query= uniprot:Q5JFW3 (362 letters) >NCBI__GCF_000009985.1:WP_083763404.1 Length = 384 Score = 263 bits (671), Expect = 8e-75 Identities = 156/373 (41%), Positives = 211/373 (56%), Gaps = 24/373 (6%) Query: 1 MPLY-RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVA 59 MP Y R L RGEG Y++ GRRYLD AG+ VN LGH HP V ++ Q K+ Sbjct: 1 MPTYARADLAFERGEGAYLFTADGRRYLDFAAGVAVNALGHCHPRLVKALTAQAAKVWHT 60 Query: 60 GPMFEHDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFAR---LATG---RSEIVAM 113 ++ +E + +L + V+ NSG EA+E +IK AR A G R I+ Sbjct: 61 SNLYRVAGQESVAAKLVERSFADTVFFCNSGAEALECSIKMARRHHFAAGNPQRYRIICA 120 Query: 114 TNAFHGRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQG 173 AFHGRTL +++A +KK+ EGF P V GF H+P+ N+ A + +IT+ETAA++ EP+QG Sbjct: 121 EGAFHGRTLATVAAGGQKKHLEGFAPAVDGFDHVPYGNLNALRASITEETAAILVEPVQG 180 Query: 174 EGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGI 232 EGGIVP D ++++ LR ++ G LLI DEVQ+G+ RTG A E G+ PDI+ + KG+ Sbjct: 181 EGGIVPGDPDYLRRLRATADEFGLLLIFDEVQTGMGRTGTLFAHEQAGIAPDIMGVAKGL 240 Query: 233 GNGFPVSLTLTDLE----IPRGKHGSTFGGNPLACRAVATTLRILRRDRLVE-------- 280 G GFPV L + + G HGSTFGGNPLA L I+ +E Sbjct: 241 GGGFPVGACLATTKAASGMVPGTHGSTFGGNPLAMAVAGEVLDIMAEPGFLEHVQAMAAL 300 Query: 281 ---KAGEKFMEFSGERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLL 337 K + F G V + RG GLM+GI R P V L E G+L AG+ ++RLL Sbjct: 301 LRSKVEDTAARFPGV-VEEVRGLGLMLGIKPRMPNTEMVARLAEGGLLTVGAGDNIVRLL 359 Query: 338 PPLIIEGDTLEEA 350 PPLII ++EA Sbjct: 360 PPLIINDAQVDEA 372 Lambda K H 0.320 0.140 0.410 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: 373 Number of extensions: 18 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: 362 Length of database: 384 Length adjustment: 30 Effective length of query: 332 Effective length of database: 354 Effective search space: 117528 Effective search space used: 117528 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 Aug 03 2021. The underlying query database was built on Aug 03 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