Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 208056 DVU2559 adenosylmethionine--8-amino-7-oxononanoate aminotransferase
Query= curated2:Q9YBY6 (388 letters) >MicrobesOnline__882:208056 Length = 542 Score = 123 bits (309), Expect = 1e-32 Identities = 124/408 (30%), Positives = 187/408 (45%), Gaps = 57/408 (13%) Query: 28 DDSGRKYLDCHAGHGAAFLGHSNPAIVEAVVRQARELVAASSSFS---TPSLEEALTEFS 84 D G +YLD + GH +P I EA+ RQ + VA S+ TPS+E A + Sbjct: 97 DTDGNRYLDGVSSLWTNVHGHRHPHIDEAIRRQL-DRVAHSTLLGLGGTPSIELA-ARLT 154 Query: 85 RIAPPWAEEIVFLNTGTEAVEAALKAAWLA--------TGKRGIVALKNSFHGRTLASLS 136 IAP + + ++G+ AVEAALK A+ + ++A N++HG T+ S+S Sbjct: 155 AIAPAGLTRVFYSDSGSTAVEAALKIAFQYHRQAPEGDARRTRVMAFSNAYHGDTIGSVS 214 Query: 137 VTWNPRYRRGV--PVLDTRFLSPSTDP-----------------GEVEKLVPE---DTAA 174 + + G+ P+L +P+ GEVE+L+ + A Sbjct: 215 LGGMSLFH-GIYGPLLFDPVRAPAPHCYRCPADLRPETCGMACLGEVERLMRHHGHELCA 273 Query: 175 IIVEP-IQGEGGLTKIYAELAKALREAADRVGALLIFDEIQTGFGRTGRVWAHESLGVEP 233 ++VEP +QG G+ + LR+ DR G ++ DE+ GFG+TG ++A E GV P Sbjct: 274 VVVEPLVQGAAGMLVQPRGWLRGLRDLCDRHGVFMVADEVAVGFGKTGTMFACEQEGVVP 333 Query: 234 DIMTAGKSIAGG-LPASAVLSRE----GVLATLASGR---HGSTHAANPLSMAAVAAASR 285 D++ K I GG LP +A L E G L A R HG T+ N L+ AA A+ Sbjct: 334 DMLCLAKGITGGYLPLAATLVTEHIHDGFLGGYADFRTFFHGHTYTGNALACAAALASLD 393 Query: 286 FLREEGVPDKARAAGALLEGLLRDRIEGLRLVRGVRGEGLMLGVEL------RLDPGPVL 339 EE + R L LL + L V +R G+M G+EL R P Sbjct: 394 VFEEERTLETLRPRIERLATLLAP-LNDLPHVGDIRRVGVMTGIELVADRETRTPYRPEE 452 Query: 340 R-----CLQESERVLALRSGATVVRLLPPYSISREDAEMVVYGLERCI 382 R L+ R + +R V+ L+PP SI+ + E +V+ + I Sbjct: 453 RIGHRVTLEARRRGVIVRPLGDVMVLMPPLSITETELETLVHTVRGAI 500 Lambda K H 0.319 0.136 0.398 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: 479 Number of extensions: 29 Number of successful extensions: 1 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: 388 Length of database: 542 Length adjustment: 33 Effective length of query: 355 Effective length of database: 509 Effective search space: 180695 Effective search space used: 180695 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 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