Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate GFF3766 HP15_3708 4-aminobutyrate aminotransferase
Query= curated2:Q8ZV07 (383 letters) >FitnessBrowser__Marino:GFF3766 Length = 425 Score = 188 bits (477), Expect = 3e-52 Identities = 129/389 (33%), Positives = 199/389 (51%), Gaps = 32/389 (8%) Query: 23 VWDDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIW-AVPLNFATPARERFIEEFS 81 +WD G+R ID GV+ +GH +PK+VEAVK Q++++ + E+ S Sbjct: 34 LWDADGKRMIDFAGGIGVLNIGHRHPKVVEAVKAQLDKLMHTCQTVMPYEGYVKLAEKLS 93 Query: 82 KLLPPK-FGVVFLQNTGTEAVEVAIKIAKKVTRKPTIVAFTNSFHGRTMGSLSITWNEK- 139 ++P + V L N+G EA+E A+KIA+ T K ++ F +HGRT ++++ Sbjct: 94 GVVPVRGHAKVMLANSGAEALENAMKIARAATGKTNVICFDGGYHGRTFYTMAMNGKAAP 153 Query: 140 YKKAFEPLYPHVRFGKFNVPH----EVDKLIG-----------EDTCCVVVEPIQGEGGV 184 Y+ F P+ V + VP+ E + L G +T +V+EP+ GEGG Sbjct: 154 YQTDFGPMPGTVYRAPYPVPYHGVSEDEALRGLKMAMKADSPAHNTAAIVIEPVLGEGGF 213 Query: 185 NPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAFQKYGVEPDIFTAGKPVAGGL 244 A FLK +R+ L+I DEVQ+GFGRTG ++A + GVEPD+ T K +A G+ Sbjct: 214 YAAPTSFLKEIRKICDENDILMIADEVQSGFGRTGKMFAIEHSGVEPDLMTMAKSMADGM 273 Query: 245 PIGLAVAREDFGDVFEPGEHGSTFAGNAVVMAAAAAASRLLREEDVPGRAERIGAELAKA 304 PI V + + D P G T+ G+ AAA A + +EED+ G+++ +G +L + Sbjct: 274 PISAIVGTDKYMDASGPNSLGGTYTGSPTACAAALAVFDVFKEEDILGKSQALGEKLKQR 333 Query: 305 LGDTGSRLA--VRVKGMGLMLGLEL-RVKADQFIQPLL---------ERGVMALTAGV-- 350 + A V+ +G M EL K + +P L E+G++ L+ G+ Sbjct: 334 FSQWQEQFAHVDNVRNLGPMAAFELVESKESRTPKPELAAAVTKKAKEKGLILLSCGMYG 393 Query: 351 NTLRFLPPYMISKEDVEVVHAAVTEVLKK 379 NTLRFL P I E +E A V E LK+ Sbjct: 394 NTLRFLMPVTIEDEVLEEGLAIVEESLKE 422 Lambda K H 0.320 0.138 0.408 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: 400 Number of extensions: 24 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: 383 Length of database: 425 Length adjustment: 31 Effective length of query: 352 Effective length of database: 394 Effective search space: 138688 Effective search space used: 138688 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 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