Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_019555867.1 F612_RS0100950 diaminobutyrate--2-oxoglutarate transaminase
Query= curated2:Q8ZV07 (383 letters) >NCBI__GCF_000381085.1:WP_019555867.1 Length = 428 Score = 179 bits (454), Expect = 1e-49 Identities = 128/404 (31%), Positives = 212/404 (52%), Gaps = 34/404 (8%) Query: 7 YYREYGIRIVKGFMQYVWDDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIW-AVP 65 Y R + K M +WD G+RYID G + GH NPKI +AV ++ Sbjct: 16 YIRSFPTIFEKSKMAEIWDVSGKRYIDFFAGAGALNYGHNNPKINDAVISYLQNDGIGHA 75 Query: 66 LNFATPARERFIEEF-SKLLPPK---FGVVFLQNTGTEAVEVAIKIAKKVTRKPTIVAFT 121 L+ T A+ F+E F + +L P+ + + F+ TGT A+E A+KIA+KV + I++FT Sbjct: 76 LDMGTVAKRDFMESFVNNILKPRDLDYKLQFVGPTGTGAIEAALKIARKVKGRKQIMSFT 135 Query: 122 NSFHGRTMGSLSITWNEKY--KKAFEPLYP-HVRFGKFNVPHEVD------KLIGEDT-- 170 N FHG +MGSLSIT N+ Y + P Y V F K+ + +VD K++ +D+ Sbjct: 136 NGFHGMSMGSLSITGNKYYHDESYGVPGYTTQVPFHKY-LGDKVDTIAYLRKILEDDSSG 194 Query: 171 ----CCVVVEPIQGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAFQK 226 +V+E +Q EGG+N A E+LK LR+ L+I D++Q G GR+G ++F++ Sbjct: 195 TELPAAIVLETVQAEGGINVAGEEWLKDLRQICDDFDILMIVDDIQVGNGRSGDFFSFER 254 Query: 227 YGVEPDIFTAGKPVAGGLPIGLAVAREDFGDVFEPGEHGSTFAGNAVVMAAAAAASRLLR 286 G++PDI T K + G P+ L + + + D++ GEH TF GN + A+ A Sbjct: 255 AGIKPDIITLSKSIGAGHPMALVLLKPEL-DIWTAGEHSGTFRGNNLAFVASTVALDTYW 313 Query: 287 EEDVPGRAERIGAELA----KALGDTGSRLAVRVKGMGLMLGLELRVKA--DQFIQPLLE 340 +D + +I A+L + L + +G+G++ G E + + E Sbjct: 314 SDDSFSKEVKIKAKLVEQRMQKLVSRFPEIINETRGLGMIWGAEFKDPSITSAICSQAFE 373 Query: 341 RGVMALTAGVNT--LRFLPPYMISKEDV----EVVHAAVTEVLK 378 G++ TAG + ++FL P ++++E + +++ A+ +VLK Sbjct: 374 DGLVIETAGAESDLIKFLGPLVMTEELINEGFDILENAIVKVLK 417 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: 372 Number of extensions: 21 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: 428 Length adjustment: 31 Effective length of query: 352 Effective length of database: 397 Effective search space: 139744 Effective search space used: 139744 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 10 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